STATO: the statistical methods ontology
type: Ontology
version IRI: stato.owl
Contributor: Brian Alper (https://orcid.org/000-0003-4300-4928)
Contributor: Camille Maumet (http://orcid.org/0000-0002-6290-553X)
Contributor: Chris Mungall (http://orcid.org/0000-0002-6601-2165)
Contributor: Gavin Lloyd
Contributor: Guillaume Bauchet
Contributor: Hanna Cwiek (https://orcid.org/0000-0001-9113-567X)
Contributor: Harold Lehmann (https://orcid.org/0000-0002-7698-219X)
Contributor: Joanne Dehnbostel (https://orcid.org/0000-0002-9896-9842)
Contributor: Kenneth Wilkins (https://orcid.org/0000-0003-0531-7165)
Contributor: Khalid Shahin (https://orcid.org/0000-0002-3526-7667)
Contributor: Nolan Nichols (http://orcid.org/0000-0003-1099-3328)
Contributor: Ralf Weber (https://orcid.org/0000-0002-8796-4771)
Contributor: Thomas Nichols (http://orcid.org/0000-0002-4516-5103)
creator: Alejandra Gonzalez-Beltran (http://orcid.org/0000-0003-3499-8262)
creator: Orlaith Burke
creator: Philippe Rocca-Serra (http://orcid.org/0000-0001-9853-5668)
description: STATO is the statistical methods ontology. It contains concepts and properties related to statistical methods, probability distributions and other concepts related to statistical analysis, including relationships to study designs and plots.
rights: This Ontology is distributed under a Creative Commons Attribution License
subject: Statistical Method, Design of Experiment, Plots, Statistical Model
license: http://creativecommons.org/licenses/by/3.0/
bug-database: https://github.com/ISA-tools/stato/issues
homepage: http://stato-ontology.org/
version info: 2025-02-23

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
has curation status: ready for release
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

example of usage
type: AnnotationProperty
editor preferred label: example
has curation status: ready for release
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred label: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
definition source: OBI_0000281

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
has curation status: ready for release
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

editor note
type: AnnotationProperty
editor preferred label: editor note
has curation status: ready for release
definition: An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred label: term editor
has curation status: ready for release
definition: Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

alternative term
type: AnnotationProperty
editor preferred label: alternative term
has curation status: pending final vetting
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred label: definition source
has curation status: ready for release
definition: formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: ready for release
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: pending final vetting
definition: An IRI or similar locator for a request or discussion of an ontology term.
term editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
comment: The 'tracker item' can associate a tracker with a specific ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: pending final vetting
definition: For external terms/classes, the ontology from which the term was imported
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: pending final vetting
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bjoern Peters
term editor: PERSON:Chris Mungall
term editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

elucidation
type: AnnotationProperty
editor preferred label: elucidation
term editor: person:Alan Ruttenberg
definition source: Person:Barry Smith
elucidation: Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms

has associated axiom(nl)
type: AnnotationProperty
editor preferred label: has associated axiom(nl)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom associated with a term expressed using natural language

has associated axiom(fol)
type: AnnotationProperty
editor preferred label: has associated axiom(fol)
term editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg
elucidation: An axiom expressed in first order logic using CLIF syntax

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: ready for release
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
term editor: Person: Alejandra Gonzalez-Beltran
term editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: ready for release
definition: An alternative term used by the IEDB.
term editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB

temporal interpretation
type: AnnotationProperty

STATO alternative term
type: AnnotationProperty
definition: an alternative term used for STATO statistical ontology and ISA team
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

R command
type: AnnotationProperty
definition: a R command syntax or link to a R documentation in support of Statistical Ontology Classes or Data Transformations
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

Python command
type: AnnotationProperty
definition: an annotation property to provide a canonical command to invoke a method implementation using Python programming language
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

preferred mathematical notation
type: AnnotationProperty
definition: the most common series or system of written mathematical symbols used to represent the entity
definition source: AGB

Contributor
type: AnnotationProperty
description: Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity.
comment: An entity responsible for making contributions to the content of the resource.

Creator
type: AnnotationProperty
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
comment: An entity primarily responsible for making the content of the resource.

Date
type: AnnotationProperty
description: Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
comment: A date associated with an event in the life cycle of the resource.

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
comment: An account of the content of the resource.

Format
type: AnnotationProperty
description: Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats).
comment: The physical or digital manifestation of the resource.

Source
type: AnnotationProperty
description: The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a resource from which the present resource is derived.

Subject and Keywords
type: AnnotationProperty
description: Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme.
comment: The topic of the content of the resource.

license
type: AnnotationProperty
term editor: Mark Miller
date: 2018-05-11T13:47:29Z

label
editor preferred label: label

part of
type: ObjectProperty
equivalent property:
  inverse of: has part
inverse of: has part
type: TransitiveProperty
editor preferred label: is part of
example of usage: my brain is part of my body (continuant parthood, two material entities)
example of usage: my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
example of usage: this day is part of this year (occurrent parthood)
definition: a core relation that holds between a part and its whole
editor note: Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
alternative term: part_of
imported from: obi.owl
temporal interpretation: axiom holds for all times

has part
type: ObjectProperty
equivalent property:
  inverse of: part of
type: TransitiveProperty
editor preferred label: has part
example of usage: my body has part my brain (continuant parthood, two material entities)
example of usage: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
example of usage: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
editor note: Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
editor note: Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
alternative term: has_part
imported from: obi.owl
temporal interpretation: axiom holds for all times

realized in
type: ObjectProperty
equivalent property:
  inverse of: realizes
inverse of: realizes
domain: realizable entity
range: process
editor preferred label: realized in
example of usage: this disease is realized in this disease course
example of usage: this fragility is realized in this shattering
example of usage: this investigator role is realized in this investigation
alternative term: is realized by
alternative term: realized_in
imported from: obi.owl
elucidation: [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

realizes
type: ObjectProperty
equivalent property:
  inverse of: realized in
domain: process
range: realizable entity
editor preferred label: realizes
example of usage: this disease course realizes this disease
example of usage: this investigation realizes this investigator role
example of usage: this shattering realizes this fragility
imported from: obi.owl
elucidation: to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process

preceded by
type: ObjectProperty
inverse of: precedes
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: preceded by
editor note: An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
alternative term: is preceded by
alternative term: preceded_by
imported from: obi.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:preceded_by

precedes
type: ObjectProperty
sub property of: temporal relation
type: TransitiveProperty
domain: occurrent
range: occurrent
editor preferred label: precedes
imported from: obi.owl

has measurement unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
range: measurement unit label
imported from: obi.owl

is about
type: ObjectProperty
domain: information content entity
example of usage: This document is about information artifacts and their representations
has curation status: pending final vetting
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
editor note: 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
term editor: person:Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: obi.owl

denotes
type: ObjectProperty
sub property of: is about
inverse of: is denoted by
example of usage: A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
definition: denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
editor note: 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r
term editor: person:Alan Ruttenberg
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
imported from: obi.owl

is quality measurement of
type: ObjectProperty
equivalent property:
  inverse of: is quality measured as
sub property of: is about
inverse of: is quality measured as
domain: measurement datum
range: quality
definition: m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q
editor note: 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later
editor note: From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes.
editor note: From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
editor note: From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input.
editor note: This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
term editor: Alan Ruttenberg
imported from: obi.owl

has coordinate unit label
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: length unit
imported from: obi.owl
comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point

is duration of
type: ObjectProperty
sub property of: is about
domain: time measurement datum
range: process
has curation status: metadata complete
definition: relates a process to a time-measurement-datum that represents the duration of the process
term editor: Person:Alan Ruttenberg
imported from: obi.owl

is quality measured as
type: ObjectProperty
equivalent property:
  inverse of: is quality measurement of
has curation status: metadata complete
definition: inverse of the relation of is quality measurement of
editor note: 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship
term editor: Person:Alan Ruttenberg
imported from: obi.owl

has time stamp
type: ObjectProperty
sub property of: has part
type: FunctionalProperty
domain: time stamped measurement datum
range: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken
term editor: Alan Ruttenberg
imported from: obi.owl

has measurement datum
type: ObjectProperty
sub property of: has part
domain: time stamped measurement datum
range: Class
  intersection of: measurement datum
  intersection of: Class
    complement of: time measurement datum
has curation status: metadata incomplete
definition: relates a time stamped measurement datum to the measurement datum that was measured
term editor: Alan Ruttenberg
imported from: obi.owl

is_supported_by_data
type: ObjectProperty
domain: conclusion based on data
range: data item
editor preferred label: is_supported_by_data
example of usage: The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA.
has curation status: ready for release
definition: The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process
term editor: OBI
definition source: OBI
definition source: Philly 2011 workshop
imported from: obi.owl

has_specified_input
type: ObjectProperty
equivalent property:
  inverse of: is_specified_input_of
sub property of: has participant
inverse of: is_specified_input_of
domain: planned process
editor preferred label: has_specified_input
example of usage: see is_input_of example_of_usage
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
editor note: 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
imported from: obi.owl

is_specified_input_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_input
sub property of: participates in
range: planned process
editor preferred label: is_specified_input_of
example of usage: some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has curation status: ready for release
definition: A relation between a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

has_specified_output
type: ObjectProperty
equivalent property:
  inverse of: is_specified_output_of
sub property of: has participant
inverse of: is_specified_output_of
domain: planned process
editor preferred label: has_specified_output
has curation status: ready for release
definition: A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
imported from: obi.owl

is_specified_output_of
type: ObjectProperty
equivalent property:
  inverse of: has_specified_output
sub property of: participates in
range: planned process
editor preferred label: is_specified_output_of
has curation status: ready for release
definition: A relation between a continuant participating in a planned process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
term editor: Alan Ruttenberg
term editor: PERSON:Bjoern Peters
imported from: obi.owl

is_proxy_for
type: ObjectProperty
domain: continuant
range: continuant
editor preferred label: is_proxy_for
example of usage: position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity
has curation status: metadata incomplete
definition: A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
editor note: A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. (another definition)
term editor: Alan Ruttenberg
imported from: obi.owl

achieves_planned_objective
type: ObjectProperty
inverse of: objective_achieved_by
domain: planned process
range: objective specification
editor preferred label: achieves_planned_objective
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
has curation status: metadata complete
definition: This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
imported from: obi.owl

has grain
type: ObjectProperty
sub property of: has part
editor preferred label: has grain
has curation status: metadata complete
definition: the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
editor note: Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
term editor: PERSON: Alan Ruttenberg
definition source: PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
imported from: obi.owl

objective_achieved_by
type: ObjectProperty
domain: objective specification
range: planned process
editor preferred label: objective_achieved_by
has curation status: ready for release
definition: This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
term editor: OBI
definition source: OBI
imported from: obi.owl

is member of organization
type: ObjectProperty
sub property of: is member of
inverse of: has organization member
domain: Class
  union of: Homo sapiens
  union of: organization
range: organization
editor preferred label: is member of organization
has curation status: metadata complete
definition: Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization.
editor note: 2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
editor note: JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it.
term editor: Person:Alan Ruttenberg
term editor: Person:Helen Parkinson
definition source: Person:Alan Ruttenberg
definition source: Person:Helen Parkinson
curator note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
imported from: obi.owl

has organization member
type: ObjectProperty
domain: organization
range: Class
  union of: Homo sapiens
  union of: organization
editor preferred label: has organization member
has curation status: metadata incomplete
definition: Relating an organization to a legal person or organization.
editor note: See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178
term editor: Person: Jie Zheng
imported from: obi.owl

specifies value of
type: ObjectProperty
sub property of: is about
inverse of: assumes values specified by
domain: value specification
editor preferred label: specifies value of
has curation status: metadata incomplete
definition: A relation between a value specification and an entity which the specification is about.
imported from: obi.owl

has value specification
type: ObjectProperty
sub property of: has part
domain: information content entity
range: value specification
editor preferred label: has value specification
has curation status: metadata complete
definition: A relation between an information content entity and a value specification that specifies its value.
term editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

inheres in
type: ObjectProperty
equivalent property:
  inverse of: bearer of
inverse of: bearer of
editor preferred label: inheres in
example of usage: this fragility inheres in this vase
example of usage: this red color inheres in this apple
definition: a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
editor note: A dependent inheres in its bearer at all times for which the dependent exists.
alternative term: inheres_in
imported from: obi.owl
temporal interpretation: axiom holds for all times

bearer of
type: ObjectProperty
equivalent property:
  inverse of: inheres in
range: specifically dependent continuant
editor preferred label: bearer of
example of usage: this apple is bearer of this red color
example of usage: this vase is bearer of this fragility
definition: a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
editor note: A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
alternative term: bearer_of
alternative term: is bearer of
imported from: obi.owl
temporal interpretation: axiom holds for all times

participates in
type: ObjectProperty
equivalent property:
  inverse of: has participant
inverse of: has participant
domain: continuant
range: occurrent
editor preferred label: participates in
example of usage: this blood clot participates in this blood coagulation
example of usage: this input material (or this output material) participates in this process
example of usage: this investigator participates in this investigation
definition: a relation between a continuant and a process, in which the continuant is somehow involved in the process
alternative term: participates_in
imported from: obi.owl

has participant
type: ObjectProperty
equivalent property:
  inverse of: participates in
domain: occurrent
range: continuant
property chain axiom: has part
editor preferred label: has participant
example of usage: this blood coagulation has participant this blood clot
example of usage: this investigation has participant this investigator
example of usage: this process has participant this input material (or this output material)
definition: a relation between a process and a continuant, in which the continuant is somehow involved in the process
editor note: Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
alternative term: has_participant
imported from: obi.owl
Source: http://www.obofoundry.org/ro/#OBO_REL:has_participant

is concretized as
type: ObjectProperty
equivalent property:
  inverse of: concretizes
inverse of: concretizes
domain: generically dependent continuant
range: specifically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants.
imported from: obi.owl

concretizes
type: ObjectProperty
equivalent property:
  inverse of: is concretized as
domain: specifically dependent continuant
range: generically dependent continuant
example of usage: A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant).
example of usage: An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process).
definition: A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant.
imported from: obi.owl

function of
type: ObjectProperty
equivalent property:
  inverse of: has function
sub property of: inheres in
inverse of: has function
domain: function
example of usage: this catalysis function is a function of this enzyme
definition: a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
editor note: A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists.
alternative term: function_of
alternative term: is function of
imported from: obi.owl

quality of
type: ObjectProperty
equivalent property:
  inverse of: has quality
sub property of: inheres in
inverse of: has quality
example of usage: this red color is a quality of this apple
definition: a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
editor note: A quality inheres in its bearer at all times for which the quality exists.
alternative term: is quality of
alternative term: quality_of
imported from: obi.owl

role of
type: ObjectProperty
equivalent property:
  inverse of: has role
sub property of: inheres in
inverse of: has role
example of usage: this investigator role is a role of this person
definition: a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
editor note: A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists.
alternative term: is role of
alternative term: role_of
imported from: obi.owl

has function
type: ObjectProperty
equivalent property:
  inverse of: function of
sub property of: bearer of
domain: independent continuant
range: function
example of usage: this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
definition: a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
editor note: A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
alternative term: has_function
imported from: obi.owl

has quality
type: ObjectProperty
equivalent property:
  inverse of: quality of
sub property of: bearer of
range: quality
example of usage: this apple has quality this red color
definition: a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
editor note: A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
alternative term: has_quality
imported from: obi.owl

has role
type: ObjectProperty
equivalent property:
  inverse of: role of
sub property of: bearer of
domain: independent continuant
range: role
example of usage: this person has role this investigator role (more colloquially: this person has this role of investigator)
definition: a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
editor note: A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
alternative term: has_role
imported from: obi.owl

derives from
type: ObjectProperty
equivalent property:
  inverse of: derives into
sub property of: topObjectProperty
inverse of: derives into
domain: independent continuant
range: independent continuant
editor preferred label: derives from
example of usage: this cell derives from this parent cell (cell division)
example of usage: this nucleus derives from this parent nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'.
alternative term: derives_from
imported from: obi.owl
imported from: ro.owl

derives into
type: ObjectProperty
equivalent property:
  inverse of: derives from
example of usage: this parent cell derives into this cell (cell division)
example of usage: this parent nucleus derives into this nucleus (nuclear division)
has curation status: pending final vetting
definition: a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity
editor note: This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'.
alternative term: derives_into
imported from: obi.owl

location of
type: ObjectProperty
equivalent property:
  inverse of: located in
inverse of: located in
type: TransitiveProperty
editor preferred label: is location of
example of usage: my head is the location of my brain
example of usage: this cage is the location of this rat
definition: a relation between two independent continuants, the location and the target, in which the target is entirely within the location
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: location_of
imported from: obi.owl
temporal interpretation: axiom holds for all times

located in
type: ObjectProperty
equivalent property:
  inverse of: location of
type: TransitiveProperty
editor preferred label: located in
example of usage: my brain is located in my head
example of usage: this rat is located in this cage
definition: a relation between two independent continuants, the target and the location, in which the target is entirely within the location
editor note: Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
editor note: Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
alternative term: located_in
imported from: obi.owl
temporal interpretation: axiom holds for all times
Source: http://www.obofoundry.org/ro/#OBO_REL:located_in

temporal relation
type: ObjectProperty
range: occurrent
has curation status: pending final vetting
editor note: move to BFO?
definition source: Allen
imported from: obi.owl
comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.

declares
type: ObjectProperty
sub property of: is about
inverse of: is declared by
definition: property to indicate that a design declares a variable; the inverse property is 'is declared by'
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

is declared by
type: ObjectProperty
definition: property to indicate the variables declared by a design; the inverse property is 'declares'
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

has numerator
type: ObjectProperty
type: AsymmetricProperty
definition: the relationship between a fraction and the number above the line
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

executes
type: ObjectProperty
property chain axiom: realizes
property chain axiom: concretizes
definition: relationship between a planned process and the plan specification that it carries out; it is defined as equivalent to the composed relationship (realizes o concretizes)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

assumes values specified by
type: ObjectProperty
example of usage: This is the inverse of 'specifies value of' and it is intended to say things such as 'compound' 'assumes values specified by' 'independent variable specification'
definition: A relation between an entity and a value specification, where the value specification is about the entity.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

is member of
type: ObjectProperty
inverse of: has member
definition: relationship between an element and a set it belongs to
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

has member
type: ObjectProperty
sub property of: topObjectProperty
definition: relationship between a set and one of its elements
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

is denoted by
type: ObjectProperty
sub property of: topObjectProperty
definition: Inverse relation of 'denotes', where denotation is what happens when someone creates an information content entity E in order to specifically refer to something (from 'denotes' definition).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

has denominator
type: ObjectProperty
definition: the relationship between a fraction and the number below the line (or divisor)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB

is model for
type: ObjectProperty
inverse of: is modeled by
domain: statistical model
range: study design dependent variable
definition: This property is the inverse relationship of 'is model by' and represents the relationship between a dependent variable and an statistical model.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

has effect on
type: ObjectProperty
sub property of: is about
domain: variable
range: variable
has curation status: requires discussion
definition: 'has effect on' is a special case of the 'is about' relationship to be used for mixed effect models
editor note: AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75 Thus the definition is temporary. The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed. Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

has fixed effect on
type: ObjectProperty
sub property of: has effect on
has curation status: requires discussion
definition: 'has fixed effect on' is a special case of the 'is about' relationship to be used with fixed effect models
editor note: AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75 Thus the definition is temporary. The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed. Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

has interaction effect on
type: ObjectProperty
sub property of: has effect on
has curation status: requires discussion
definition: 'has interaction effect on' is a special case of the 'is about' relationship to be used for mixed effect models
editor note: AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75 Thus the definition is temporary. The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed. Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

has random effect on
type: ObjectProperty
sub property of: has effect on
has curation status: requires discussion
definition: 'has random effect on' is a special case of the 'is about' relationship to be used for random effect models
editor note: AGB: this relationship requires more discussion in light of potentially adding the Effect class as per the issue: https://github.com/ISA-tools/stato/issues/75 Thus the definition is temporary. The domain and range were 'variable' but removing now to discuss the specific restrictions when the issue is discussed. Not extracting to separate ontology (stato-experimental.owl) due to IDs already assigned. If deemed not necessary in the future, the IDs should be deprecated.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

has order in sequence
type: ObjectProperty
sub property of: is about
domain: Class
  union of: model random effect term
  union of: model fixed effect term
  union of: model interaction effect term
  union of: model error term
range: count
definition: 'has order in sequence' is a special case of the 'is about' relation being used to be able to enumerate the different terms within a linear mixed model formula (thus assinging and order to random effect terms, fixed effect terms, interaction effect terms and error terms).
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Ćwiek
term editor: Philippe Rocca-Serra

estimate of
type: ObjectProperty
sub property of: topObjectProperty
domain: statistic
range: model parameter
definition: Relationship between a parameter of a model and the estimate produced by estimation process as used in statistical modeling.

is modeled by
type: ObjectProperty
sub property of: is about
domain: study design dependent variable
range: statistical model
definition: This property is a specialization of the 'is about' property to represent the relationship between a dependent variable and an statistical model.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

computed from
type: ObjectProperty
sub property of: topObjectProperty
domain: information content entity
range: information content entity
definition: computed_from is a relation between 2 information content entity denoting how one is derived from another on through the application of a data transformation or computation process.

has measurement value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: scalar measurement datum
range: double
imported from: obi.owl

has x coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float
imported from: obi.owl

has y coordinate value
type: DatatypeProperty
sub property of: topDataProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float
imported from: obi.owl

has specified numeric value
type: DatatypeProperty
sub property of: has specified value
domain: value specification
range: real
editor preferred label: has specified numeric value
has curation status: metadata complete
definition: A relation between a value specification and a number that quantifies it.
editor note: A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning.
term editor: PERSON: James A. Overton
definition source: OBI
imported from: obi.owl

has specified value
type: DatatypeProperty
domain: value specification
editor preferred label: has specified value
has curation status: metadata incomplete
definition: A relation between a value specification and a literal.
editor note: This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject.
definition source: OBI
imported from: obi.owl

has value
type: DatatypeProperty
definition: A relationship (data property) between an entity and its value.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

entity
type: Class
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
imported from: obi.owl
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

continuant
type: Class
subclass of: entity
disjoint with: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
definition: An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240]
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
imported from: obi.owl
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

occurrent
type: Class
subclass of: entity
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
definition: An entity that has temporal parts and that happens, unfolds or develops through time.
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
imported from: obi.owl
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

independent continuant
type: Class
subclass of: continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
editor note: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
imported from: obi.owl
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

spatial region
type: Class
subclass of: immaterial entity
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
imported from: obi.owl
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

two-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
imported from: obi.owl
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
editor note: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
imported from: obi.owl
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

disposition
type: Class
subclass of: realizable entity
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
imported from: obi.owl
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

realizable entity
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
definition: A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
imported from: obi.owl
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

zero-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
imported from: obi.owl
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
imported from: obi.owl
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

specifically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
editor note: b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])
imported from: obi.owl
has associated axiom(fol): (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004]
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
is defined by: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
definition: A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
imported from: obi.owl
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

one-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
imported from: obi.owl
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
imported from: obi.owl
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
editor note: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
imported from: obi.owl
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
imported from: obi.owl
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

material entity
type: Class
subclass of: independent continuant
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
imported from: obi.owl
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
imported from: obi.owl

peptide
type: Class
subclass of: macromolecule
editor preferred label: peptide
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl
imported from: obi.owl

deoxyribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: deoxyribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
imported from: chebi.owl
imported from: obi.owl

molecular entity
type: Class
subclass of: material entity
editor preferred label: molecular entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
imported from: chebi.owl
imported from: obi.owl

atom
type: Class
subclass of: material entity
editor preferred label: atom
definition: A chemical entity constituting the smallest component of an element having the chemical properties of the element.
imported from: chebi.owl
imported from: obi.owl

nucleic acid
type: Class
subclass of: macromolecule
editor preferred label: nucleic acid
definition: A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
imported from: chebi.owl
imported from: obi.owl

ribonucleic acid
type: Class
subclass of: nucleic acid
editor preferred label: ribonucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.
imported from: chebi.owl
imported from: obi.owl

macromolecule
type: Class
subclass of: molecular entity
editor preferred label: macromolecule
definition: A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
alternative term: polymer
imported from: chebi.owl
imported from: obi.owl

cell
type: Class
subclass of: material entity
editor preferred label: cell
example of usage: PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
definition: A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
imported from: cl.owl
imported from: obi.owl

cultured cell
type: Class
subclass of: experimentally modified cell in vitro
subclass of: Class
  union of: Restriction
    on property: is_specified_output_of
    some values from: establishing cell culture
  union of: Restriction
    on property: derives from
    some values from: Restriction
      on property: is_specified_output_of
      some values from: establishing cell culture
editor preferred label: cultured cell
definition: A cell in vitro that is or has been maintained or propagated as part of a cell culture.
imported from: cl.owl
imported from: obi.owl

experimentally modified cell in vitro
type: Class
subclass of: cell
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: experimentally modified cell in vitro
definition: A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure.
imported from: cl.owl
imported from: obi.owl

GO:molecular_function
type: Class
subclass of: process
editor preferred label: molecular_function
definition: A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
imported from: go.owl
imported from: obi.owl

catalytic activity
type: Class
subclass of: GO:molecular_function
editor preferred label: catalytic activity
definition: Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
imported from: go.owl
imported from: obi.owl

biological_process
type: Class
subclass of: process
editor preferred label: biological_process
definition: A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
imported from: go.owl
imported from: obi.owl

gene expression
type: Class
subclass of: biological_process
editor preferred label: gene expression
definition: The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
imported from: go.owl
imported from: obi.owl

protein complex
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: protein
editor preferred label: protein complex
example of usage: A ribosome is a protein complex
definition: A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
imported from: go.owl
imported from: obi.owl

conditional specification
type: Class
subclass of: directive information entity
editor preferred label: conditional specification
has curation status: metadata complete
definition: a directive information entity that specifies what should happen if the trigger condition is fulfilled
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
definition source: OBI_0000349
imported from: obi.owl

measurement unit label
type: Class
subclass of: datum label
editor preferred label: measurement unit label
example of usage: Examples of measurement unit labels are liters, inches, weight per volume.
has curation status: pending final vetting
definition: A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure.
editor note: 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term.
editor note: 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: obi.owl

objective specification
type: Class
subclass of: directive information entity
editor preferred label: objective specification
example of usage: In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
has curation status: ready for release
definition: a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
editor note: 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed."
editor note: 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that.
editor note: Answers the question, why did you do this experiment?
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
alternative term: goal specification
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
imported from: obi.owl

action specification
type: Class
subclass of: directive information entity
example of usage: Pour the contents of flask 1 into flask 2
has curation status: ready for release
definition: a directive information entity that describes an action the bearer will take
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
imported from: obi.owl

datum label
type: Class
subclass of: information content entity
editor preferred label: datum label
has curation status: metadata incomplete
definition: A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
term editor: GROUP: IAO
curator note: 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
imported from: obi.owl

information carrier
type: Class
equivalent class: Class
  intersection of: quality
  intersection of: Restriction
    on property: concretizes
    some values from: information content entity
subclass of: quality
subclass of: Restriction
  on property: part of
  some values from: regression model
editor preferred label: information carrier
example of usage: In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case.
has curation status: pending final vetting
definition: A quality of an information bearer that imparts the information content
editor note: 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'.
editor note: 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.
term editor: PERSON: Alan Ruttenberg
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
imported from: obi.owl

data item
type: Class
subclass of: information content entity
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: pending final vetting
definition: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
alternative term: data
imported from: obi.owl

symbol
type: Class
subclass of: information content entity
editor preferred label: symbol
example of usage: a serial number such as "12324X"
example of usage: a stop sign
example of usage: a written proper name such as "OBI"
has curation status: pending final vetting
definition: An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
editor note: 20091104, MC: this needs work and will most probably change
editor note: 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154).
term editor: PERSON: James A. Overton
term editor: PERSON: Jonathan Rees
definition source: based on Oxford English Dictionary
imported from: obi.owl

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: ready for release
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
term editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: obi.owl

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: scalar value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
example of usage: 10 feet. 3 ml.
has curation status: metadata complete
definition: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
editor note: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
editor note: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Melanie Courtot
imported from: obi.owl

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
has curation status: ready for release
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
editor note: 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
editor note: Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
imported from: obi.owl

dot plot
type: Class
subclass of: graph
editor preferred label: dot plot
example of usage: Dot plot of SSC-H and FSC-H.
has curation status: example to be eventually removed
definition: A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000123
definition source: group:OBI
imported from: obi.owl

graph
type: Class
subclass of: diagram
editor preferred label: graph
has curation status: pending final vetting
definition: A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way.
term editor: PERSON: Lawrence Hunter
term editor: person:Alan Ruttenberg
term editor: person:Allyson Lister
definition source: OBI_0000240
definition source: group:OBI
imported from: obi.owl

rule
type: Class
subclass of: conditional specification
editor preferred label: rule
example of usage: example to be added
has curation status: metadata incomplete
definition: a rule is an executable which guides, defines, restricts actions
editor note: MSI
term editor: PRS
definition source: OBI_0500021
definition source: PRS
imported from: obi.owl

algorithm
type: Class
subclass of: plan specification
editor preferred label: algorithm
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
has curation status: metadata complete
definition: A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: OBI_0000270
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
imported from: obi.owl

curation status specification
type: Class
equivalent class: Class
  one of: example to be eventually removed
  one of: metadata complete
  one of: organizational term
  one of: ready for release
  one of: metadata incomplete
  one of: uncurated
  one of: pending final vetting
  one of: to be replaced with external ontology term
  one of: requires discussion
subclass of: data about an ontology part
editor preferred label: curation status specification
has curation status: pending final vetting
definition: The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
term editor: PERSON:Bill Bug
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
imported from: obi.owl

data set
type: Class
subclass of: data item
editor preferred label: data set
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
has curation status: pending final vetting
definition: A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
editor note: 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
editor note: 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
definition source: OBI_0000042
definition source: group:OBI
imported from: obi.owl

image
type: Class
subclass of: figure
editor preferred label: image
has curation status: ready for release
definition: An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface.
term editor: person:Alan Ruttenberg
term editor: person:Allyson
term editor: person:Chris Stoeckert
definition source: OBI_0000030
definition source: group:OBI
imported from: obi.owl

data about an ontology part
type: Class
subclass of: data item
definition: data about an ontology part is a data item about a part of an ontology, for example a term
term editor: Person:Alan Ruttenberg
imported from: obi.owl

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: objective specification
subclass of: Restriction
  on property: has part
  some values from: action specification
editor preferred label: plan specification
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
has curation status: ready for release
definition: A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
editor note: 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
editor note: 2014-03-31: A plan specification can have other parts, such as conditional specifications.
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
imported from: obi.owl
comment: 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them

measurement datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: has value specification
  some values from: value specification
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: pending final vetting
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
term editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: obi.owl

version number
type: Class
subclass of: symbol
editor preferred label: version number
has curation status: metadata incomplete
definition: A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
editor note: Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
term editor: GROUP: IAO
imported from: obi.owl

conclusion textual entity
type: Class
subclass of: textual entity
subclass of: conclusion based on data
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: metadata complete
definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
editor note: 2009/10/23 Alan Ruttenberg: We need to work on the definition still
term editor: Person:Alan Ruttenberg
imported from: obi.owl

scatter plot
type: Class
subclass of: graph
editor preferred label: scatter plot
example of usage: Comparison of gene expression values in two samples can be displayed in a scatter plot
has curation status: ready for release
definition: A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
alternative term: scattergraph
definition source: WEB: http://en.wikipedia.org/wiki/Scatterplot
imported from: obi.owl

textual entity
type: Class
subclass of: information content entity
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: metadata incomplete
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
term editor: PERSON: Lawrence Hunter
alternative term: text
imported from: obi.owl

table
type: Class
subclass of: textual entity
editor preferred label: table
example of usage: | T F --+----- T | T F F | F F
has curation status: pending final vetting
definition: A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

figure
type: Class
subclass of: information content entity
editor preferred label: figure
example of usage: Any picture, diagram or table
has curation status: metadata complete
definition: An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

diagram
type: Class
subclass of: figure
editor preferred label: diagram
example of usage: A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space.
has curation status: metadata complete
definition: A figure that expresses one or more propositions
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

document
type: Class
subclass of: information content entity
editor preferred label: document
example of usage: A journal article, patent application, laboratory notebook, or a book
has curation status: metadata complete
definition: A collection of information content entities intended to be understood together as a whole
term editor: PERSON: Lawrence Hunter
imported from: obi.owl

cartesian spatial coordinate datum
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: zero-dimensional spatial region
subclass of: Restriction
  on property: has coordinate unit label
  cardinality: 1
has curation status: metadata complete
definition: A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
editor note: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
term editor: Alan Ruttenberg
curator note: AR notes: We need to discuss whether it should include site.
imported from: obi.owl

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: one-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
term editor: Alan Ruttenberg
imported from: obi.owl

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: zero-dimensional spatial region
    intersection of: Restriction
      on property: part of
      some values from: two-dimensional spatial region
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
has curation status: metadata incomplete
definition: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
term editor: Alan Ruttenberg
imported from: obi.owl

mass measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: mass unit
  intersection of: Restriction
    on property: is quality measurement of
    all values from: mass
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measurement of mass quality
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
imported from: obi.owl

time measurement datum
type: Class
subclass of: scalar measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has measurement unit label
    all values from: time unit
  intersection of: Restriction
    on property: is duration of
    all values from: process
has curation status: metadata incomplete
definition: A scalar measurement datum that is the result of measuring a temporal interval
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
term editor: Person:Alan Ruttenberg
imported from: obi.owl

documenting
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  some values from: document
example of usage: Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
has curation status: pending final vetting
definition: a planned process in which a document is created or added to by including the specified input in it.
editor note: 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
term editor: Bjoern Peters
definition source: wikipedia http://en.wikipedia.org/wiki/Documenting
imported from: obi.owl

line graph
type: Class
subclass of: graph
subclass of: Restriction
  on property: is denoted by
  some values from: slope
subclass of: Restriction
  on property: is denoted by
  some values from: intercept
editor preferred label: line graph
has curation status: ready for release
definition: A line graph is a type of graph created by connecting a series of data points together with a line.
term editor: PERSON:Chris Stoeckert
term editor: PERSON:Melanie Courtot
alternative term: line chart
definition source: GROUP:OBI
definition source: WEB: http://en.wikipedia.org/wiki/Line_chart
imported from: obi.owl

centrally registered identifier symbol
type: Class
subclass of: symbol
subclass of: Restriction
  on property: part of
  some values from: centrally registered identifier
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: metadata complete
definition: A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID symbol
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: obi.owl

centrally registered identifier
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier symbol
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: centrally registered identifier registry
example of usage: The sentence "The article has Pubmed ID 12345." contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed.
has curation status: metadata complete
definition: An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
editor note: 2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records').
editor note: Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
editor note: Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: obi.owl

centrally registered identifier registry
type: Class
subclass of: data set
example of usage: PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles.
has curation status: metadata complete
definition: A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
alternative term: CRID registry
definition source: Original proposal from Bjoern, discussions at IAO calls
imported from: obi.owl

time stamped measurement datum
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: Restriction
    on property: has time stamp
    some values from: time measurement datum
  intersection of: Restriction
    on property: has measurement datum
    some values from: measurement datum
has curation status: metadata incomplete
imported from: obi.owl

time sampled measurement data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: time stamped measurement datum
example of usage: pmid:20604925 - time-lapse live cell microscopy
has curation status: metadata complete
definition: A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time.
term editor: Alan Ruttenberg
alternative term: experimental time series
imported from: obi.owl

Viruses
type: Class
subclass of: organism
editor preferred label: Viruses
imported from: ncbitaxon.owl
imported from: obi.owl

Euteleostomi
type: Class
subclass of: Vertebrata <Metazoa>
editor preferred label: Euteleostomi
alternative term: bony vertebrates
imported from: ncbitaxon.owl
imported from: obi.owl

Bacteria
type: Class
subclass of: organism
editor preferred label: Bacteria
alternative term: eubacteria
imported from: ncbitaxon.owl
imported from: obi.owl

Archaea
type: Class
subclass of: organism
editor preferred label: Archaea
imported from: ncbitaxon.owl
imported from: obi.owl

Eukaryota
type: Class
subclass of: organism
editor preferred label: Eukaryota
alternative term: eucaryotes
alternative term: eukaryotes
imported from: ncbitaxon.owl
imported from: obi.owl

Euarchontoglires
type: Class
subclass of: Mammalia
editor preferred label: Euarchontoglires
imported from: ncbitaxon.owl
imported from: obi.owl

Tetrapoda
type: Class
subclass of: Euteleostomi
editor preferred label: Tetrapoda
alternative term: tetrapods
imported from: ncbitaxon.owl
imported from: obi.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred label: Amniota
alternative term: amniotes
imported from: ncbitaxon.owl
imported from: obi.owl

Opisthokonta
type: Class
subclass of: Eukaryota
editor preferred label: Opisthokonta
imported from: ncbitaxon.owl
imported from: obi.owl

Bilateria
type: Class
subclass of: Opisthokonta
editor preferred label: Bilateria
imported from: ncbitaxon.owl
imported from: obi.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred label: Mammalia
alternative term: mammals
imported from: ncbitaxon.owl
imported from: obi.owl

Vertebrata <Metazoa>
type: Class
subclass of: Bilateria
editor preferred label: Vertebrata <Metazoa>
alternative term: Vertebrata
alternative term: vertebrates
imported from: ncbitaxon.owl
imported from: obi.owl

Homo sapiens
type: Class
subclass of: Euarchontoglires
editor preferred label: Homo sapiens
alternative term: human
alternative term: human being
alternative term: man
imported from: ncbitaxon.owl
imported from: obi.owl

fluorescent reporter intensity
type: Class
subclass of: measurement datum
editor preferred label: fluorescent reporter intensity
has curation status: pending final vetting
definition: A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
term editor: person:Chris Stoeckert
definition source: group:OBI
curator note: From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
imported from: obi.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: plan specification
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: ready for release
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
term editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

biological feature identification objective
type: Class
subclass of: objective specification
editor preferred label: biological feature identification objective
has curation status: metadata incomplete
definition: Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
term editor: Jennifer Fostel
imported from: obi.owl

processed material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: material processing
subclass of: material entity
editor preferred label: processed material
example of usage: Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
has curation status: ready for release
definition: Is a material entity that is created or changed during material processing.
term editor: PERSON: Alan Ruttenberg
imported from: obi.owl

investigation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: documenting
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion based on data
subclass of: Restriction
  on property: has part
  some values from: study design execution
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: planning
    intersection of: Restriction
      on property: has_specified_output
      some values from: study design
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: ready for release
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
term editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
ISA alternative term: study

evaluant role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: assay
editor preferred label: evaluant role
example of usage: When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source.
has curation status: ready for release
definition: a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role
editor note: Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
editor note: examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: evaluant role
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: ready for release
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
term editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

quantitative confidence value
type: Class
subclass of: measure of hypothesis testing
editor preferred label: quantitative confidence value
has curation status: pending final vetting
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
term editor: person:Chris Stoeckert
definition source: group:OBI
imported from: obi.owl

culture medium
type: Class
subclass of: processed material
editor preferred label: culture medium
example of usage: A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
has curation status: ready for release
definition: a processed material that provides the needed nourishment for microorganisms or cells grown in vitro.
editor note: changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178 Modification made by JZ.
term editor: Person: Jennifer Fostel, Jie Zheng
definition source: OBI
imported from: obi.owl

reagent role
type: Class
subclass of: role
editor preferred label: reagent role
example of usage: Buffer, dye, a catalyst, a solvating agent.
has curation status: metadata complete
definition: A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer.
term editor: PERSON:Matthew Brush
alternative term: reagent
definition source: PERSON:Matthew Brush
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term. May 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities ("a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.
imported from: obi.owl
comment: (copied from ReO) Reagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique. Reagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated. In regard to the statement that reagents are 'distinct' from the specified outputs of a technique, note that a reagent may be incorporated into a material output of a technique, as long as the IDENTITY of this output is distinct from that of the bearer of the reagent role. For example, dNTPs input into a PCR are reagents that become part of the material output of this technique, but this output has a new identity (ie that of a 'nucleic acid molecule') that is distinct from the identity of the dNTPs that comprise it. Similarly, a biotin molecule input into a cell labeling technique are reagents that become part of the specified output, but the identity of the output is t…

material processing
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: processed material
subclass of: Restriction
  on property: has_specified_input
  all values from: material entity
subclass of: Restriction
  on property: has_specified_output
  all values from: material entity
editor preferred label: material processing
example of usage: A cell lysis, production of a cloning vector, creating a buffer.
has curation status: ready for release
definition: A planned process which results in physical changes in a specified input material
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca Serra
alternative term: material transformation
definition source: OBI branch derived
imported from: obi.owl

participant under investigation role
type: Class
subclass of: role
subclass of: Restriction
  on property: realized in
  all values from: study design execution
editor preferred label: study subject role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: ready for release
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl

specimen role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: specimen collection process
editor preferred label: specimen role
example of usage: liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
has curation status: ready for release
definition: a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation
editor note: 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen.
editor note: parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject.
term editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

sequence feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: sequence feature identification objective
has curation status: metadata incomplete
definition: Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
term editor: Jennifer Fostel
imported from: obi.owl

intervention design
type: Class
equivalent class: Class
  intersection of: study design
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: study design independent variable
      intersection of: Restriction
        on property: is about
        some values from: study intervention
subclass of: study design
disjoint with: observation design
editor preferred label: intervention design
example of usage: PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
has curation status: pending final vetting
definition: An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
term editor: Philppe Rocca-Serra
definition source: OBI branch derived
imported from: obi.owl

gene list
type: Class
subclass of: data set
editor preferred label: gene list
example of usage: Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
has curation status: pending final vetting
definition: A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
term editor: person:Chris Stoeckert
definition source: group:OBI
curator note: kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.
imported from: obi.owl

molecular feature identification objective
type: Class
subclass of: biological feature identification objective
editor preferred label: molecular feature identification objective
has curation status: metadata incomplete
definition: Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
term editor: Jennifer Fostel
imported from: obi.owl

cDNA library
type: Class
subclass of: recombinant vector
subclass of: Restriction
  on property: is_specified_output_of
  some values from: recombinant vector cloning
subclass of: Restriction
  on property: has grain
  some values from: recombinant vector
editor preferred label: cDNA library
example of usage: PMID:6110205. collection of cDNA derived from mouse splenocytes.
has curation status: metadata incomplete
definition: Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process. ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
term editor: PERSON: Luisa Montecchi
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: PSI
curator note: PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
imported from: obi.owl

population
type: Class
subclass of: material entity
editor preferred label: population
example of usage: PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
has curation status: pending final vetting
definition: a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
editor note: 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from Oxford English Dictionnary
curator note: rem1: collection somehow always involve a selection process
imported from: obi.owl

imaging assay
type: Class
subclass of: assay
subclass of: Restriction
  on property: has_specified_output
  some values from: image
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
editor preferred label: imaging assay
has curation status: pending final vetting
definition: An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

organization
type: Class
subclass of: material entity
editor preferred label: organization
example of usage: PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
has curation status: ready for release
definition: An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
editor note: BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition source: GROUP: OBI
imported from: obi.owl

dye role
type: Class
subclass of: molecular label role
editor preferred label: dye role
has curation status: metadata complete
definition: A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest.
term editor: Jennifer Fostel
alternative term: dye
definition source: A substance used to color materials www.answers.com/topic/dye 19feb09
imported from: obi.owl

protocol
type: Class
subclass of: plan specification
editor preferred label: protocol
example of usage: PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
has curation status: ready for release
definition: A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process.
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
imported from: obi.owl
ISA alternative term: study protocol

adding a material entity into a target
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: adding material objective
subclass of: material combination
subclass of: Restriction
  on property: realizes
  some values from: material to be added role
subclass of: Restriction
  on property: realizes
  some values from: target of material addition role
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: material to be added role
    intersection of: Restriction
      on property: located in
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: adding a material entity into a target
example of usage: Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
has curation status: ready for release
definition: is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
editor note: Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
term editor: BP
definition source: branch derived
imported from: obi.owl

analyte role
type: Class
subclass of: measurand role
subclass of: Restriction
  on property: role of
  some values from: Class
    union of: molecular entity
    union of: atom
subclass of: Restriction
  on property: realized in
  all values from: analyte assay
editor preferred label: analyte role
example of usage: Glucose in blood (measured in an assay to determine the concentration of glucose).
has curation status: ready for release
definition: A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role.
editor note: interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
editor note: pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
editor note: qualities such as weight, color are not assayed but measured, so they do not fall into this category.
term editor: GROUP: Role Branch
definition source: OBI
curator note: Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.
imported from: obi.owl

material to be added role
type: Class
subclass of: role
editor preferred label: material to be added role
example of usage: drug added to a buffer contained in a tube; substance injected into an animal;
has curation status: metadata complete
definition: material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
term editor: Role Branch
definition source: OBI
curator note: 9 March 09 from discussion with PA branch
imported from: obi.owl

drawing a conclusion based on data
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion based on data
editor preferred label: interpreting data
example of usage: Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene.
has curation status: ready for release
definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition source: Bjoern Peters
imported from: obi.owl

planning
type: Class
subclass of: process
subclass of: Class
  intersection of: process
  intersection of: Restriction
    on property: has participant
    some values from: plan specification
editor preferred label: planning
example of usage: The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software.
has curation status: ready for release
definition: a process of creating or modifying a plan specification
editor note: 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
term editor: Bjoern Peters
definition source: Bjoern Peters
definition source: Plans and Planned Processes Branch
imported from: obi.owl

light emission function
type: Class
subclass of: excitation function
editor preferred label: light emission function
has curation status: ready for release
definition: A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

contain function
type: Class
subclass of: function
editor preferred label: contain function
example of usage: A syringe, a beaker
has curation status: ready for release
definition: A contain function is a function to constrain a material entities location in space
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

heat function
type: Class
subclass of: function
editor preferred label: heat function
has curation status: ready for release
definition: A heat function is a function that increases the internal kinetic energy of a material
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

material separation function
type: Class
subclass of: function
editor preferred label: material separation function
has curation status: ready for release
definition: A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

excitation function
type: Class
subclass of: function
editor preferred label: excitation function
has curation status: ready for release
definition: A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

filter function
type: Class
subclass of: material separation function
editor preferred label: filter function
has curation status: ready for release
definition: A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
term editor: Frank Gibson
imported from: obi.owl

cool function
type: Class
subclass of: function
editor preferred label: cool function
has curation status: ready for release
definition: A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

solid support function
type: Class
subclass of: function
editor preferred label: solid support function
example of usage: Taped, glued, pinned, dried or molecularly bonded to a solid support
has curation status: ready for release
definition: A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

environment control function
type: Class
subclass of: function
editor preferred label: environment control function
has curation status: ready for release
definition: An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
term editor: Bill Bug
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

sort function
type: Class
subclass of: material separation function
editor preferred label: sort function
has curation status: ready for release
definition: A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
term editor: Daniel Schober
term editor: Frank Gibson
term editor: Melanie Courtot
imported from: obi.owl

cloning vector role
type: Class
subclass of: material to be added role
subclass of: Class
  intersection of: Restriction
    on property: inheres in
    some values from: nucleic acid
  intersection of: Restriction
    on property: realized in
    all values from: recombinant vector cloning
editor preferred label: cloning vector role
example of usage: pBluescript plays the role of a cloning vector
has curation status: metadata incomplete
definition: A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
editor note: JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/
term editor: PERSON: Helen Parkinson
imported from: obi.owl

cloning insert role
type: Class
subclass of: role
editor preferred label: cloning insert role
has curation status: organizational term
definition: cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
editor note: Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
term editor: GROUP: Role branch
definition source: OBII and Wikipedia
imported from: obi.owl

extract
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: extraction
editor preferred label: extract
example of usage: Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
has curation status: metadata complete
definition: an extract is a material entity which results from an extraction process
term editor: PERSON: Philippe Rocca-Serra
alternative term: extracted material
definition source: GROUP: OBI Biomatrial Branch
imported from: obi.owl

transcription profiling assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: transcription profiling identification objective
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: measurement datum
    intersection of: Restriction
      on property: is about
      some values from: gene expression
editor preferred label: transcription profiling assay
example of usage: Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
has curation status: metadata complete
definition: An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
term editor: Philippe Rocca-Serra
alternative term: gene expression profiling
definition source: OBI
imported from: obi.owl
ISA alternative term: transcription profiling

averaging objective
type: Class
subclass of: data transformation objective
editor preferred label: averaging objective
example of usage: A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
has curation status: ready for release
definition: An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

enzyme
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Class
    union of: ribonucleic acid
    union of: protein complex
    union of: protein
    union of: Restriction
      on property: has part
      some values from: ribonucleic acid
    union of: Restriction
      on property: has part
      some values from: protein complex
    union of: Restriction
      on property: has part
      some values from: protein
  intersection of: Restriction
    on property: has function
    some values from: Restriction
      on property: realized in
      all values from: catalytic activity
subclass of: material entity
editor preferred label: enzyme
has curation status: pending final vetting
definition: (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity)
editor note: MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
term editor: person: Melanie Courtot
definition source: GROUP:OBI
imported from: obi.owl

adding material objective
type: Class
subclass of: material combination objective
editor preferred label: adding material objective
example of usage: creating a mouse infected with LCM virus
has curation status: ready for release
definition: is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
term editor: BP
imported from: obi.owl

genotyping assay
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: genotype information
subclass of: analyte assay
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: genotype information
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence feature identification objective
editor preferred label: genotyping assay
example of usage: High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
has curation status: metadata complete
definition: an assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
term editor: Philippe Rocca-Serra
alternative term: genotype profiling, SNP genotyping
definition source: OBI Biomaterial
imported from: obi.owl
ISA alternative term: SNP analysis

analyte measurement objective
type: Class
subclass of: assay objective
editor preferred label: analyte measurement objective
example of usage: The objective to measure the concentration of glucose in a blood sample
has curation status: ready for release
definition: an assay objective to determine the presence or concentration of an analyte in the evaluant
term editor: PERSON: Bjoern Peters
definition source: PPPB branch
imported from: obi.owl

assay objective
type: Class
subclass of: objective specification
editor preferred label: assay objective
example of usage: the objective to determine the weight of a mouse.
has curation status: ready for release
definition: an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)
term editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

analyte assay
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: analyte measurement objective
subclass of: assay
subclass of: Restriction
  on property: realizes
  some values from: analyte role
subclass of: Restriction
  on property: has_specified_output
  some values from: measurement datum
editor preferred label: analyte assay
example of usage: example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
has curation status: ready for release
definition: An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
editor note: 2013-09-23: simplify equivalent axiom
editor note: Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
editor note: logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum and ('has measurement unit label' some 'measurement unit label') and ('is quality measurement of' some 'molecular concentration'))
term editor: PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
definition source: PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch
imported from: obi.owl

target of material addition role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: material entity
subclass of: Restriction
  on property: realized in
  all values from: adding a material entity into a target
editor preferred label: target of material addition role
example of usage: peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
has curation status: metadata complete
definition: target of material addition role is a role realized by an entity into which a material is added in a material addition process
editor note: From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
term editor: GROUP: Role Branch
definition source: OBI
imported from: obi.owl

normalized data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: normalization data transformation
subclass of: data set
editor preferred label: normalized data set
has curation status: pending final vetting
definition: A data set that is produced as the output of a normalization data transformation.
term editor: PERSON: James Malone
term editor: PERSON: Melanie Courtot
imported from: obi.owl

measure function
type: Class
subclass of: function
subclass of: Restriction
  on property: function of
  some values from: processed material
subclass of: Restriction
  on property: realized in
  all values from: Restriction
    on property: has_specified_output
    some values from: measurement datum
editor preferred label: measure function
example of usage: A glucometer measures blood glucose concentration, the glucometer has a measure function.
has curation status: ready for release
definition: Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
term editor: PERSON: Daniel Schober
term editor: PERSON: Helen Parkinson
term editor: PERSON: Melanie Courtot
term editor: PERSON:Frank Gibson
imported from: obi.owl

material transformation objective
type: Class
subclass of: objective specification
editor preferred label: material transformation objective
example of usage: The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
has curation status: ready for release
definition: an objective specifiction that creates an specific output object from input materials.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Frank Gibson
term editor: PERSON: Jennifer Fostel
term editor: PERSON: Melanie Courtot
term editor: PERSON: Philippe Rocca-Serra
alternative term: artifact creation objective
definition source: GROUP: OBI PlanAndPlannedProcess Branch
imported from: obi.owl

study design execution
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: study design
subclass of: planned process
editor preferred label: study design execution
example of usage: injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
has curation status: ready for release
definition: a planned process that carries out a study design
editor note: removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
definition source: branch derived
curator note: 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation.
imported from: obi.owl

DNA sequencing
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: deoxyribonucleic acid
      intersection of: Restriction
        on property: has role
        some values from: evaluant role
  intersection of: Restriction
    on property: has_specified_output
    some values from: DNA sequence data
subclass of: sequencing assay
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: assay objective
subclass of: Restriction
  on property: has participant
  some values from: DNA sequencer
editor preferred label: DNA sequencing
example of usage: Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
has curation status: metadata incomplete
definition: DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
term editor: Philippe Rocca-Serra
definition source: OBI Branch derived
imported from: obi.owl
ISA alternative term: nucleotide sequencing

material separation objective
type: Class
equivalent class: Class
  union of: portioning objective
  union of: separation into different composition objective
subclass of: material transformation objective
editor preferred label: material separation objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
has curation status: ready for release
definition: is an objective to transform a material entity into spatially separated components.
term editor: PPPB branch
definition source: PPPB branch
imported from: obi.owl

clustered data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: class discovery data transformation
subclass of: data set
editor preferred label: clustered data set
example of usage: A clustered data set is the output of a K means clustering data transformation
has curation status: pending final vetting
definition: A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: data set with assigned discovered class labels
curator note: AR thinks could be a data item instead
imported from: obi.owl

data set of features
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: descriptive statistical calculation data transformation
subclass of: data set
editor preferred label: data set of features
has curation status: pending final vetting
definition: A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
imported from: obi.owl

differential expression analysis data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: differential expression analysis objective
subclass of: data transformation
editor preferred label: differential expression analysis data transformation
has curation status: ready for release
definition: A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
term editor: James Malone
term editor: Melanie Courtot
term editor: Monnie McGee
definition source: WEB:
imported from: obi.owl

material combination
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material combination objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material combination
example of usage: Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
has curation status: ready for release
definition: is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
editor note: created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
term editor: bp
definition source: bp
imported from: obi.owl

specimen collection process
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: specimen collection objective
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
editor preferred label: specimen collection process
example of usage: drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation
has curation status: ready for release
definition: A planned process with the objective of collecting a specimen.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
editor note: Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role.
editor note: Philly2013: The specimen_role for the specimen is created during the specimen collection process.
editor note: label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/
term editor: Bjoern Peters
alternative term: specimen collection
curator note: 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession
curator note: 6/9/09: used at workshop
imported from: obi.owl

error corrected data set
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: error correction data transformation
subclass of: data set
editor preferred label: error corrected data set
has curation status: pending final vetting
definition: A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
imported from: obi.owl

error correction data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: error correction objective
subclass of: data transformation
editor preferred label: error correction data transformation
has curation status: ready for release
definition: An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
term editor: James Malone
term editor: Monnie McGee
definition source: EDITORS
imported from: obi.owl

sample from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: collecting specimen from organism
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: material sample
subclass of: specimen from organism
subclass of: Restriction
  on property: derives from
  some values from: material anatomical entity
editor preferred label: sample from organism
has curation status: example to be eventually removed
definition: a material obtained from an organism in order to be a representative of the whole
editor note: 5/29: This is a helper class for now
editor note: we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
imported from: obi.owl

statistical test hypothesis
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: data transformation
subclass of: Restriction
  on property: has part
  some values from: drawing a conclusion
subclass of: Restriction
  on property: has part
  some values from: assess statistical evidence
subclass of: Restriction
  on property: has part
  some values from: specifying null and alternate hypothesis
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: degree of freedom approximation
    union of: degree of freedom calculation
editor preferred label: statistical hypothesis test
has curation status: metadata complete
definition: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
term editor: Alejandra Gonzalez-Beltran
term editor: James Malone
term editor: Philippe Rocca-Serra
definition source: PERSON: James Malone
definition source: http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm
imported from: obi.owl
STATO alternative term: NHST
STATO alternative term: Null Hypothesis Statistical Testing
STATO alternative term: statistical hypothesis testing

center value
type: Class
equivalent class: center value
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: center calculation data transformation
subclass of: measure of central tendency
subclass of: quartile
editor preferred label: center value
has curation status: pending final vetting
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: median
imported from: obi.owl

statistical hypothesis test objective
type: Class
subclass of: data transformation objective
subclass of: Restriction
  on property: has part
  some values from: absence of difference hypothesis
editor preferred label: statistical hypothesis test objective
has curation status: metadata incomplete
definition: is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
term editor: James Malone
term editor: Person:Helen Parkinson
alternative term: hypothesis test objective
definition source: WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
imported from: obi.owl

portioning objective
type: Class
subclass of: material separation objective
editor preferred label: portioning objective
example of usage: The objective to obtain multiple aliquots of an enzyme preparation.
has curation status: metadata incomplete
definition: A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material.
imported from: obi.owl

average value
type: Class
equivalent class: average value
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: averaging data transformation
subclass of: measure of central tendency
editor preferred label: average value
has curation status: pending final vetting
definition: A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
term editor: PERSON: James Malone
term editor: PERSON: Monnie McGee
alternative term: arithmetic mean
imported from: obi.owl

separation into different composition objective
type: Class
subclass of: material separation objective
editor preferred label: separation into different composition objective
example of usage: The objective to obtain cells contained in a sample of blood.
has curation status: metadata complete
definition: A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities).
editor note: We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
imported from: obi.owl

specimen collection objective
type: Class
subclass of: objective specification
editor preferred label: specimen collection objective
example of usage: The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
has curation status: ready for release
definition: A objective specification to obtain a material entity for potential use as an input during an investigation.
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

material combination objective
type: Class
subclass of: material transformation objective
editor preferred label: material combination objective
has curation status: ready for release
definition: is an objective to obtain an output material that contains several input materials.
term editor: PPPB branch
definition source: bp
imported from: obi.owl

paired-end library
type: Class
subclass of: processed material
editor preferred label: paired-end library
example of usage: PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
has curation status: metadata incomplete
definition: is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
term editor: Philippe Rocca-Serra
alternative term: mate-paired library
alternative term: paired-end tag (PET) library
definition source: adapted from information provided by Solid web site
imported from: obi.owl

k-nearest neighbors
type: Class
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
editor preferred label: k-nearest neighbors
has curation status: pending final vetting
definition: A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
term editor: James Malone
alternative term: k-NN
definition source: PERSON: James Malone
imported from: obi.owl

recombinant vector
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: recombinant vector cloning
subclass of: processed material
editor preferred label: recombinant vector
has curation status: metadata incomplete
definition: A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
imported from: obi.owl

single fragment library
type: Class
subclass of: processed material
editor preferred label: single fragment library
has curation status: metadata incomplete
definition: is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
term editor: Philippe Rocca-Serra
alternative term: fragment library
imported from: obi.owl

cloning vector
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: cloning vector role
subclass of: processed material
subclass of: material to be added
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
editor preferred label: cloning vector
has curation status: metadata incomplete
definition: A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
imported from: obi.owl

Student's t-test
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: Student's t distribution
  intersection of: Restriction
    on property: has_specified_input
    some values from: t-statistic
subclass of: statistical test hypothesis
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    qualified cardinality: 1
    on class: study group population
  intersection of: Restriction
    on property: has_specified_input
    qualified cardinality: 2
    on class: Class
      intersection of: data set
      intersection of: Restriction
        on property: has part
        some values from: Class
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: normal distribution hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Student's t distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: t-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: normal distribution hypothesis
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: dichotomous variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: population
editor preferred label: Student's t-test
has curation status: ready for release
has curation status: metadata incomplete
definition: Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
term editor: Alejandra Gonzalez-Beltran
term editor: James Malone
term editor: Philippe Rocca-Serra
alternative term: t-test
definition source: WEB: http://en.wikipedia.org/wiki/T-test
imported from: obi.owl
R command: t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html

material sample role
type: Class
subclass of: specimen role
editor preferred label: material sample role
example of usage: a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: pending final vetting
definition: A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
editor note: 7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
imported from: obi.owl

material sampling process
type: Class
equivalent class: Class
  intersection of: specimen collection process
  intersection of: Restriction
    on property: has_specified_input
    some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: material sample
subclass of: specimen collection process
editor preferred label: material sampling process
has curation status: metadata incomplete
definition: A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
imported from: obi.owl

material sample
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: material sample role
subclass of: specimen
editor preferred label: material sample
example of usage: blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
has curation status: metadata incomplete
definition: A material entity that has the material sample role
term editor: OBI: workshop
alternative term: sample population
imported from: obi.owl
ISA alternative term: sample

study design independent variable
type: Class
subclass of: directive information entity
subclass of: variable
subclass of: Restriction
  on property: part of
  some values from: study design
subclass of: Restriction
  on property: has part
  some values from: data set
disjoint with: study design dependent variable
editor preferred label: independent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable.
has curation status: ready for release
definition: a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
editor note: 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
editor note: an independent variable is a variable which assumes only values set by the operator according to a plan and which are expected to (or are being tested for) influence the ranges of values assumed by one or more dependent variables (also known as 'response variables').
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative term: experimental factor
alternative term: independent variable
definition source: Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
imported from: obi.owl
ISA alternative term: study factor
STATO alternative term: explanatory variable
STATO alternative term: factor

study design dependent variable
type: Class
subclass of: directive information entity
subclass of: variable
subclass of: Restriction
  on property: part of
  some values from: study design
editor preferred label: dependent variable specification
example of usage: In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, the gene expression is the dependent variable.
has curation status: ready for release
definition: dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
editor note: 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
editor note: In the Philly 2013 workshop the label was chosen to distinguish it from "dependent variable" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
alternative term: dependent variable
definition source: WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
curator note: 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI.
imported from: obi.owl
STATO alternative term: response variable

survival rate
type: Class
subclass of: rate
subclass of: Restriction
  on property: has numerator
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is about
      some values from: study group population
subclass of: Restriction
  on property: has denominator
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is about
      some values from: study group population
editor preferred label: survival rate
has curation status: metadata complete
definition: A rate that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
term editor: Oliver He
definition source: adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate
imported from: obi.owl

multiple testing correction objective
type: Class
subclass of: error correction objective
editor preferred label: multiple testing correction objective
example of usage: Application of the Bonferroni correction
has curation status: metadata complete
definition: A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
alternative term: multiple comparison correction objective
definition source: http://en.wikipedia.org/wiki/Multiple_Testing_Correction
imported from: obi.owl

material maintenance objective
type: Class
subclass of: objective specification
editor preferred label: material maintenance objective
has curation status: ready for release
definition: An objective specification maintains some or all of the qualities of a material over time.
term editor: PERSON: Bjoern Peters
definition source: PERSON: Bjoern Peters
imported from: obi.owl

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acid
subclass of: region
editor preferred label: primary structure of DNA macromolecule
has curation status: metadata incomplete
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
term editor: BP et al
imported from: obi.owl

measurement device
type: Class
equivalent class: Class
  intersection of: device
  intersection of: Restriction
    on property: has function
    some values from: measure function
subclass of: device
editor preferred label: measurement device
example of usage: A ruler, a microarray scanner, a Geiger counter.
has curation status: ready for release
definition: A device in which a measure function inheres.
term editor: GROUP:OBI Philly workshop
definition source: OBI
imported from: obi.owl

material maintenance
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
subclass of: planned process
editor preferred label: material maintenance
has curation status: metadata incomplete
definition: a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
imported from: obi.owl

polyA RNA extraction
type: Class
subclass of: RNA extraction
editor preferred label: polyA RNA extraction
has curation status: metadata complete
definition: A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
term editor: Person: Chris Stoeckert
term editor: Person: Jie Zheng
definition source: UPenn Group
imported from: obi.owl

Likelihood-ratio test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: contingency table
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
editor preferred label: Likelihood-ratio test
has curation status: ready for release
has curation status: metadata incomplete
definition: Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.
editor note: date: March 2013 AGB and PRS provide formal definition expressed the test in terms of output and input, specifying the nature of the variables, the purpose of the test and the distribution used.
term editor: Alejandra Gonzales-Beltran
term editor: Philippe Rocca-Serra
term editor: Tina Boussard
imported from: obi.owl
R command: lrtest() http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/lrtest.html

survival curve
type: Class
subclass of: data item
subclass of: line graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: time measurement datum
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: survival rate
subclass of: Restriction
  on property: is about
  some values from: survival rate
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: survival analysis data transformation
editor preferred label: survival curve
has curation status: ready for release
definition: A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
term editor: Alejandra Gonzalez-Beltran
term editor: PERSON:Chris Stoeckert
term editor: PERSON:James Malone
term editor: PERSON:Melanie Courtot
term editor: Philippe Rocca-Serra
definition source: WEB: http://www.graphpad.com/www/book/survive.htm
imported from: obi.owl

flow cytometry assay
type: Class
equivalent class: Class
  intersection of: cytometry assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: function
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: flow cytometer
  intersection of: Restriction
    on property: has part
    some values from: fluorescence detection assay
subclass of: cytometry assay
editor preferred label: flow cytometry assay
example of usage: Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
has curation status: metadata complete
definition: A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
term editor: IEDB
definition source: IEDB
imported from: obi.owl

labeled specimen
type: Class
equivalent class: Class
  intersection of: specimen
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: addition of molecular label
subclass of: processed specimen
subclass of: molecular-labeled material
editor preferred label: labeled specimen
has curation status: metadata incomplete
definition: A specimen that has been modified in order to be able to detect it in future experiments
editor note: added during call 3/1/2010
term editor: OBI group
imported from: obi.owl

study intervention
type: Class
subclass of: planned process
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: specimen
  intersection of: Restriction
    on property: has_specified_output
    some values from: specimen
subclass of: Restriction
  on property: part of
  some values from: Class
    intersection of: study design execution
    intersection of: Restriction
      on property: realizes
      some values from: Restriction
        on property: concretizes
        some values from: intervention design
editor preferred label: study intervention
has curation status: metadata complete
definition: the part of the execution of an intervention design study which is varied between two or more subjects in the study
term editor: PERSON: Bjoern Peters
definition source: GROUP: OBI
imported from: obi.owl

material separation device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: material separation function
subclass of: device
editor preferred label: material separation device
example of usage: flow cytometer
has curation status: metadata incomplete
definition: A device with a separation function realized in a planed process
imported from: obi.owl

categorical measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has value specification
  some values from: categorical value specification
editor preferred label: categorical measurement datum
has curation status: metadata complete
definition: A measurement datum that is reported on a categorical scale
term editor: Bjoern Peters
alternative term: nominal mesurement datum
definition source: Bjoern Peters
imported from: obi.owl

processed specimen
type: Class
equivalent class: Class
  intersection of: processed material
  intersection of: specimen
subclass of: processed material
subclass of: specimen
editor preferred label: processed specimen
example of usage: A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells.
has curation status: ready for release
definition: A specimen that has been intentionally physically modified.
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl
comment: A tissue sample that has been sliced and stained for a histology study.

categorical label
type: Class
subclass of: datum label
editor preferred label: categorical label
example of usage: The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
has curation status: metadata complete
definition: A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale.
term editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

in live cell assay
type: Class
subclass of: assay
editor preferred label: in live cell assay
has curation status: metadata incomplete
definition: An assay in which a measurement is made by observing entities located in a live cell.
imported from: obi.owl

container
type: Class
equivalent class: Restriction
  on property: has function
  some values from: contain function
subclass of: device
editor preferred label: container
has curation status: metadata incomplete
definition: A device that can be used to restrict the location of material entities over time
editor note: 03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
term editor: PERSON: Bjoern Peters
imported from: obi.owl

device
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: material processing
subclass of: Restriction
  on property: has function
  some values from: function
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: ready for release
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
term editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: sequence data
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
has curation status: metadata complete
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
term editor: Person:Chris Stoeckert
definition source: GROUP: OBI
imported from: obi.owl

dose
type: Class
subclass of: measurement datum
editor preferred label: dose
example of usage: An organism has been injected 1ml of vaccine
has curation status: metadata incomplete
definition: A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
imported from: obi.owl

nucleic acid extract
type: Class
subclass of: extract
subclass of: processed specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: nucleic acid extraction
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
editor preferred label: nucleic acid extract
has curation status: metadata complete
definition: An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
term editor: PERSON: Jie Zheng
definition source: UPenn Group
imported from: obi.owl

light emission device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: light emission function
subclass of: device
editor preferred label: light emission device
example of usage: A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
has curation status: metadata complete
definition: a device which has a function to emit light.
term editor: Person:Helen Parkinson
definition source: OBI
imported from: obi.owl

environmental control device
type: Class
equivalent class: Restriction
  on property: has function
  some values from: Class
    union of: heat function
    union of: cool function
    union of: environment control function
subclass of: device
editor preferred label: environmental control device
example of usage: A growth chamber is an environmental control device.
has curation status: metadata complete
definition: An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
term editor: Helen Parkinson
definition source: OBI
imported from: obi.owl

labeled nucleic acid extract
type: Class
subclass of: labeled specimen
subclass of: Class
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: addition of molecular label
      intersection of: Restriction
        on property: has_specified_input
        some values from: nucleic acid extract
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: Restriction
  on property: has grain
  some values from: nucleic acid
editor preferred label: labeled nucleic acid extract
has curation status: metadata complete
definition: a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
term editor: Person: Jie Zheng
alternative term: labeled extract
definition source: MO_221 labeledExtract
imported from: obi.owl
ISA alternative term: labeled extract

dose response curve
type: Class
subclass of: line graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: dose
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: study design dependent variable
subclass of: Restriction
  on property: is_specified_output_of
  some values from: data visualization
editor preferred label: dose response curve
has curation status: metadata complete
has curation status: ready for release
definition: A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
term editor: Bjoern Peters; Randi Vita
term editor: Philippe Rocca-Serra, Alejandra Gonzalez-Beltran
imported from: obi.owl

genetic population background information
type: Class
subclass of: genetic characteristics information
subclass of: Restriction
  on property: part of
  some values from: genotype information
editor preferred label: genetic population background information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
has curation status: metadata complete
definition: a genetic characteristics information which is a part of genotype information that identifies the population of organisms
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

FWER adjusted p-value
type: Class
subclass of: quantitative confidence value
subclass of: error corrected data set
subclass of: Restriction
  on property: is about
  some values from: null hypothesis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Holm-Bonferroni family-wise error rate correction method
editor preferred label: FWER adjusted p-value
example of usage: http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
has curation status: ready for release
definition: A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
editor note: Addition of restriction 'output of null hypothesis testing' and specified output by AGB and PRS while working on STATO
term editor: PERS:Philippe Rocca-Serra
definition source: adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
imported from: obi.owl
STATO alternative term: Family-wise type I error rate

RNA-seq assay
type: Class
subclass of: transcription profiling assay
subclass of: sequencing assay
subclass of: Restriction
  on property: has part
  some values from: polyA RNA extraction
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: analyte role
    intersection of: Restriction
      on property: role of
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: specimen
    intersection of: Restriction
      on property: has part
      some values from: ribonucleic acid
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: sequence data
    intersection of: Restriction
      on property: is about
      some values from: gene expression
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: transcription profiling identification objective
subclass of: Restriction
  on property: has participant
  some values from: DNA sequencer
editor preferred label: RNA-seq assay
has curation status: metadata complete
definition: An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
term editor: PERSON: James Malone
alternative term: transcription profiling by high throughput sequencing
definition source: EFO_0002770 transcription profiling by high throughput sequencing
curator note: JZ: should be inferred as 'DNA sequencing'. Will check in the future.
curator note: an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. WEB: http://en.wikipedia.org/wiki/RNA-Seq
imported from: obi.owl

genotype information
type: Class
subclass of: genetic characteristics information
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: genetic population background information
  intersection of: Restriction
    on property: has part
    some values from: genetic alteration information
editor preferred label: genotype information
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
has curation status: metadata complete
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

transcription profiling identification objective
type: Class
subclass of: molecular feature identification objective
editor preferred label: transcription profiling identification objective
has curation status: metadata complete
definition: A molecular feature identification objective that aims to characterize the abundance of transcripts
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: Group: Penn Group
imported from: obi.owl

allele information
type: Class
subclass of: genetic alteration information
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: genotype information
  intersection of: Restriction
    on property: is about
    some values from: region
editor preferred label: allele information
example of usage: genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
has curation status: metadata complete
definition: a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
editor note: discussed on San Diego OBI workshop, March 2011
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_58 Allele
imported from: obi.owl

genetic alteration information
type: Class
subclass of: genetic characteristics information
editor preferred label: genetic alteration information
has curation status: metadata complete
definition: a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
editor note: proposed and discussed on San Diego OBI workshop, March 2011
term editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

genetic characteristics information
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: region
    intersection of: Restriction
      on property: is concretized as
      some values from: Restriction
        on property: inheres in
        some values from: Class
editor preferred label: genetic characteristics information
has curation status: metadata complete
definition: a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_66 IndividualGeneticCharacteristics
curator note: MO definition: The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. examples in ArrayExpress wild_type MutaMouse (CD2F1 mice with lambda-gt10LacZ integration) AlfpCre; SNF5 flox/knockout p53 knock out C57Bl/6 gp130lox/lox MLC2vCRE/+ fer-15; fem-1 df/df pat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)
imported from: obi.owl

q-value
type: Class
subclass of: quantitative confidence value
subclass of: error corrected data set
subclass of: Restriction
  on property: is about
  some values from: null hypothesis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    union of: Benjamini and Hochberg false discovery rate correction method
    union of: Benjamini and Yekutieli false discovery rate correction method
editor preferred label: q-value
example of usage: PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines. "After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
has curation status: ready for release
definition: A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
editor note: Addition of restriction 'output of null hypothesis testing' by AGB and PRS while working on STATO
term editor: PERS:Philippe Rocca-Serra
alternative term: FDR adjusted p-value
definition source: Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
imported from: obi.owl
preferred mathematical notation: q

genotyping design
type: Class
subclass of: study design
subclass of: Restriction
  on property: has part
  some values from: sequence feature identification objective
subclass of: Restriction
  on property: is concretized as
  some values from: Restriction
    on property: realized in
    some values from: Restriction
      on property: has part
      some values from: genotyping assay
subclass of: Restriction
  on property: declares
  some values from: Class
    intersection of: study design dependent variable
    intersection of: dichotomous variable
    intersection of: Restriction
      on property: is about
      some values from: genotype information
editor preferred label: genotyping design
has curation status: metadata complete
definition: A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
term editor: Person: Chris Stoeckert, Jie Zheng
definition source: MO_560 genotyping_design
imported from: obi.owl

specimen from organism
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has role
    some values from: specimen role
  intersection of: Restriction
    on property: derives from
    some values from: Class
      union of: material anatomical entity
      union of: anatomical cluster
subclass of: specimen
editor preferred label: specimen from organism
has curation status: ready for release
definition: A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
term editor: PERSON: Chris Stoeckert, Jie Zheng
alternative term: tissue specimen
definition source: MO_954 organism_part
imported from: obi.owl

fluorescence detection assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: fluorescence
    intersection of: Restriction
      on property: has_specified_input
      some values from: material entity
  intersection of: Restriction
    on property: has_specified_output
    some values from: Restriction
      on property: is about
      some values from: fluorescence
subclass of: assay
editor preferred label: fluorescence detection assay
example of usage: Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
has curation status: metadata complete
definition: An assay in which a material's fluorescence is determined.
term editor: IEDB
definition source: IEDB
imported from: obi.owl

rate measurement datum
type: Class
subclass of: scalar measurement datum
editor preferred label: rate measurement datum
example of usage: The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time.
has curation status: metadata complete
definition: A scalar measurement datum that represents the number of events occuring over a time interval
term editor: PERSON: Bjoern Peters, Randi Vita
definition source: IEDB
imported from: obi.owl

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
editor preferred label: DNA sequence data
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: metadata complete
definition: A sequence data item that is about the primary structure of DNA
term editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
curator note: 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
imported from: obi.owl

selection criterion
type: Class
subclass of: directive information entity
editor preferred label: selection criterion
example of usage: rats should be aged between 6 and 8 weeks and weight between 180-250grams
has curation status: ready for release
definition: A directive information entity which defines and states a principle of standard by which selection process may take place.
term editor: Person: Philippe Rocca-Serra
alternative term: selection rule
definition source: OBI discussion summarized under the following tracker item : http://sourceforge.net/p/obi/obi-terms/678/
imported from: obi.owl

drawing a conclusion
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: conclusion textual entity
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: information content entity
editor preferred label: drawing a conclusion
example of usage: Concluding that the length of the hypotenuse is equal to the square root of the sum of squares of the other two sides in a right-triangle. Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting.
has curation status: metadata incomplete
definition: A planned process in which new information is inferred from existing information.
imported from: obi.owl

assay array
type: Class
subclass of: device
subclass of: Restriction
  on property: has function
  some values from: solid support function
editor preferred label: assay array
has curation status: metadata complete
definition: A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface.
term editor: PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg
definition source: Penn Group
imported from: obi.owl

conclusion based on data
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_supported_by_data
  some values from: data item
subclass of: Restriction
  on property: is_specified_output_of
  some values from: drawing a conclusion based on data
editor preferred label: conclusion based on data
example of usage: The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime".
has curation status: ready for release
definition: An information content entity that is inferred from data.
editor note: In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate.
term editor: Group:2013 Philly Workshop group
definition source: Group:2013 Philly Workshop group
imported from: obi.owl

cell freezing medium
type: Class
subclass of: processed material
editor preferred label: cell freezing medium
has curation status: metadata complete
definition: A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles.
term editor: PERSON: Matthew Brush
imported from: obi.owl

categorical value specification
type: Class
subclass of: value specification
editor preferred label: categorical value specification
has curation status: metadata incomplete
definition: A value specification that is specifies one category out of a fixed number of nominal categories
term editor: PERSON:Bjoern Peters
imported from: obi.owl

scalar value specification
type: Class
subclass of: value specification
subclass of: Restriction
  on property: has measurement unit label
  min cardinality: 1
subclass of: Restriction
  on property: has specified numeric value
  min cardinality: 1
editor preferred label: scalar value specification
has curation status: metadata incomplete
definition: A value specification that consists of two parts: a numeral and a unit label
term editor: PERSON:Bjoern Peters
imported from: obi.owl

value specification
type: Class
subclass of: information content entity
editor preferred label: value specification
example of usage: The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass.
has curation status: ready for release
definition: An information content entity that specifies a value within a classification scheme or on a quantitative scale.
editor note: This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement.
term editor: PERSON:Bjoern Peters
imported from: obi.owl

molecular-labeled material
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has part
    some values from: molecular label
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: addition of molecular label
subclass of: processed material
editor preferred label: molecular-labeled material
has curation status: pending final vetting
definition: a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay
term editor: PERSON:Matthew Brush
definition source: OBI developer call, 3-12-12
imported from: obi.owl

cytometry assay
type: Class
equivalent class: Class
  intersection of: assay
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: Class
        intersection of: evaluant role
        intersection of: Restriction
    intersection of: Restriction
      on property: has_specified_input
      some values from: Class
        intersection of: cell
        intersection of: Restriction
subclass of: assay
editor preferred label: cytometry assay
example of usage: An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells.
has curation status: metadata complete
definition: An assay that measures properties of cells.
term editor: IEDB
definition source: IEDB
imported from: obi.owl

physical store
type: Class
equivalent class: Restriction
  on property: has function
  some values from: environment control function
subclass of: container
subclass of: environmental control device
editor preferred label: physical store
example of usage: a freezer. a humidity controlled box.
has curation status: ready for release
definition: A container with an environmental control function.
editor note: For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/
term editor: Chris Stoeckert
definition source: Duke Biobank, OBIB
imported from: obi.owl
Source: Biobank

measurand role
type: Class
subclass of: role
subclass of: Restriction
  on property: role of
  some values from: material entity
editor preferred label: measurand role
has curation status: metadata complete
definition: A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role.
term editor: Person: Alan Ruttenberg, Jie Zheng
definition source: https://en.wiktionary.org/wiki/measurand
term tracker item: https://github.com/obi-ontology/obi/issues/778
imported from: obi.owl

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor preferred label: organism
example of usage: animal
example of usage: fungus
example of usage: plant
example of usage: virus
has curation status: ready for release
definition: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
editor note: 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
editor note: 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.
term editor: GROUP: OBI Biomaterial Branch
definition source: WEB: http://en.wikipedia.org/wiki/Organism
imported from: obi.owl

specimen
type: Class
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has role
    some values from: specimen role
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: ready for release
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
term editor: PERSON: James Malone
term editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
imported from: obi.owl

cultured cell population
type: Class
subclass of: processed material
subclass of: Restriction
  on property: is_specified_output_of
  some values from: maintaining cell culture
subclass of: Restriction
  on property: has grain
  some values from: cultured cell
subclass of: Restriction
  on property: has grain
  all values from: cultured cell
editor preferred label: cultured cell population
example of usage: A cultured cell population applied in an experiment: "293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest." (Lee, Ramee, et al. "Regulation of cell survival by secreted proneurotrophins." Science 294.5548 (2001): 1945-1948). A cultured cell population maintained in vitro: "Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks" (Dichter, Marc A. "Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation." Brain Research 149.2 (1978): 279-293).
has curation status: metadata complete
definition: A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history.
editor note: 2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line.
term editor: PERSON:Matthew Brush
alternative term: cell culture sample
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally.

screening library
type: Class
subclass of: processed material
editor preferred label: screening library
example of usage: PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
has curation status: metadata incomplete
definition: a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
editor note: PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application change biomaterial to material in definition
term editor: PERSON: Bjoern Peters
definition source: GROUP: IEDB
curator note: 7/13/09: Need to clarify if this meets reagent role definition
imported from: obi.owl

data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
subclass of: planned process
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: algorithm
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: data item
editor preferred label: data transformation
example of usage: The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
has curation status: ready for release
definition: A planned process that produces output data from input data.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
definition source: Branch editors
imported from: obi.owl

differential expression analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: differential expression analysis objective
example of usage: Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
has curation status: ready for release
definition: A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

Benjamini and Hochberg false discovery rate correction method
type: Class
subclass of: false discovery rate correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: has_specified_output
  some values from: error corrected data set
subclass of: Restriction
  on property: has_specified_output
  some values from: q-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: Benjamini and Hochberg false discovery rate correction method
example of usage: Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
has curation status: metadata complete
definition: A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
editor note: 2011-03-31: [PRS]. specified input and output of dt which were missing
term editor: Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: Helen Parkinson
imported from: obi.owl

k-means clustering
type: Class
subclass of: partitioning data transformation
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
editor preferred label: k-means clustering
has curation status: pending final vetting
definition: A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/K-means
imported from: obi.owl

hierarchical clustering
type: Class
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: hierarchical clustering
has curation status: pending final vetting
definition: A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
term editor: James Malone
definition source: WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
imported from: obi.owl

average linkage hierarchical clustering
type: Class
subclass of: agglomerative hierarchical clustering
editor preferred label: average linkage hierarchical clustering
has curation status: pending final vetting
definition: An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

complete linkage hierarchical clustering
type: Class
subclass of: agglomerative hierarchical clustering
editor preferred label: complete linkage hierarchical clustering
has curation status: metadata complete
definition: an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

single linkage hierarchical clustering
type: Class
subclass of: agglomerative hierarchical clustering
editor preferred label: single linkage hierarchical clustering
has curation status: pending final vetting
definition: A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
term editor: Elisabetta Manduchi
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

Benjamini and Yekutieli false discovery rate correction method
type: Class
subclass of: false discovery rate correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: has_specified_output
  some values from: error corrected data set
subclass of: Restriction
  on property: has_specified_output
  some values from: q-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: Benjamini and Yekutieli false discovery rate correction method
example of usage: The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
has curation status: metadata complete
definition: A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
editor note: 2011-03-31: [PRS]. specified input and output of dt which were missing
term editor: Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: Helen Parkinson
imported from: obi.owl

dimensionality reduction
type: Class
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: dimensionality reduction
has curation status: ready for release
definition: A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative term: data projection
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
imported from: obi.owl

principal components analysis dimensionality reduction
type: Class
subclass of: dimensionality reduction
subclass of: Restriction
  on property: has_specified_input
  some values from: number of orthogonal components
subclass of: Restriction
  on property: has_specified_output
  some values from: eigen value
subclass of: Restriction
  on property: has_specified_output
  some values from: loadings
subclass of: Restriction
  on property: has_specified_output
  some values from: score
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      some values from: variance
editor preferred label: principal components analysis dimensionality reduction
has curation status: ready for release
definition: A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Philippe Rocca-Serra
alternative term: pca data reduction
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
imported from: obi.owl

Holm-Bonferroni family-wise error rate correction method
type: Class
subclass of: family wise error rate correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: has_specified_output
  some values from: FWER adjusted p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: Holm-Bonferroni family-wise error rate correction method
example of usage: t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
has curation status: metadata complete
definition: a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
editor note: 2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition Also added restriction to specify the output to be a FWER adjusted p-value The 'editor preferred term' should be removed
term editor: Person:Helen Parkinson
term editor: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
imported from: obi.owl
STATO alternative term: Bonferroni adjustment method

family wise error rate correction method
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: FWER adjusted p-value
subclass of: multiple testing correction method
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: family wise error rate correction method
has curation status: pending final vetting
definition: A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
editor note: 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt
term editor: Monnie McGee
term editor: Philippe Rocca-Serra
alternative term: FWER correction
definition source: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
imported from: obi.owl

descriptive statistical calculation objective
type: Class
subclass of: data transformation objective
editor preferred label: descriptive statistical calculation objective
has curation status: ready for release
definition: A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Monnie McGee
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Monnie McGee
imported from: obi.owl

survival analysis objective
type: Class
subclass of: data transformation objective
editor preferred label: survival analysis objective
example of usage: Kaplan meier data transformation
has curation status: metadata complete
definition: A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
term editor: PERSON: James Malone
term editor: PERSON: Tina Boussard
alternative term: survival analysis
definition source: http://en.wikipedia.org/wiki/Survival_analysis
imported from: obi.owl

multiple testing correction method
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
subclass of: error correction data transformation
editor preferred label: multiple testing correction method
has curation status: metadata incomplete
definition: A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
term editor: Monnie McGee
alternative term: multiple testing procedure
definition source: PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
imported from: obi.owl

logarithmic transformation
type: Class
subclass of: normalization data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data normalization objective
editor preferred label: logarithmic transformation
has curation status: ready for release
definition: A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
term editor: Elisabetta Manduchi
definition source: WEB: http://en.wikipedia.org/wiki/Logarithm
imported from: obi.owl

regression analysis method
type: Class
subclass of: data transformation
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: model parameter estimation
      intersection of: model fitting
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: statistical model
      intersection of: Restriction
        on property: is about
        some values from: study design dependent variable
editor preferred label: regression analysis method
has curation status: pending final vetting
definition: Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
editor note: Date:2013-11-15 Person: AGB,PRS Adding restrictions, specifying model + parameter estimation process change of label from 'regression analysis method' to 'regression analysis'
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
term editor: Tina Hernandez-Boussard
definition source: BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
imported from: obi.owl
STATO alternative term: regression analysis

principal component regression
type: Class
subclass of: regression analysis method
subclass of: class discovery data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
editor preferred label: principal component regression
has curation status: pending final vetting
definition: The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
term editor: Tina Hernandez-Boussard
definition source: WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html
imported from: obi.owl

data visualization
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: graph
    union of: image
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: Class
    union of: graph
    union of: image
editor preferred label: data visualization
example of usage: Generation of a heatmap from a microarray dataset
has curation status: ready for release
definition: An planned process that creates images, diagrams or animations from the input data.
term editor: Elisabetta Manduchi
term editor: James Malone
term editor: Melanie Courtot
term editor: Tina Boussard
alternative term: data encoding as image
alternative term: visualization
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
definition source: PERSON: Tina Boussard
curator note: Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding
imported from: obi.owl

mode calculation
type: Class
subclass of: center calculation data transformation
subclass of: descriptive statistical calculation data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: center value
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: center calculation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: mode
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: descriptive statistical calculation objective
editor preferred label: mode calculation
has curation status: metadata complete
definition: A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
term editor: James Malone
term editor: Monnie McGee
definition source: PERSON: James Malone
definition source: PERSON: Monnie McGee
curator note: From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
imported from: obi.owl

median calculation
type: Class
subclass of: center calculation data transformation
subclass of: descriptive statistical calculation data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: center value
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: center calculation objective
subclass of: Restriction
  on property: has_specified_output
  some values from: center value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: descriptive statistical calculation objective
editor preferred label: median calculation
has curation status: metadata complete
definition: A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
term editor: James Malone
term editor: Monnie McGee
definition source: PERSON: James Malone
definition source: PERSON: Monnie McGee
curator note: From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
imported from: obi.owl

agglomerative hierarchical clustering
type: Class
subclass of: hierarchical clustering
editor preferred label: agglomerative hierarchical clustering
has curation status: pending final vetting
definition: An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.
term editor: Elisabetta Manduchi
term editor: James Malone
alternative term: bottom-up hierarchical clustering
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

divisive hierarchical clustering
type: Class
subclass of: hierarchical clustering
editor preferred label: divisive hierarchical clustering
has curation status: pending final vetting
definition: A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.
term editor: Elisabetta Manduchi
term editor: James Malone
alternative term: top-down hierarchical clustering
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

false discovery rate correction method
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: q-value
subclass of: multiple testing correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple testing correction objective
editor preferred label: false discovery rate correction method
has curation status: pending final vetting
definition: The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
editor note: 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt
term editor: Monnie McGee
term editor: Philippe Rocca-Serra
alternative term: FDR correction method
definition source: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
imported from: obi.owl

data transformation objective
type: Class
subclass of: objective specification
editor preferred label: data transformation objective
example of usage: normalize objective
has curation status: ready for release
definition: An objective specification to transformation input data into output data
editor note: Modified definition in 2013 Philly OBI workshop
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

data normalization objective
type: Class
subclass of: data transformation objective
editor preferred label: data normalization objective
example of usage: Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
has curation status: ready for release
definition: A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons.
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: Helen Parkinson
definition source: PERSON: James Malone
imported from: obi.owl

correction objective
type: Class
subclass of: data transformation objective
editor preferred label: correction objective
example of usage: Type I error correction
has curation status: metadata incomplete
definition: A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
term editor: James Malone
definition source: PERSON: James Malone
definition source: PERSON: Melanie Courtot
imported from: obi.owl

normalization data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: normalized data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: data normalization objective
subclass of: data transformation
editor preferred label: normalization data transformation
has curation status: metadata incomplete
definition: A normalization data transformation is a data transformation that has objective normalization.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

averaging data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: average value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: averaging objective
subclass of: data transformation
editor preferred label: averaging data transformation
has curation status: metadata incomplete
definition: An averaging data transformation is a data transformation that has objective averaging.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

partitioning data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: partitioning objective
subclass of: data transformation
editor preferred label: partitioning data transformation
has curation status: metadata incomplete
definition: A partitioning data transformation is a data transformation that has objective partitioning.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

partitioning objective
type: Class
subclass of: data transformation objective
editor preferred label: partitioning objective
example of usage: A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
has curation status: ready for release
definition: A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
term editor: Elisabetta Manduchi
term editor: James Malone
definition source: PERSON: Elisabetta Manduchi
imported from: obi.owl

class discovery data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: clustered data set
  union of: Restriction
    on property: achieves_planned_objective
    some values from: class discovery objective
subclass of: data transformation
editor preferred label: class discovery data transformation
has curation status: ready for release
definition: A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
term editor: James Malone
alternative term: clustering data transformation
alternative term: unsupervised classification data transformation
definition source: PERSON: James Malone
imported from: obi.owl

center calculation objective
type: Class
subclass of: data transformation objective
editor preferred label: center calculation objective
example of usage: A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
has curation status: ready for release
definition: A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

class discovery objective
type: Class
subclass of: data transformation objective
editor preferred label: class discovery objective
has curation status: ready for release
definition: A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
term editor: James Malone
alternative term: clustering objective
alternative term: discriminant analysis objective
alternative term: unsupervised classification objective
definition source: PERSON: Elisabetta Manduchi
definition source: PERSON: James Malone
imported from: obi.owl

center calculation data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: center value
  union of: Restriction
    on property: achieves_planned_objective
    some values from: center calculation objective
subclass of: data transformation
editor preferred label: center calculation data transformation
has curation status: metadata incomplete
definition: A center calculation data transformation is a data transformation that has objective of center calculation.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

descriptive statistical calculation data transformation
type: Class
equivalent class: Class
  union of: Restriction
    on property: has_specified_output
    some values from: data set of features
  union of: Restriction
    on property: achieves_planned_objective
    some values from: descriptive statistical calculation objective
subclass of: data transformation
editor preferred label: descriptive statistical calculation data transformation
has curation status: ready for release
definition: A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

error correction objective
type: Class
subclass of: correction objective
editor preferred label: error correction objective
example of usage: Application of a multiple testing correction method
has curation status: pending final vetting
definition: An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
term editor: James Malone, Helen Parkinson
definition source: PERSON: James Malone
imported from: obi.owl

gene list visualization
type: Class
subclass of: data visualization
subclass of: Restriction
  on property: has_specified_output
  some values from: table
subclass of: Restriction
  on property: has_specified_input
  all values from: gene list
editor preferred label: gene list visualization
has curation status: metadata incomplete
definition: Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
term editor: James Malone
imported from: obi.owl

survival analysis data transformation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: survival analysis objective
subclass of: data transformation
editor preferred label: survival analysis data transformation
has curation status: metadata complete
definition: A data transformation which has the objective of performing survival analysis.
term editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

chi square test
type: Class
subclass of: statistical test hypothesis
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
editor preferred label: chi square test
has curation status: metadata incomplete
definition: The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
editor note: negociation with OBI hence definition and definition source are missing from this class
term editor: PERSON: James Malone
term editor: PERSON: Tina Boussard
imported from: obi.owl

ANOVA
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: F-test
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: between group comparison objective
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    min qualified cardinality: 1
    on class: Class
      intersection of: study design independent variable
      intersection of: categorical variable
  intersection of: Restriction
    on property: has_specified_input
    min qualified cardinality: 1
    on class: Class
      intersection of: study design dependent variable
      intersection of: continuous variable
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: homoskedasticity hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: Class
      intersection of: normal distribution hypothesis
      intersection of: Restriction
        on property: has value
        has value: true
    intersection of: Restriction
      on property: is about
      some values from: residual
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: Levene's test
    union of: Barlett's test
    union of: Brown Forsythe test
    union of: Kolmogorov-Smirnov test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_input
  some values from: F-distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: standardized mean difference
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is about
      some values from: absence of between group difference hypothesis
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: population
editor preferred label: ANOVA
has curation status: metadata incomplete
has curation status: pending final vetting
definition: ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal.
editor note: AGB and PRS augmented the class with formal definitions as part of STATO extension
term editor: Alejandra Gonzalez-Beltran
term editor: James Malone
term editor: Philippe Rocca-Serra
alternative term: Analysis of Variance
imported from: obi.owl
R command: stat.anova()

observation design
type: Class
subclass of: study design
editor preferred label: observation design
example of usage: PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
has curation status: pending final vetting
definition: observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
term editor: Philippe Rocca-Serra
definition source: OBI branch derived
imported from: obi.owl

extraction
type: Class
subclass of: material component separation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: separation into different composition objective
editor preferred label: extraction
example of usage: nucleic acid extraction using phenol chloroform
has curation status: metadata incomplete
definition: A material separation in which a desired component of an input material is separated from the remainder
editor note: Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. 'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future.
term editor: Person:Bjoern Peters
term editor: Philippe Rocca-Serra
imported from: obi.owl

group randomization
type: Class
subclass of: group assignment
editor preferred label: group randomization
example of usage: PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
has curation status: metadata complete
definition: A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
imported from: obi.owl

nucleic acid hybridization
type: Class
subclass of: material processing
subclass of: Restriction
  on property: realizes
  some values from: Class
    intersection of: function
    intersection of: Restriction
      on property: inheres in
      some values from: hybridization chamber
editor preferred label: nucleic acid hybridization
example of usage: PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
has curation status: metadata complete
definition: a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
imported from: obi.owl
ISA alternative term: hybridization assay

flow cell
type: Class
subclass of: container
subclass of: Restriction
  on property: has function
  some values from: contain function
editor preferred label: flow cell
example of usage: Biofilm Flow Cell
has curation status: metadata incomplete
definition: Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
term editor: Person:John Quinn
alternative term: flow_cell
definition source: http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
imported from: obi.owl

flow cytometer
type: Class
subclass of: cytometer
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: flow cell
  intersection of: Restriction
    on property: has part
    some values from: light source
  intersection of: Restriction
    on property: has part
    some values from: optical filter
  intersection of: Restriction
    on property: has part
    some values from: photodetector
subclass of: Restriction
  on property: has part
  some values from: obscuration bar
subclass of: Restriction
  on property: has part
  some values from: droplet sorter
editor preferred label: flow cytometer
example of usage: FACS Calibur
has curation status: ready for release
definition: A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
term editor: John Quinn
definition source: http://en.wikipedia.org/wiki/Flow_cytometer
imported from: obi.owl

light source
type: Class
subclass of: light emission device
subclass of: Restriction
  on property: has function
  some values from: light emission function
editor preferred label: light source
has curation status: metadata incomplete
definition: A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
term editor: Elizabeth M. Goralczyk
term editor: John Quinn
term editor: Olga Tchuvatkina
definition source: Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
imported from: obi.owl

obscuration bar
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
editor preferred label: obscuration bar
example of usage: obscuration bar in a flow cytometer
has curation status: metadata incomplete
definition: An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
term editor: Daniel Schober
definition source: Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
definition source: John Quinn
imported from: obi.owl

optical filter
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: filter function
editor preferred label: optical filter
example of usage: 720 LP filter, 580/30 BP filter
has curation status: metadata incomplete
definition: An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
term editor: John Quinn
definition source: http://en.wikipedia.org/wiki/Optical_filter
imported from: obi.owl

photodetector
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: photodetector
example of usage: A photomultiplier tube, a photo diode
has curation status: metadata incomplete
definition: A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
term editor: John Quinn
definition source: http://einstein.stanford.edu/content/glossary/glossary.html
imported from: obi.owl

DNA sequencer
type: Class
subclass of: measurement device
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: DNA sequencer
example of usage: ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
has curation status: ready for release
definition: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
term editor: Trish Whetzel
definition source: MO
imported from: obi.owl

hybridization chamber
type: Class
subclass of: physical store
subclass of: Restriction
  on property: has function
  some values from: contain function
subclass of: Restriction
  on property: has function
  some values from: environment control function
editor preferred label: hybridization chamber
example of usage: Glass Array Hybridization Cassette
has curation status: metadata complete
definition: A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
term editor: Trish Whetzel
definition source: MO_563 hybridization_chamber
imported from: obi.owl

cytometer
type: Class
subclass of: measurement device
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: light source
  intersection of: Restriction
    on property: has part
    some values from: optical filter
  intersection of: Restriction
    on property: has part
    some values from: photodetector
subclass of: Restriction
  on property: has function
  some values from: measure function
editor preferred label: cytometer
has curation status: ready for release
definition: A cytometer is an instrument for counting and measuring cells.
term editor: Melanie Courtot
definition source: http://medical.merriam-webster.com/medical/cytometer
imported from: obi.owl

microarray
type: Class
subclass of: assay array
editor preferred label: microarray
example of usage: An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
has curation status: ready for release
definition: A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
term editor: Daniel Schober
definition source: PERSON: Chris Stoeckert
imported from: obi.owl

DNA microarray
type: Class
subclass of: microarray
editor preferred label: DNA microarray
example of usage: Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
has curation status: metadata incomplete
definition: A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
term editor: PERSON: Daniel Schober
term editor: PERSON: Frank Gibson
alternative term: DNA Chip
alternative term: DNA-array
definition source: Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
imported from: obi.owl

droplet sorter
type: Class
subclass of: material separation device
subclass of: Restriction
  on property: has function
  some values from: sort function
editor preferred label: droplet sorter
has curation status: metadata incomplete
definition: A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original sample for particles of interest based on qualities determined by gating) or disposal.
term editor: OBI Instrument branch
definition source: OBI Instrument branch
imported from: obi.owl

study design
type: Class
equivalent class: Class
  intersection of: plan specification
  intersection of: Class
    union of: parallel group design
    union of: Class
      complement of: parallel group design
  intersection of: Restriction
    on property: has part
    some values from: protocol
subclass of: plan specification
subclass of: Restriction
  on property: has part
  some values from: protocol
subclass of: Restriction
  on property: is about
  some values from: investigation
subclass of: Restriction
  on property: denotes
  some values from: study group population
subclass of: Restriction
  on property: declares
  some values from: study design independent variable
subclass of: Restriction
  on property: declares
  some values from: study design dependent variable
editor preferred label: study design
example of usage: a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
has curation status: ready for release
definition: A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
editor note: Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
term editor: PERSON: Chris Stoeckert
alternative term: experimental design
curator note: rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol.
imported from: obi.owl

repeated measure design
type: Class
subclass of: intervention design
subclass of: study design
subclass of: Class
  union of: Restriction
    on property: has part
    some values from: association between categorical variables testing objective
  union of: Restriction
    on property: has part
    some values from: within subject comparison objective
editor preferred label: repeated measure design
example of usage: PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
has curation status: metadata complete
definition: a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
term editor: PlanAndPlannedProcess Branch
definition source: http://www.holah.karoo.net/experimentaldesigns.htm
imported from: obi.owl

cross over design
type: Class
subclass of: intervention design
subclass of: repeated measure design
subclass of: time series design
subclass of: block design
subclass of: Restriction
  on property: has part
  some values from: within subject comparison objective
subclass of: Restriction
  on property: declares
  some values from: Class
    intersection of: Class
      intersection of: study design independent variable
      intersection of: blocking variable
    intersection of: Restriction
      on property: is about
      some values from: time sampled measurement data set
editor preferred label: cross over design
example of usage: PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
has curation status: metadata complete
definition: a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
term editor: Philippe Rocca-Serra
definition source: (source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
imported from: obi.owl

matched pairs design
type: Class
subclass of: study design
subclass of: block design
subclass of: Restriction
  on property: has part
  some values from: pairing rule
subclass of: Restriction
  on property: declares
  some values from: Class
    intersection of: blocking variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: material entity
        intersection of: Restriction
editor preferred label: matched pairs design
example of usage: PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknow…
has curation status: pending final vetting
definition: A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
term editor: Philippe Rocca-Serra
definition source: http://www.holah.karoo.net/experimentaldesigns.htm
imported from: obi.owl

parallel group design
type: Class
subclass of: study design
editor preferred label: parallel group design
example of usage: PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
has curation status: pending final vetting
definition: A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
term editor: Philippe Rocca-Serra
alternative term: independent measure design
definition source: http://www.holah.karoo.net/experimentaldesigns.htm
imported from: obi.owl

randomized complete block design
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realized in
    some values from: complete randomization
  intersection of: Restriction
    on property: declares
    some values from: blocking variable
subclass of: realizable entity
subclass of: intervention design
subclass of: study design
subclass of: block design
editor preferred label: randomized complete block design
example of usage: http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
has curation status: pending final vetting
definition: A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
term editor: Philippe Rocca-Serra
definition source: http://www.tufts.edu/~gdallal/ranblock.htm
imported from: obi.owl

latin square design
type: Class
subclass of: study design
subclass of: randomized complete block design
subclass of: Restriction
  on property: realized in
  some values from: complete randomization
subclass of: Restriction
  on property: declares
  some values from: study design independent variable
subclass of: Restriction
  on property: declares
  qualified cardinality: 2
  on class: blocking variable
editor preferred label: latin square design
example of usage: PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
has curation status: pending final vetting
definition: Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
term editor: Philippe Rocca-Serra
definition source: Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
imported from: obi.owl

graeco latin square design
type: Class
subclass of: randomized complete block design
subclass of: Restriction
  on property: declares
  qualified cardinality: 3
  on class: blocking variable
editor preferred label: graeco latin square design
example of usage: PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
has curation status: pending final vetting
definition: Greco-Latin square design is a study design which relates to Latin square design
term editor: Philippe Rocca-Serra
definition source: Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
curator note: only 2 articles in pubmed ->probably irrelevant
imported from: obi.owl
STATO alternative term: Euler square design
STATO alternative term: orthogonal latin squares design

hyper graeco latin square design
type: Class
subclass of: study design
subclass of: randomized complete block design
subclass of: Restriction
  on property: realized in
  some values from: complete randomization
subclass of: Restriction
  on property: declares
  qualified cardinality: 4
  on class: blocking variable
editor preferred label: hyper graeco latin square design
has curation status: pending final vetting
definition: PRS to do
term editor: Philippe Rocca-Serra
definition source: Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
curator note: no example found in pubmed->not in use in the community
imported from: obi.owl

factorial design
type: Class
equivalent class: Class
  union of: fractional factorial design
  union of: full factorial design
subclass of: study design
subclass of: Restriction
  on property: has part
  some values from: number of factor level combinations
subclass of: Restriction
  on property: has part
  some values from: between group comparison objective
subclass of: Restriction
  on property: has part
  some values from: factor level combination
subclass of: Restriction
  on property: declares
  min qualified cardinality: 1
  on class: study design dependent variable
subclass of: Restriction
  on property: declares
  min qualified cardinality: 2
  on class: study design independent variable
disjoint with: single factor design
editor preferred label: factorial design
example of usage: PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
has curation status: pending final vetting
definition: factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
term editor: Philippe Rocca-Serra
definition source: http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
imported from: obi.owl

2x2 factorial design
type: Class
subclass of: factorial design
subclass of: full factorial design
subclass of: Restriction
  on property: has part
  some values from: factor level combination
subclass of: Restriction
  on property: declares
  qualified cardinality: 2
  on class: Class
    intersection of: study design independent variable
    intersection of: dichotomous variable
editor preferred label: 2x2 factorial design
example of usage: PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
has curation status: metadata complete
definition: a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
term editor: Philippe Rocca-Serra
definition source: PMID: 17561240
imported from: obi.owl

fractional factorial design
type: Class
subclass of: factorial design
editor preferred label: fractional factorial design
has curation status: pending final vetting
definition: A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
term editor: Philippe Rocca-Serra
definition source: http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
imported from: obi.owl

dye swap design
type: Class
subclass of: study design
subclass of: block design
subclass of: Restriction
  on property: declares
  some values from: Class
    intersection of: blocking variable
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: molecular entity
        intersection of: Restriction
editor preferred label: dye swap design
example of usage: PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
has curation status: pending final vetting
definition: An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
term editor: Philippe Rocca-Serra on behalf of MO
definition source: MO_858
imported from: obi.owl

time series design
type: Class
equivalent class: Restriction
  on property: declares
  some values from: Class
    intersection of: study design independent variable
    intersection of: Restriction
      on property: is about
      some values from: time sampled measurement data set
subclass of: study design
editor preferred label: time series design
example of usage: PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limite…
has curation status: pending final vetting
definition: Groups of assays that are related as part of a time series.
editor note: PRS-AGB adding formal restriction on independent variable specification about time (march 2013) and making time series design class a defined class.
term editor: Philippe Rocca-Serra on behalf of MO
definition source: MO_887
imported from: obi.owl

collecting specimen from organism
type: Class
subclass of: specimen collection process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: specimen
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: specimen collection objective
editor preferred label: collecting specimen from organism
example of usage: taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
has curation status: ready for release
definition: a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
term editor: PERSON:Bjoern Peters
definition source: IEDB
imported from: obi.owl

material component separation
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: material separation objective
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: material entity
subclass of: Restriction
  on property: has_specified_output
  some values from: material entity
editor preferred label: material component separation
example of usage: Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
has curation status: ready for release
definition: a material processing in which components of an input material become segregated in space
term editor: Bjoern Peters
definition source: IEDB
imported from: obi.owl

group assignment
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: role
    intersection of: Restriction
      on property: inheres in
      some values from: organism
editor preferred label: group assignment
example of usage: Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
has curation status: ready for release
definition: group assignment is a process which has an organism as specified input and during which a role is assigned
term editor: Philippe Rocca-Serra
alternative term: cohort assignment
alternative term: study assignment
definition source: OBI Plan
imported from: obi.owl

maintaining cell culture
type: Class
subclass of: material maintenance
subclass of: Restriction
  on property: has_specified_input
  some values from: cultured cell population
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: culture medium
    union of: cell freezing medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material maintenance objective
editor preferred label: maintaining cell culture
example of usage: When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
has curation status: pending final vetting
definition: a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

establishing cell culture
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: cell
subclass of: Restriction
  on property: has_specified_input
  some values from: culture medium
subclass of: Restriction
  on property: has_specified_output
  some values from: cultured cell population
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: 'establishing cell culture'
has curation status: metadata complete
definition: a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line).
term editor: PERSON:Matthew Brush
definition source: PERSON:Matthew Brush
imported from: obi.owl
comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms.

addition of molecular label
type: Class
subclass of: material processing
subclass of: Restriction
  on property: has_specified_input
  some values from: target of material addition
subclass of: Restriction
  on property: has_specified_input
  some values from: molecular label
subclass of: Restriction
  on property: has_specified_output
  some values from: molecular-labeled material
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: addition of molecular label
example of usage: The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
has curation status: pending final vetting
definition: a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay
term editor: PERSON:Matthew Brush
alternative term: labeling
definition source: OBI developer call, 3-12-12
imported from: obi.owl

sequencing assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has_specified_output
    some values from: sequence data
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: assay objective
subclass of: assay
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: Class
      union of: deoxyribonucleic acid
      union of: ribonucleic acid
      union of: protein
    intersection of: Restriction
      on property: has role
      some values from: evaluant role
editor preferred label: sequencing assay
example of usage: The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
has curation status: pending final vetting
definition: the use of a chemical or biochemical means to infer the sequence of a biomaterial
editor note: has_output should be sequence of input; we don't have sequence well defined yet
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

recombinant vector cloning
type: Class
subclass of: material processing
subclass of: Restriction
  on property: realizes
  some values from: cloning vector role
subclass of: Restriction
  on property: has_specified_input
  some values from: cloning vector
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has role
      some values from: cloning insert role
subclass of: Restriction
  on property: has_specified_output
  some values from: recombinant vector
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: material transformation objective
editor preferred label: recombinant vector cloning
has curation status: metadata complete
definition: a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
term editor: pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
alternative term: molecular cloning
definition source: OBI branch derived
imported from: obi.owl

RNA extraction
type: Class
subclass of: nucleic acid extraction
subclass of: Restriction
  on property: has_specified_output
  some values from: ribonucleic acid
editor preferred label: RNA extraction
has curation status: pending final vetting
definition: A RNA extraction is a nucleic acid extraction where the desired output material is RNA
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO
imported from: obi.owl

nucleic acid extraction
type: Class
subclass of: extraction
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: sample from organism
    union of: organism
    union of: cultured cell population
subclass of: Restriction
  on property: has_specified_output
  some values from: nucleic acid
editor preferred label: nucleic acid extraction
example of usage: Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
has curation status: pending final vetting
definition: a material separation to recover the nucleic acid fraction of an input material
term editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
curator note: requested by Helen Parkinson for MO. Could be defined class
imported from: obi.owl

phage display library
type: Class
subclass of: recombinant vector
subclass of: Restriction
  on property: is_specified_output_of
  some values from: recombinant vector cloning
subclass of: Restriction
  on property: has grain
  some values from: recombinant vector
editor preferred label: phage display library
example of usage: PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
has curation status: metadata complete
definition: a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
alternative term: display library
definition source: WEB: http://www.immuneepitope.org/home.do
curator note: PRS: 22022008. class moved under population, modification of definition and replacement of biomaterials in previous definition with 'material' addition of has_role restriction
imported from: obi.owl

material to be added
type: Class
equivalent class: Restriction
  on property: has role
  some values from: material to be added role
subclass of: material entity
editor preferred label: material to be added
example of usage: A mixture of peptides that is being added into a cell culture.
has curation status: ready for release
definition: a material that is added to another one in a material combination process
editor note: 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
editor note: 2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
definition source: IEDB
imported from: obi.owl

target of material addition
type: Class
equivalent class: Restriction
  on property: has role
  some values from: target of material addition role
subclass of: material entity
editor preferred label: target of material addition
example of usage: A cell culture into which a mixture of peptides is being added.
has curation status: ready for release
definition: A material entity into which another is being added in a material combinatino process
editor note: 10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
definition source: IEDB
imported from: obi.owl

phenotype
type: Class
subclass of: quality
editor preferred label: phenotype
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
imported from: obi.owl
imported from: ogms.owl

fluorescence
type: Class
subclass of: disposition
editor preferred label: fluorescence
definition: A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
imported from: obi.owl
imported from: pato.owl

mass
type: Class
subclass of: quality
editor preferred label: mass
definition: A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.
imported from: obi.owl
imported from: pato.owl

protein
type: Class
subclass of: peptide
editor preferred label: protein
example of usage: antithrombin III is a protein
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
imported from: obi.owl
imported from: pr.owl

molecular label role
type: Class
subclass of: role
editor preferred label: molecular label role
definition: a reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay.
editor note: MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)
alternative term: molecular tracer role
definition source: OBI developer call, 3-12-12
imported from: obi.owl
imported from: reo.owl

molecular label
type: Class
equivalent class: Class
  intersection of: molecular entity
  intersection of: Restriction
    on property: has role
    some values from: molecular label role
subclass of: molecular entity
editor preferred label: molecular label
definition: a molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay
alternative term: molecular tracer
definition source: OBI developer call, 3-12-12
imported from: obi.owl
imported from: reo.owl

region
type: Class
subclass of: generically dependent continuant
editor preferred label: region
definition: A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
alternative term: primary structure of sequence macromolecule
alternative term: sequence
imported from: obi.owl
imported from: so.owl

digital file
type: Class
subclass of: information content entity
example of usage: digital images may be stored as electronic file in TIFF format on mass memory storage devices
has curation status: ready for release
definition: an electronic file is an information content entity which conforms to a specification or format and which is meant to hold data and information in digital form, accessible to software agents
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

balanced design
type: Class
subclass of: study design
has curation status: ready for release
definition: a balanced design is a an experimental design where all experimental group have the an equal number of subject observations
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

single factor design
type: Class
equivalent class: Restriction
  on property: declares
  qualified cardinality: 1
  on class: study design independent variable
subclass of: study design
has curation status: ready for release
definition: a single factor design is a study design which declares exactly 1 independent variable
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

x-axis
type: Class
subclass of: cartesian coordinate axis
has curation status: ready for release
definition: x-axis is a cartesian coordinate axis which is orthogonal to the y-axis and the z-axis
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

axis
type: Class
subclass of: line graph
has curation status: ready for release
definition: an axis is a line graph used as reference line for the measurement of coordinates.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.oxforddictionaries.com/definition/english/axis

y-axis
type: Class
subclass of: cartesian coordinate axis
has curation status: ready for release
definition: y-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the z-axis
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

cartesian coordinate system
type: Class
subclass of: coordinate system
subclass of: Restriction
  on property: has part
  some values from: cartesian coordinate axis
subclass of: Restriction
  on property: has part
  some values from: cartesian spatial coordinate origin
has curation status: ready for release
definition: A Cartesian coordinate system is a coordinate system that specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Cartesian_coordinate_system

coordinate system
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: spatial region
has curation status: ready for release
definition: In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element on a manifold such as Euclidean space.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Coordinate_system

cartesian coordinate axis
type: Class
subclass of: axis
has curation status: ready for release
definition: a cartesian axis is one of 3 the axis in a cartesian coordinate system defining a referential in 3 dimensions. each of the axis is orthogonal to the other 2
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: rectangular coordinate axis
definition source: adapted from Wolfram Alpha: https://www.wolframalpha.com/input/?i=cartesian+coordinates&lk=4&num=6&lk=4&num=6

z-axis
type: Class
subclass of: cartesian coordinate axis
has curation status: ready for release
definition: z-axis is a cartesian coordinate axis which is orthogonal to the x-axis and the y-axis
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

two dimensional cartesian coordinate system
type: Class
subclass of: cartesian coordinate system
subclass of: Restriction
  on property: has part
  some values from: y-axis
subclass of: Restriction
  on property: has part
  some values from: two dimensional cartesian spatial coordinate origin
subclass of: Restriction
  on property: is about
  some values from: two-dimensional spatial region
has curation status: ready for release
definition: a 2 dimensional cartesian coordinate system is a cartesian coordinate system which defines 2 orthogonal one dimensional axes and which may be used to describe a 2 dimensional spatial region.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

spherical coordinate system
type: Class
subclass of: coordinate system
has curation status: IAO_0000226
definition: In mathematics, a spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Spherical_coordinate_system

cylindrical coordinate system
type: Class
subclass of: coordinate system
has curation status: metadata incomplete
definition: A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis. The latter distance is given as a positive or negative number depending on which side of the reference plane faces the point.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Cylindrical_coordinate_system

polar coordinate system
type: Class
subclass of: coordinate system
has curation status: pending final vetting
definition: In mathematics, the polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Polar_coordinate_system

Wilk's lambda distribution
type: Class
subclass of: probability distribution
has curation status: ready for release
definition: Wilks' lambda distribution (named for Samuel S. Wilks), is a probability distribution used in multivariate hypothesis testing, especially with regard to the likelihood-ratio test and Multivariate analysis of variance. It is a multivariate generalization of the univariate F-distribution, and generalizes the F-distribution in the same way that the Hotelling's T-squared distribution generalizes Student's t-distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: wikipedia: last accessed: 2013-09-11 http://en.wikipedia.org/wiki/Wilks%27_lambda_distribution

three dimensional cartesian spatial coordinate origin
type: Class
subclass of: cartesian spatial coordinate origin
has curation status: requires discussion
definition: A cartesian spatial coordinate datum chosen as a fixed point of reference in a three dimensional spatial region.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

normal distribution hypothesis
type: Class
subclass of: goodness of fit hypothesis
has curation status: ready for release
definition: normal distribution hypothesis is a goodness of fit hypothesis stating that the distribution computed from the sample population fits a normal distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

two dimensional cartesian spatial coordinate origin
type: Class
subclass of: cartesian spatial coordinate origin
has curation status: requires discussion
definition: A cartesian spatial coordinate datum chosen as a fixed point of reference in a two dimensional spatial region.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

90% confidence interval
type: Class
subclass of: confidence interval
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: confidence level
    intersection of: Restriction
      on property: has specified value
      has value: 90
has curation status: ready for release
definition: a confidence interval which covers 90% of the sampling distribution, meaning that there is a 90% risk of false positive (type I error)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

one dimensional cartesian coordinate system
type: Class
subclass of: cartesian coordinate system
subclass of: Restriction
  on property: has part
  some values from: x-axis
subclass of: Restriction
  on property: has part
  some values from: one dimensional cartesian spatial coordinate origin
subclass of: Restriction
  on property: is about
  some values from: one-dimensional spatial region
has curation status: ready for release
definition: A one dimensional cartesian coordinate system is a cartesian coordinate system which defines a one dimensional axis and which may be used to describe a one dimensional spatial region, i.e. a straight line. It is defined by a point O, the origin, a unit of length and the orientation for the one dimensional space.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

studentized range distribution
type: Class
subclass of: continuous probability distribution
example of usage: http://www.stat.duke.edu/courses/Spring98/sta110c/qtable.html
has curation status: ready for release
definition: The studentized range (q) distribution is a probability distribution used by the Tukey Honestly Significant Difference test. The distribution of the statistic [x̄(k)- x̄(1)]/(s/√n) where random samples of size n have been taken from k independent and identically distributed normal populations, with x̄(1) and x̄(k) being, respectively, the smallest and largest of the k sample means, and s2 being the pooled estimate of the common variance. This statistic is particularly used in multiple comparison tests.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: q distribution
definition source: A Dictionary of Statistics (2 rev ed.), OUP. ISBN-13: 9780199541454 http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1588
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Tukey.html

three dimensional cartesian coordinate system
type: Class
subclass of: cartesian coordinate system
subclass of: Restriction
  on property: has part
  some values from: z-axis
subclass of: Restriction
  on property: has part
  some values from: three dimensional cartesian spatial coordinate origin
subclass of: Restriction
  on property: is about
  some values from: three-dimensional spatial region
has curation status: ready for release
definition: a three dimensional cartesian coordinate system is a cartesian coordinate system which defines 3 orthogonal one dimensional axes and which may be used to describe a 3 dimensional spatial region.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

one dimensional cartesian spatial coordinate origin
type: Class
subclass of: cartesian spatial coordinate origin
has curation status: requires discussion
definition: A cartesian spatial coordinate datum chosen as a fixed point of reference in a one dimensional spatial region.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

cartesian spatial coordinate origin
type: Class
subclass of: cartesian spatial coordinate datum
has curation status: requires discussion
definition: A cartesian spatial coordinate datum chosen as a fixed point of reference in a spatial region.
editor note: placeholder, more work needed
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

test of association between categorical variables
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: linkage between 2 categorical variable test is a statistical test which evaluates if there is an association between a predictor variable assuming discrete values and a response variable also assuming discrete values
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: test of association
definition source: STATO
STATO alternative term: test of independence
STATO alternative term: test of independence between variables

measure of dispersion
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: data set
    union of: probability distribution
has curation status: ready for release
definition: measure of variation or statistical dispersion is a data item which describes how much a theoritical distribution or dataset is spread.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: measure of variation

measure of central tendency
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: data set
    union of: probability distribution
has curation status: ready for release
definition: a measure of central tendency is a data item which attempts to describe a set of data by identifying the value of its centre.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
STATO alternative term: measure of central tendency

Chi-Squared statistic
type: Class
subclass of: measure of hypothesis testing
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Cochran-Armitage test for trend
has curation status: ready for release
definition: Chi-squared statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Chi-Squared distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

binary classification
type: Class
subclass of: data transformation
has curation status: ready for release
definition: binary classification (or binomial classification) is a data transformation which aims to cast members of a set into 2 disjoint groups depending on whether the element have a given property/feature or not.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Binary_classifier last accessed: 2013-11-21
STATO alternative term: binomial classification

mode
type: Class
equivalent class: Restriction
  on property: is_specified_output_of
  some values from: mode calculation
subclass of: data set of features
subclass of: center value
subclass of: measure of central tendency
has curation status: ready for release
definition: The mode is a data item which corresponds to the most frequently occurring number in a set of numbers.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.sagepub.com/upm-data/47775_ch_3.pdf
STATO alternative term: mode
Python command: scipy.stats.mode(a, axis=0) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mode.html#scipy.stats.mode source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L586

model parameter
type: Class
subclass of: data item
subclass of: Restriction
  on property: part of
  some values from: model term
subclass of: Restriction
  on property: is about
  some values from: factor level
has curation status: requires discussion
definition: a model parameter is a data item which is part of a model and which is meant to characterize an theoritecal or unknown population. a model parameter may be estimated by considering the properties of samples presumably taken from the theoritecal population
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

range
type: Class
subclass of: measure of dispersion
has curation status: ready for release
definition: the range is a measure of variation which describes the difference between the lowest score and the highest score in a set of numbers (a data set)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.sagepub.com/upm-data/47775_ch_3.pdf
R command: range(..., na.rm = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/base/html/range.html

outlier
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: data set
has curation status: ready for release
definition: Outliers are deviant scores that have been legitimately gathered and are not due to equipment failures.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.sagepub.com/upm-data/47775_ch_3.pdf

standard error of the mean
type: Class
subclass of: standard error of estimate
subclass of: Restriction
  on property: is about
  some values from: sample mean
subclass of: Restriction
  on property: estimate of
  some values from: statistic
example of usage: http://stats.stackexchange.com/questions/50623/r-calculating-mean-and-standard-error-of-mean-for-factors-with-lm-vs-direct
has curation status: ready for release
definition: The standard error of the mean (SEM) is data item denoting the standard deviation of the sample-mean's estimate of a population mean. It is calculated by dividing the sample standard deviation (i.e., the sample-based estimate of the standard deviation of the population) by the square root of n , the size (number of observations) of the sample. A measure of dispersion applied to means across hypothetical repeated random samples.
term editor: Alejandra Gonzalez-Beltran
term editor: Brian S. Alper, Harold Lehmann, Muhammad Afzal, Xing Song, Kenneth Wilkins, Joanne Dehnbostel
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: SEM
definition source: adapted from wikipedia (https://en.wikipedia.org/wiki/Standard_error)
STATO alternative term: SEM
Python command: scipy.stats.sem(a, axis=0, ddof=1) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.sem.html#scipy.stats.sem source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L1928

matched pair of subjects
type: Class
subclass of: population
subclass of: Restriction
  on property: is_specified_output_of
  some values from: subject pairing
has curation status: requires discussion
definition: a set of 2 subjects which result from a pairing process which assigns subject to a set based on a pairing rule/criteria
editor note: possibly submit to 'Population and Community Ontology'
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

statistic
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: data set
has curation status: ready for release
definition: a statistic is a measurement datum to describe a dataset or a variable. It is generated by a calculation on set of observed data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Statistic).
STATO alternative term: statistic

MA plot
type: Class
subclass of: scatter plot
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: average log signal intensity
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Class
      union of: log signal intensity ratio
      union of: Restriction
        on property: denotes
        some values from: Class
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: gene list visualization
    intersection of: Restriction
      on property: preceded by
      some values from: differential expression analysis data transformation
has curation status: ready for release
definition: an MA plot is a scatter plot of the log intensity ratios M = log_2(T/R) versus the average log intensities A = log_2(T*T)/2, where T and R represent the signal intensities in the test and reference channels respectively.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: M vs A plot
definition source: http://www.stat.berkeley.edu/users/terry/zarray/Software/SMAcode/html/plot.mva.html
STATO alternative term: MA plot
R command: plot.mva()

Anderson-Darling test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: data set
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: probability distribution
has curation status: pending final vetting
definition: The Anderson–Darling test is a statistical test of whether a given sample of data is drawn from a given probability distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Anderson_Darling_test
R command: ad.test(x) function, where x is a numeric vector
Python command: scipy.stats.anderson(x, dist='norm') http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.anderson.html#scipy.stats.anderson source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1017

one-way ANOVA
type: Class
subclass of: data transformation
subclass of: ANOVA
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: F-test
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: between group comparison objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: homoskedasticity hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: Class
      intersection of: normal distribution hypothesis
      intersection of: Restriction
        on property: has value
        has value: true
    intersection of: Restriction
      on property: is about
      some values from: residual
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: Levene's test
    union of: Barlett's test
    union of: Brown Forsythe test
    union of: Kolmogorov-Smirnov test
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: standardized mean difference
    union of: root-mean-square standardized effect
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: categorical variable
has curation status: ready for release
definition: one-way anova is an analysis of variance where the different groups being compared are associated with the factor levels of only one independent variable. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: one factor ANOVA
definition source: STATO
R command: http://statland.org/R/R/R1way.htm
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f_oneway.html#scipy.stats.f_oneway

two-way ANOVA
type: Class
subclass of: data transformation
subclass of: ANOVA
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: F-test
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: between group comparison objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: homoskedasticity hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: Class
      intersection of: normal distribution hypothesis
      intersection of: Restriction
        on property: has value
        has value: true
    intersection of: Restriction
      on property: is about
      some values from: residual
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: Levene's test
    union of: Barlett's test
    union of: Brown Forsythe test
    union of: Kolmogorov-Smirnov test
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: standardized mean difference
    union of: root-mean-square standardized effect
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: study design independent variable
    intersection of: categorical variable
has curation status: ready for release
definition: two-way anova is an analysis of variance where the different groups being compared are associated the factor levels of exatly 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: two factor ANOVA
definition source: STATO
R command: http://courses.statistics.com/software/R/Rtwoway.htm

block design
type: Class
equivalent class: Class
  union of: Restriction
    on property: has part
    some values from: group assignment based on blocking variable specification
  union of: Restriction
    on property: declares
    some values from: blocking variable
subclass of: study design
has curation status: pending final vetting
definition: a block design is a kind of study design which declares a blocking variable (also known as nuisance variable) in order to account for a known source of variation and reduce its impact on the acquisition of the signal
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from several sources including Wikipedia

count
type: Class
subclass of: statistic
subclass of: Restriction
  on property: has value
  qualified cardinality: 1
  on data range: integer
example of usage: a count of 4 resulting from counting limbs in humans
has curation status: ready for release
definition: a count is a data item denoted by an integer and representing the number of instances or occurences of an entity
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

multiway ANOVA
type: Class
subclass of: data transformation
subclass of: ANOVA
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: F-test
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: between group comparison objective
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: homoskedasticity hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: Class
      intersection of: normal distribution hypothesis
      intersection of: Restriction
        on property: has value
        has value: true
    intersection of: Restriction
      on property: is about
      some values from: residual
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: Levene's test
    union of: Barlett's test
    union of: Brown Forsythe test
    union of: Kolmogorov-Smirnov test
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: standardized mean difference
    union of: root-mean-square standardized effect
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 3
  on class: Class
    intersection of: study design independent variable
    intersection of: categorical variable
has curation status: ready for release
definition: Multi-way anova is an analysis of variance where the difference groups being compared are associated to the factor levels of more than 2 independent variables. The null hypothesis is an absence of difference between the means calculated for each of the groups. The test assumes normality and equivariance of the data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Hardy-Weinberg equilibrium hypothesis
type: Class
subclass of: goodness of fit hypothesis
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581961/
has curation status: ready for release
definition: Hardy-Weinberg equilibrium hypothesis is a good of fit hypothesis which states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences (non-random mating, mutation, selection, genetic drift, gene flow and meiotic drive).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)

signal to noise ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: signal to noise ratio is a measurement datum comparing the amount of meaningful, useful or interesting data (the signal) to the amount of irrelevant or false data (the noise). Depending on the field and domain of application, different variables will be used to determinate a 'signal to noise ratio'. In statistics, the definition of signal to noise ratio is the ratio of the mean of a measurement to its standard deviation. It thus corresponds to the inverse of the coefficient of variation
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Signal-to-noise_ratio#Alternative_definition last accessed: 2013-10-18
STATO alternative term: S/N
STATO alternative term: SNR
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.signaltonoise.html#scipy.stats.signaltonoise

Poisson distribution
type: Class
subclass of: discrete probability distribution
has curation status: ready for release
definition: Poisson distribution is a probability distribution used to model the number of events occurring within a given time interval. It is defined by a real number (λ) and an integer k representing the number of events and a function. The expected value of a Poisson-distributed random variable is equal to λ and so is its variance.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
R command: dpois(x, lambda, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Poisson.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.poisson.html#scipy.stats.poisson
Source: NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda366j.htm

Z-test
type: Class
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: normal distribution hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Z-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: ready for release
definition: Z-test is a statistical test which evaluate the null hypothesis that the means of 2 populations are equal and returns a p-value.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://reference.wolfram.com/mathematica/ref/ZTest.html
R command: simple.z.test(x, sigma, conf.level=0.95) http://www.inside-r.org/packages/cran/UsingR/docs/simple.z.test

false positive rate
type: Class
subclass of: proportion
subclass of: Restriction
  on property: is about
  some values from: statistical test hypothesis
has curation status: ready for release
definition: a false positive rate is a data item which accounts for the proportion of incorrect rejection of a true null hypothesis.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: PRS,AGB adapted from wikipedia and wolfram alpha
STATO alternative term: significance level
STATO alternative term: type I error rate
STATO alternative term: α

homoskedasticity hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: equal variance testing objective
has curation status: ready for release
definition: homoskedasticity states that all variances under consideration are homogenous.
editor note: definition edited according to the discussion documented in: https://github.com/ISA-tools/stato/issues/39
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: equality of variance
definition source: STATO

chromosome coordinate system
type: Class
subclass of: genomic coordinate system
subclass of: Restriction
  on property: has part
  some values from: version number
example of usage: http://www.ncbi.nlm.nih.gov/assembly/model/ chrX:35,000,000-36,000,000.
has curation status: pending final vetting
definition: chromosome coordinate system is a genomic coordinate which uses chromosome of a particular assembly build process to define start and end positions. This coordinate system is unstable and will change with each new genome sequence assembly build.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

absence of association hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: association between categorical variables testing objective
has curation status: ready for release
definition: a null hypothesis which states that no linkage exists between 2 categorical variables
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: no relationship between the variables
STATO alternative term: variables are independent

null hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: statistical hypothesis test objective
disjoint with: alternative hypothesis
has curation status: ready for release
definition: A null hypothesis is a statistical hypothesis that is tested for possible rejection under the assumption that it is true (usually that observations are the result of chance). The concept was introduced by R. A. Fisher. The hypothesis contrary to the null hypothesis, usually that the observations are the result of a real effect, is known as the alternative hypothesis.[wolfram alpha]
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/NullHypothesis.html

goodness of fit hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: goodness of fit hypothesis is a null hypothesis stating that the distribution computed from the sample population fits a theoretical distribution or that a dataset can be correctly explained by a model
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Student's t distribution
type: Class
subclass of: continuous probability distribution
subclass of: symmetric distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution location parameter
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 0
has curation status: ready for release
definition: the Student's t distribution is a continuous probability distribution which arises when estimating the mean of a normally distributed population in situations where the sample size is small and population standard deviation is unknown.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Student's_t-distribution)
STATO alternative term: t distribution
R command: dt(x, df, ncp, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TDist.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.t.html#scipy.stats.t

hypergeometric distribution
type: Class
subclass of: discrete probability distribution
has curation status: ready for release
definition: hypergeometric distribution is a probability distribution that describes the probability of k successes in n draws from a finite population of size N containing K successes without replacement
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Hypergeometric_distribution
R command: dhyper(x, m, n, k, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.hypergeom.html#scipy.stats.hypergeom

absence of between group difference hypothesis
type: Class
subclass of: hypothesis
subclass of: Class
  intersection of: hypothesis
  intersection of: Restriction
    on property: part of
    some values from: between group comparison objective
has curation status: ready for release
definition: It is a null hypothesis stating that there are no differences observed between group of subjects.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

absence of within subject difference hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: within subject comparison objective
has curation status: ready for release
definition: is a null hypothesis stating that there are no difference observed across a series of measurements made one same subject.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

genomic coordinate datum
type: Class
subclass of: data item
has curation status: ready for release
definition: genomic coordinate datum is a data item which denotes a genomic position expressed using a genomic coordinate system
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

sequence read count
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA sequencing
example of usage: http://left.subtree.org/2012/04/13/counting-the-number-of-reads-in-a-bam-file/
has curation status: ready for release
definition: sequence read count is a data item determining how many sequence reads have been generated by a DNA sequencing assay for a given stretch of DNA
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB-PRS, STATO

hypothesis
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has value
  some values from: boolean
has curation status: ready for release
definition: In statistics, a statement that can be tested.[wolfram alpha]
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
definition source: http://mathworld.wolfram.com/Hypothesis.html

Cleveland dot plot
type: Class
subclass of: dot plot
has curation status: ready for release
definition: Cleveland dot plot is a dot plot which plots points that each belong to one of several categories. They are an alternative to bar charts or pie charts, and look somewhat like a horizontal bar chart where the bars are replaced by a dots at the values associated with each category. Compared to (vertical) bar charts and pie charts, Cleveland argues that dot plots allow more accurate interpretation of the graph by readers by making the labels easier to read, reducing non-data ink (or graph clutter) and supporting table look-up.which
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Dot_plot_(statistics) and Cleveland, William S. (1993). Visualizing Data. Hobart Press. ISBN 0-9634884-0-6. hdl:2027/mdp.39015026891187.
R command: http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/dotchart.html dotchart(x, labels = NULL, groups = NULL, gdata = NULL, cex = par("cex"), pch = 21, gpch = 21, bg = par("bg"), color = par("fg"), gcolor = par("fg"), lcolor = "gray", xlim = range(x[is.finite(x)]), main = NULL, xlab = NULL, ylab = NULL, ...)

continuous probability distribution
type: Class
subclass of: probability distribution
has curation status: ready for release
definition: a continuous probability distribution is a probability distribution which is defined by a probability density function
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Continuous_probability_distribution last accessed: 14/01/2014

skewness
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: data set
    union of: probability distribution
has curation status: ready for release
definition: Skewness is a data item indicating of the degree of asymmetry of a distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/Skewness.html
R command: skewness(x, na.rm = FALSE, type = 3) http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/e1071/html/skewness.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.skew.html#scipy.stats.skew

number of degrees of freedom
type: Class
subclass of: count
has curation status: ready for release
definition: The number degree of freedom is a count evaluating the number of values in a calculation that can vary. In statistics, the number of degrees of freedom ν is equal to N-1 in the case of the direct measurement of a quantity estimated by the arithmetic mean of N independent observations.
editor note: AGB: Addressing issue https://github.com/ISA-tools/stato/issues/77, removed 'number of degrees of freedom' subClassOf 'count' and added 'number of degrees of freedom' subClassOf 'measurement datum' instead. For more details, see https://stats.stackexchange.com/questions/116511/explanation-for-non-integer-degrees-of-freedom-in-t-test-with-unequal-variances
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Ćwiek
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://stats.stackexchange.com/questions/16921/how-to-understand-degrees-of-freedom
definition source: http://www.optique-ingenieur.org/en/courses/OPI_ang_M07_C01/co/Contenu_07.html
definition source: the rank of the quadratic form (mathematical definition)
STATO alternative term: degrees of freedom

Yate's corrected Chi-Squared test
type: Class
subclass of: Pearson's Chi square test of independence between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_input
  some values from: 2 by 2 contingency table
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
has curation status: ready for release
definition: Yate's corrected Chi-Squared test is a statistical test which is used to test the association/linkage/independence of 2 dichotomous variables while introducing a correction for using the continous Chi-squared distribution for the test. To reduce the error in approximation, Frank Yates, an English statistician, suggested a correction for continuity that adjusts the formula for Pearson's chi-squared test by subtracting 0.5 from the difference between each observed value and its expected value in a 2 × 2 contingency table. This reduces the chi-squared value obtained and thus increases its p-value.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Yates's_correction_for_continuity) polled in June 2013
STATO alternative term: Yate's correction for continuity
R command: chisq.test(x, y = NULL, correct = TRUE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html

reaction rate
type: Class
subclass of: rate
has curation status: ready for release
definition: reaction rate is a measurement datum which represents the speed of a chemical reaction turning reactive species into product species of event (i.e the number of such conversions)s occuring over a time interval
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

substrate concentration
type: Class
subclass of: concentration
has curation status: ready for release
definition: substrate concentration is a scalar measurement datum which denotes the amount of molecular entity involved in an enzymatic reaction (or catalytic chemical reaction) and whose role in that reaction is as substrate.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Fisher's exact test
type: Class
subclass of: data transformation
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has part
  some values from: specifying null and alternate hypothesis
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: hypergeometric distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: contingency table
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study group population
        intersection of: Restriction
has curation status: ready for release
definition: Fisher's exact test is a statistical test used to determine if there are nonrandom associations between two categorical variables.
editor note: duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/FishersExactTest.html
R command: fisher.test(x) function, where x is a matrix
Python command: scipy.stats.fisher_exact(table, alternative='two-sided') http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.fisher_exact.html#scipy.stats.fisher_exact source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2485

Cochran-Mantel-Haenzel test for repeated tests of independence
type: Class
subclass of: data transformation
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: odds ratio homogeneity hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: 2 by 2 contingency table
    intersection of: Restriction
      on property: denotes
      qualified cardinality: 1
      on class: stratum population
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: categorical variable
    intersection of: Restriction
      on property: denotes
      min qualified cardinality: 2
      on class: stratum population
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: dichotomous variable
disjoint with: Cochran-Armitage test for trend
has curation status: ready for release
definition: Cochran-Mantel-Haenzel test for repeated tests of independence is a statitiscal test which allows the comparison of two groups on a dichotomous/categorical response. It is used when the effect of the explanatory variable on the response variable is influenced by covariates that can be controlled. It is often used in observational studies where random assignment of subjects to different treatments cannot be controlled, but influencing covariates can. The null hypothesis is that the two nominal variables that are tested within each repetition are independent of each other. So there are 3 variables to consider: two categorical variables to be tested for independence of each other, and the third variable identifies the repeats.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO adapted from wikipedia (http://en.wikipedia.org/wiki/Cochran–Mantel–Haenszel_statistics) and from the Handbook of Biological Statistics (http://udel.edu/~mcdonald/statcmh.html)
STATO alternative term: CHM test
STATO alternative term: Mantel–Haenszel test
R command: cmh.test(x,y,z)

rarefaction curve
type: Class
subclass of: line graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: Class
        intersection of: count
        intersection of: Restriction
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: is_specified_output_of
  some values from: data visualization
has curation status: requires discussion
definition: a rarefaction curve is a graph used for estimating species richness in ecology studies
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
R command: >library(vegan) >rarefaction(x, subsample=5, plot=TRUE, color=TRUE, error=FALSE, legend=TRUE, symbol) http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vegan/html/vegan-package.html

Mann-Whitney U-test
type: Class
subclass of: data transformation
subclass of: non-parametric test
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: ranking
    intersection of: Restriction
      on property: has_specified_input
      min qualified cardinality: 1
      on class: Class
        intersection of: Class
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: dichotomous variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: population
has curation status: ready for release
definition: The Mann-Whitney U-test is a null hypothesis statistical testing procedure which allows two groups (or conditions or treatments) to be compared without making the assumption that values are normally distributed. The Mann-Whitney test is the non-parametric equivalent of the t-test for independent samples
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: U test
alternative term: Wilcoxon rank-sum test
alternative term: rank-sum test for the comparison of two samples
definition source: adapted from http://udel.edu/~mcdonald/statkruskalwallis.html and from http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U last accessed [2014-03-04]
STATO alternative term: Wilcoxon Rank-Sum test
R command: wilcox.test(dependent variable ~ independant variable, data = dataset) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/wilcox.test.html
Python command: scipy.stats.mannwhitneyu(x, y, use_continuity=True) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mannwhitneyu.html#scipy.stats.mannwhitneyu source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4049
Python command: scipy.stats.ranksums(x, y) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ranksums.html#scipy.stats.ranksums source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4103

Shapiro-Wilk test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is about
      some values from: goodness of fit hypothesis
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: Shapiro-Wilk test is a goodness of fit test which evaluates the null hypothesis that the sample is drawn from a population following a normal distribution
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: S-W test
definition source: STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Shapiro–Wilk_test)
R command: shapiro.test(x) function, where x is a numeric vector https://stat.ethz.ch/R-manual/R-devel/library/stats/html/shapiro.test.html
Python command: scipy.stats.shapiro(x, a=None, reta=False) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.shapiro.html#scipy.stats.shapiro source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L944

Levene's test
type: Class
subclass of: data transformation
subclass of: homoskedasticity test
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: equal variance testing objective
has curation status: ready for release
definition: Levene's test is a null hypothesis statistical test which evaluates the null hypothesis of equality of variance in several populations.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Levene_test
R command: levene.test(x) function, where x is a numeric vector
Python command: scipy.stats.levene(*args, **kwds) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.levene.html#scipy.stats.levene source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1496

Barlett's test
type: Class
subclass of: data transformation
subclass of: homoskedasticity test
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: continuous variable
subclass of: Restriction
  on property: has_specified_input
  some values from: categorical variable
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: equal variance testing objective
has curation status: ready for release
definition: Bartlett's test (see Snedecor and Cochran, 1989) is used to test if k samples are from populations with equal variances. Equal variances across samples is called homoscedasticity or homogeneity of variances. Some statistical tests, for example the analysis of variance, assume that variances are equal across groups or samples. The Bartlett test can be used to verify that assumption. Bartlett's test is sensitive to departures from normality. That is, if the samples come from non-normal distributions, then Bartlett's test may simply be testing for non-normality. Levene's test and the Brown–Forsythe test are alternatives to the Bartlett test that are less sensitive to departures from normality.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Bartlett_test
R command: bartlett.test(x) function, where x is a numeric vector
Python command: scipy.stats.bartlett(*args) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.bartlett.html#scipy.stats.bartlett source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1450

Brown Forsythe test
type: Class
subclass of: data transformation
subclass of: homoskedasticity test
subclass of: Restriction
  on property: has part
  some values from: median calculation
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: equal variance testing objective
has curation status: ready for release
definition: the Brown Forsythe test is a statistical test which evaluates if the variance of different groups are equal. It relies on computing the median rather than the mean, as used in the Levene's test for homoschedacity. This test maybe used to, for instance, ensure that the conditions of applications of ANOVA are met.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia and Brown, M. B., and A. B. Forsythe. 1974a. The small sample behavior of some statistics which test the equality of several means. Technometrics, 16, 129-132.
R command: http://www.statmethods.net/stats/anovaAssumptions.html The hovPlot( ) function in the HH package provides a graphic test of homogeneity of variances based on Brown-Forsyth. In the following example, y is numeric and G is a grouping factor. Note that G must be of type factor. # Homogeneity of Variance Plot library(HH) hov(y~G, data=mydata) hovPlot(y~G,data=mydata)

Pearson's Chi square test of independence between categorical variables
type: Class
subclass of: chi square test
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_input
  some values from: contingency table
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
has curation status: ready for release
definition: Pearson's Chi-Squared test is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution or used to test independence of 2 categorical variables (ie absence of association between those variables).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Chi2 test for independence
definition source: adapted from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html and http://en.wikipedia.org/wiki/Pearson's_chi-squared_test
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html chisq.test(x, y = NULL, correct = TRUE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000)
R command: http://www.inside-r.org/packages/cran/nortest/docs/pearson.test pearson.test(x) function, where x is a numeric vector
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chi2_contingency.html#scipy.stats.chi2_contingency

fixed effect model
type: Class
subclass of: statistical model
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: model error term
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: model fixed effect term
      intersection of: Restriction
        on property: is about
        some values from: study design independent variable
  intersection of: Restriction
    on property: has part
    some values from: Class
      intersection of: model interaction effect term
      intersection of: Restriction
        on property: is about
        qualified cardinality: 2
        on class: study design independent variable
subclass of: Restriction
  on property: is model for
  some values from: Class
    union of: study design dependent variable
    union of: Class
      intersection of: study design independent variable
      intersection of: Restriction
        on property: has fixed effect on
        some values from: study design dependent variable
has curation status: requires discussion
definition: a fixed effect model is a statistical model which represents the observed quantities in terms of explanatory variables that are treated as if the quantities were non-random.
editor note: PRS: this is a stub and more work is needed to reconcile conflicting definitions
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Fixed_effects_model

Kolmogorov-Smirnov test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: continuous probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: Kolmogorov-Smirnov test is a goodness of fit test which evaluates the null hypothesis that a sample is drawn from a population that follows a specific continuous probability distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: K-S test
definition source: STATO, adapted from wikipedia (https://en.wikipedia.org/wiki/Kolmogorov–Smirnov_test)
definition source: http://www.itl.nist.gov/div898/handbook/eda/section3/eda35g.htm
R command: ks.test(dataset, distribution)
Python command: scipy.stats.kstwobign = <scipy.stats._continuous_distns.kstwobign_gen object at 0x7f6169f842d0> http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kstwobign.html#scipy.stats.kstwobign source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/_continuous_distns.py
Python command: scipy.stats.mstats.ks_twosamp(data1, data2,alternative='two-sided') http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mstats.ks_twosamp.html source code: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/mstats_basic.py#L821

multinomial probit regression for analysis of polychotomous dependent variable
type: Class
subclass of: regression analysis method
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design dependent variable
        intersection of: polychotomous variable
has curation status: requires discussion
definition: multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is probit function.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_probit) polled in June 2013
R command: http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf

effect size estimate
type: Class
equivalent class: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
subclass of: estimate
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
has curation status: ready for release
definition: effect size estimate is a data item about the direction and strength of the consequences of a causative agent as explored by statistical methods. Those methods produce estimates of the effect size, e.g. confidence interval
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB,PRS
STATO alternative term: effect size

F-test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: F-distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: F-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: an F-test is a statistical test which evaluates that the computed test statistics follows an F-distribution under the null hypothesis. The F-test is sensitive to departure from normality. F-test arise when decomposing the variability in a data set in terms of sum of squares.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

polychotomous variable
type: Class
equivalent class: Class
  intersection of: categorical variable
  intersection of: Restriction
    on property: declares
    min qualified cardinality: 2
    on class: data item
subclass of: categorical variable
has curation status: ready for release
definition: a polychotomous variable is a categorical variable which is defined to have minimally 2 categories or possible values
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
definition source: http://udel.edu/~mcdonald/statvartypes.html

study group population size
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: study group population
has curation status: ready for release
definition: statistical sample size is a count evaluating the number of individual experimental units
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB-PRS
STATO alternative term: statistical sample size

case-control study design
type: Class
subclass of: parallel group design
subclass of: Restriction
  on property: denotes
  qualified cardinality: 2
  on class: study group population
subclass of: Restriction
  on property: declares
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: dichotomous variable
has curation status: pending final vetting
definition: a case-control study design is a observation study design which assess the risk of particular outcome (a trait or a disease) associated with an event (either an exposure or endogenous factor). A case-control study design therefore declares an exposure variable which is dichotomous in nature (exposed/non-exposed) and an outcome variable, which is also dichotomous (case or control), thus giving the name to the design. During the execution of the design, a case control study defines a population and counts the events to determine their frequency.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from: http://www.drcath.net/toolkit/casecontrol.html

dichotomous variable
type: Class
subclass of: polychotomous variable
subclass of: Class
  intersection of: categorical variable
  intersection of: Restriction
    on property: declares
    qualified cardinality: 2
    on class: data item
has curation status: ready for release
definition: a dichotomous variable is a categorical variable which is defined to have only 2 categories or possible values
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB-PRS
definition source: http://udel.edu/~mcdonald/statvartypes.html
comment: 'has part' exactly 1 ('categorical measurement datum' and ('has category label' exactly 2 'categorical label'))

genome-wide association study
type: Class
subclass of: genetic association study
subclass of: Restriction
  on property: has_specified_output
  some values from: allele frequency
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: odds ratio
    intersection of: confidence interval
    intersection of: relative risk
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Class
      union of: odds ratio homogeneity test
      union of: Restriction
        on property: is_specified_output_of
        some values from: test of association between categorical variables
subclass of: Restriction
  on property: executes
  some values from: Class
    intersection of: genotyping design
    intersection of: case-control study design
definition: Genome wide association study is a kind of study whose objective is to detect association between genetic markers (SNP or otherwise) accross the genome and a trait which may be a disease or another phenotype (e.g. trait of agronomic relevance in animal or plant studies). Genome wide association study compare the allele frequencies in 2 populations, one free of the trait used as control, the other one showing the trait use as 'case'. GWAS studies implement case-control design
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB, PRS
STATO alternative term: GWAS study
STATO alternative term: whole genome association study

Wilcoxon signed rank test
type: Class
subclass of: data transformation
subclass of: within subject comparison statistical test
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: ranking
    intersection of: Restriction
      on property: has_specified_input
      min qualified cardinality: 1
      on class: Class
        intersection of: study design dependent variable
        intersection of: continuous variable
    intersection of: Restriction
      on property: has_specified_input
      qualified cardinality: 2
      on class: Class
        intersection of: study design independent variable
        intersection of: categorical variable
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: within subject comparison objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: paired observation comparison objective
has curation status: ready for release
definition: The Wilcoxon signed rank test is a statistical test which tests the null hypothesis that the median difference between pairs of observations is zero. This is the non-parametric analogue to the paired t-test, and should be used if the distribution of differences between pairs may be non-normally distributed. The procedure involves a ranking, hence the name. The absolute value of the differences between observations are ranked from smallest to largest, with the smallest difference getting a rank of 1, then next larger difference getting a rank of 2, etc. Ties are given average ranks. The ranks of all differences in one direction are summed, and the ranks of all differences in the other direction are summed. The smaller of these two sums is the test statistic, W (sometimes symbolized Ts). Unlike most test statistics, smaller values of W are less likely under the null hypothesis.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://udel.edu/~mcdonald/statsignedrank.html
R command: signrank()
Python command: scipy.stats.wilcoxon(x, y=None, zero_method='wilcox', correction=False) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.wilcoxon.html#scipy.stats.wilcoxon source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L4103

date
type: Class
subclass of: time stamped measurement datum
has curation status: metadata incomplete
definition: Information about a calendar date or timestamp indicating day, month, year and time of an event.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Kruskal Wallis test
type: Class
subclass of: data transformation
subclass of: non-parametric test
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: ranking
    intersection of: Restriction
      on property: has_specified_input
      min qualified cardinality: 1
      on class: Class
        intersection of: study design dependent variable
        intersection of: continuous variable
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: population
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: polychotomous variable
has curation status: pending final vetting
definition: The Kruskal–Wallis test is a null hypothesis statistical testing objective which allows multiple (n>=2) groups (or conditions or treatments) to be compared, without making the assumption that values are normally distributed. The Kruskal–Wallis test is the non-parametric equivalent of the independent samples ANOVA. The Kruskal–Wallis test is most commonly used when there is one nominal variable and one measurement variable, and the measurement variable does not meet the normality assumption of an anova.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: H test
alternative term: rank-sum test for the comparison of multiple (more than 2) samples.
definition source: http://udel.edu/~mcdonald/statkruskalwallis.html
R command: kruskal.test() http://stat.ethz.ch/R-manual/R-patched/library/stats/html/kruskal.test.html
Python command: scipy.stats.mstats.kruskalwallis(*args) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.mstats.kruskalwallis.html source code: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/mstats_basic.py#L800

paired t-test
type: Class
subclass of: Student's t-test
subclass of: data transformation
subclass of: within subject comparison statistical test
subclass of: Restriction
  on property: has part
  some values from: subject pairing
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: normal distribution hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Student's t distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: t-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: within subject comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: normal distribution hypothesis
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: dichotomous variable
has curation status: ready for release
definition: paired t-test is a statistical test which is specifically designed to analysis differences between paired observations in the case of studies realizing repeated measures design with only 2 repeated measurements per subject (before and after treatment for example)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://udel.edu/~mcdonald/statpaired.html
definition source: http://udel.edu/~mcdonald/statsignedrank.html
STATO alternative term: t-test for dependent means
STATO alternative term: t-test for repeated measures
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html t.test(dependent variable ~ independant variable, data = dataset, var.equal = FALSE, paired= TRUE)
Python command: scipy.stats.ttest_rel(a, b, axis=0) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_rel.html#scipy.stats.ttest_rel source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3389

population stratification prior to sampling
type: Class
subclass of: material processing
subclass of: Restriction
  on property: precedes
  some values from: material sampling process
subclass of: Restriction
  on property: executes
  some values from: stratification rule
subclass of: Restriction
  on property: has_specified_output
  min qualified cardinality: 2
  on class: population
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: population
has curation status: ready for release
definition: stratification is a planned process which executes a stratification rule using as input a population and assign it member to mutually exclusive subpopulation based on the values defined by the stratification rule
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: PRS+AGB adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013
STATO alternative term: stratifying population

statistical test power analysis
type: Class
subclass of: data transformation
subclass of: Class
  union of: Restriction
    on property: has_specified_input
    some values from: false positive rate
  union of: Restriction
    on property: has_specified_input
    some values from: effect size estimate
  union of: Restriction
    on property: has_specified_input
    some values from: study group population size
  union of: Restriction
    on property: has_specified_input
    some values from: statistical test power
subclass of: Class
  union of: Restriction
    on property: has_specified_output
    some values from: false positive rate
  union of: Restriction
    on property: has_specified_output
    some values from: effect size estimate
  union of: Restriction
    on property: has_specified_output
    some values from: study group population size
  union of: Restriction
    on property: has_specified_output
    some values from: statistical test power
has curation status: ready for release
definition: A stastical test power analysis is a data transformation which aims to determine the size of a statistical sample required to reach a desired significance level given a particular statistical test
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.statmethods.net/stats/power.html
R command: http://www.statmethods.net/stats/power.html

two sample Hotelling T2 test
type: Class
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Hotelling T2 distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      some values from: population
    intersection of: Restriction
      on property: is denoted by
      min qualified cardinality: 2
      on class: study design dependent variable
example of usage: http://arxiv.org/pdf/1007.1094.pdf
has curation status: ready for release
definition: Hotelling's T2 test is a statistical test which is a generalization of Student's T-test to a assess if the means of a set of variables remains unchanged when studying 2 populations. It is a type of multivariate analysis
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
R command: http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html

random effect model
type: Class
subclass of: statistical model
subclass of: Class
  intersection of: Class
    intersection of: Restriction
      on property: has part
      some values from: model error term
    intersection of: Restriction
      on property: has part
      some values from: Class
        intersection of: model random effect term
        intersection of: Restriction
  intersection of: Restriction
    on property: is about
    some values from: study design dependent variable
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: model parameter
    intersection of: Restriction
      on property: is denoted by
      some values from: random variable
subclass of: Restriction
  on property: is model for
  some values from: Class
    union of: study design dependent variable
    union of: Class
      intersection of: study design independent variable
      intersection of: Restriction
        on property: has random effect on
        some values from: study design dependent variable
has curation status: requires discussion
definition: a random effect(s) model, also called a variance components model, is a kind of hierarchical linear model. It assumes that the dataset being analysed consists of a hierarchy of different populations whose differences relate to that hierarchy.
editor note: PRS: this is a stub and more work is needed to reconcile conflicting definitions
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: variance components model
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Random_effects_model#Qualitative_description

standardized mean difference
type: Class
subclass of: effect size estimate
subclass of: difference
subclass of: Restriction
  on property: is about
  some values from: effect size estimate
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: study group population
definition: standardized mean difference is statistic computed by forming the difference between two means, divided by an estimate of the within-group standard deviation. It is used to provide an estimation of the effect size between two treatments when the predictor (independent variable) is categorical and the response(dependent) variable is continuous. A standardized mean difference is a statistic that is a difference between two means, divided by a statistical measure of dispersion. The term Standardized Mean Difference is a description of the concept without an explicit type of statistical measure of dispersion. If the statistical measure of dispersion is specified, then a type (child term) of Standardized Mean Difference is preferred.
term editor: Alejandra Gonzalez-Beltran
term editor: Brian S. Alper, Kenneth Wilkins, Harold Lehmann, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: SMD
definition source: ready for release
definition source: adapted from "Effect size, confidence interval and statistical significance: a practical guide for biologists" Nakagawa and Cuthill DOI: 10.1111/j.1469-185X.2007.00027.x
definition source: adapted from http://htaglossary.net/standardised+mean+difference+(SMD) revised during alignment and collaboration with the COKA/SEVCO group
STATO alternative term: Cohen's d statistic

multinomial distribution
type: Class
subclass of: discrete probability distribution
has curation status: ready for release
definition: the multinomial distribution is a probability distribution which gives the probability of any particular combination of numbers of successes for various categories defined in the context of n independent trials each of which leads to a success for exactly one of k categories, with each category having a given fixed success probability.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from http://mathworld.wolfram.com/MultinomialDistribution.html and http://en.wikipedia.org/wiki/Multinomial_distribution
R command: dmultinom(x, size = NULL, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Multinom.html

z-score
type: Class
subclass of: measure of hypothesis testing
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: standard error of the mean
    intersection of: standard deviation
subclass of: Restriction
  on property: is about
  some values from: data set
has curation status: ready for release
definition: A z-score (also known as z-value, standard score, or normal score) is a measure of the divergence of an individual experimental result from the most probable result, the mean. Z is expressed in terms of the number of standard deviations from the mean value.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://controls.engin.umich.edu/wiki/index.php/Basic_statistics:_mean,_median,_average,_standard_deviation,_z-scores,_and_p-value#Z-Scores
STATO alternative term: normal score
STATO alternative term: standard score
Python command: scipy.stats.zscore(a, axis=0, ddof=0) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.zscore.html#scipy.stats.zscore source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L1977

log signal intensity ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: log signal intensity ratio is a data item which corresponding the logarithmitic base 2 of the ratio between 2 signal intensity, each corresponding to a condition.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/MA_plot last accessed: 2014-03-13
STATO alternative term: M-value

probit regression for analysis of polychotomous dependent variable
type: Class
subclass of: regression analysis method
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design dependent variable
        intersection of: polychotomous variable
has curation status: requires discussion
definition: probit regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the probit function aka the quantile function, i.e., the inverse cumulative distribution function (CDF), associated with the standard normal distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013

statistical model
type: Class
subclass of: data item
subclass of: information content entity
subclass of: Restriction
  on property: has part
  some values from: model parameter
subclass of: Restriction
  on property: is_specified_input_of
  some values from: model fitting
subclass of: Restriction
  on property: is denoted by
  some values from: design matrix
subclass of: Restriction
  on property: is model for
  some values from: study design dependent variable
has curation status: requires discussion
definition: a statistical model is an information content entity which is a formalization of relationships between variables in the form of mathematical equations. A statistical model describes how one or more random variables are related to one or more other variables. The model is statistical as the variables are not deterministically but stochastically related.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Statistical_model last accessed: 14/01/2014
STATO alternative term: statistical model

linear regression for analysis of continuous dependent variable
type: Class
subclass of: regression analysis method
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design dependent variable
        intersection of: continuous variable
has curation status: requires discussion
definition: linear regression model is a model which attempts to explain data distribution associated with response/dependent variable in terms of values assumed by the independent variable uses a linear function or linear combination of the regression parameters and the predictor/independent variable(s). linear regression modeling makes a number of assumptions, which includes homoskedasticity (constance of variance)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Linear_regression) polled in June 2013

multinomial logistic regression for analysis of dichotomous dependent variable
type: Class
subclass of: regression analysis method
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design dependent variable
        intersection of: dichotomous variable
has curation status: requires discussion
definition: multinomial logistic regression model is a model which attempts to explain data distribution associated with *polychotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Multinomial_logistic_regression) polled in June 2013
R command: http://cran.r-project.org/web/packages/mlogit/vignettes/mlogit.pdf

sequence read
type: Class
subclass of: DNA sequence data
subclass of: Restriction
  on property: is_specified_output_of
  some values from: DNA sequencing
definition: a sequence read is a DNA sequence data which is generated by a DNA sequencer
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

Funnel plot
type: Class
subclass of: scatter plot
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: effect size estimate
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: Restriction
      on property: preceded by
      some values from: meta analysis
has curation status: ready for release
definition: a Funnel plot is a scatter plot of treatment effect versus a measure of study size and aims to provide a visual aid to detecting bias or systematic heterogeneity. A symmetric inverted funnel shape arises from a ‘well-behaved’ data set, in which publication bias is unlikely. An asymmetric funnel indicates a relationship between treatment effect and study size. Known caveats: If high precision studies really are different from low precision studies with respect to effect size (e.g., due to different populations examined) a funnel plot may give a wrong impression of publication bias. The appearance of the funnel plot can change quite dramatically depending on the scale on the y-axis — whether it is the inverse square error or the trial size. Funnel plot was introduced by Light and Palmer in 1984.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Funnel_plot

variance
type: Class
subclass of: measure of dispersion
has curation status: ready for release
definition: variance is a data item about a random variable or probability distribution. it is equivalent to the square of the standard deviation. It is one of several descriptors of a probability distribution, describing how far the numbers lie from the mean (expected value).The variance is the second moment of a distribution.
term editor: Alejandra Gonzalez-Belran
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: σ2
R command: var(x, y = NULL, na.rm = FALSE, use) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html

assess statistical evidence
type: Class
subclass of: planned process
has curation status: requires discussion
definition: the process of using statistical analysis for interpreting and communicating "what the data say".
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: From "The strenght of statistical evidence" by Richard Royall. https://www.stat.fi/isi99/proceedings/arkisto/varasto/roya0578.pdf
STATO alternative term: assess stastistical evidence

discrete probability distribution
type: Class
subclass of: probability distribution
has curation status: ready for release
definition: a discrete probability distribution is a probability distribution which is defined by a probability mass function where the random variable can only assume a finite number of values or infinitely countable values
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia http://en.wikipedia.org/wiki/Probability_distribution#Discrete_probability_distribution last accessed: 14/01/2014

ranking
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_output
  all values from: ordinal variable
has curation status: ready for release
definition: ranking is a data transformation which turns a non-ordinal variable into a Ordinal variable by sorting the values of the input variable and replacing their value by their position in the sorting result
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

model parameter estimation
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
has curation status: pending final vetting
definition: model parameter estimation is a data transformation that finds parameter values (the model parameter estimates) most compatible with the data as judged by the model.
editor note: textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

bean plot
type: Class
subclass of: graph
example of usage: http://www.r-bloggers.com/boxplots-beyond-iv-beanplots/
has curation status: ready for release
definition: beanplot is a plot in which (one or) multiple batches ("beans") are shown. Each bean consists of a density trace, which is mirrored to form a polygon shape. Next to that, a one-dimensional scatter plot shows all the individual measurements, like in a stripchart. The name beanplot stems from green beans. The density shape can be seen as the pod of a green bean, while the scatter plot shows the seeds inside the pod.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.jstatsoft.org/v28/c01/paper
R command: http://cran.r-project.org/web/packages/beanplot/index.html

association between categorical variables testing objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: absence of association hypothesis
has curation status: ready for release
definition: the objective of a data transformation to evaluate a null hypothesis of absence of linkage between variables.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

pedigree chart
type: Class
subclass of: graph
subclass of: Restriction
  on property: is about
  some values from: family
has curation status: ready for release
definition: a pedigree chart is a graph which plots parent child relations
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO adapted from wikipedia (https://en.wikipedia.org/wiki/Pedigree_chart)
STATO alternative term: family tree
R command: plot.pedigree {kinship} http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/kinship/html/plot.pedigree.html

r2 measure of linkage desequilibrium
type: Class
subclass of: correlation coefficient
subclass of: Class
  intersection of: Restriction
    on property: part of
    some values from: LD plot
  intersection of: Restriction
    on property: is_specified_input_of
    some values from: data visualization
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: dichotomous variable
has curation status: ready for release
definition: r2 is a correlation coefficient which is computed over the frequency of 2 dichotomous variable and is used as a measure of Linkage Disequilibrium and as input data item to the creation of an LD plot
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: R squared measure of LD
definition source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2580747/
STATO alternative term: r2 measure of LD

stratification rule
type: Class
subclass of: rule
has curation status: pending final vetting
definition: a stratification rule/criteria is a criteria used to determine population strata so that a stratification process implementing the rule can result in any member of the total population being assigned to one and only one stratum
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Stratified_sampling polled on June 7th,2013

Wilkinson dot plot
type: Class
subclass of: dot plot
has curation status: ready for release
definition: The dot plot as a representation of a distribution consists of group of data points plotted on a simple scale. Dot plots are used for continuous, quantitative, univariate data. Data points may be labelled if there are few of them.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: Wilkinson, Leland (1999). "Dot plots". The American Statistician (American Statistical Association) 53 (3): 276–281. doi:10.2307/2686111

volcano plot
type: Class
subclass of: scatter plot
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: Class
        intersection of: fold change
        intersection of: Restriction
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: Class
        intersection of: Class
        intersection of: Restriction
subclass of: Restriction
  on property: is about
  some values from: gene expression
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: gene list visualization
    intersection of: Restriction
      on property: preceded by
      some values from: differential expression analysis data transformation
has curation status: ready for release
definition: volcano plot is a kind of scatter plot which graphs the negative log of the p-value (significance) on the y-axis versus log2 of fold-change between 2 conditions on the x-axis. It is a popular method for visualizing differential occurence of variables between 2 conditions.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Volcano_plot_(statistics)
R command: volcanoplot(fit, coef=1, highlight=0, names=fit$genes$ID, ...) http://rss.acs.unt.edu/Rdoc/library/limma/html/volcanoplot.html

99% confidence interval
type: Class
subclass of: confidence interval
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: confidence level
    intersection of: Restriction
      on property: has specified value
      has value: 99
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
has curation status: ready for release
definition: a confidence interval which covers 99% of the sampling distribution, meaning that there is a 1% risk of false positive (type I error)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: confidence interval at 1% of type I error rate
definition source: STATO

Altman box and whisker plot
type: Class
subclass of: box and whisker plot
has curation status: ready for release
definition: Altman Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Altman to create the 'whisker' of the plot.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Altman, D.G. Practical Statistics for Medical Research (Chapman and Hall, 1991).

Breslow-Day test for homogeneity of odds ratio
type: Class
subclass of: data transformation
subclass of: odds ratio homogeneity test
subclass of: homogeneity test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: homogeneity test objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: 2 by 2 contingency table
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: odds ratio
example of usage: http://www.biomedcentral.com/1471-2288/11/58#B9
has curation status: ready for release
definition: the Breslow-Day test is a statistical test which evaluates if the odds ratios are homogenous across N 2x2 contingency tables, for instance several 2x2 contingency tables associated with different strata of a stratified population when evaluating the relationship between exposure and outcome or associated with the different samples coming from several centres in a multicentric study in clinical trial context.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Odds_ratio#Statistical_inference polled on June 8th,2013
STATO alternative term: Breslow-Day test
R command: http://www.math.montana.edu/~jimrc/classes/stat524/Rcode/breslowday.test.r

sphericity test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: sphericity testing objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: a sphericity test is a null hypothesis statistical testing procedure which posits a null hypothesis of equality of the variances of the differences between levels of the repeated measures factor
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Sphericity#Sphericity_in_statistics)
STATO alternative term: test of data sphericity

Hotelling T2 distribution
type: Class
subclass of: probability distribution
has curation status: ready for release
definition: Hotelling T squared distribution is a probability distribution used in multivariate hypothesis testing, which is a univariate distribution proportional to the F-distribution and arises importantly as the distribution of a set of statistics which are natural generalizations of the statistics underlying Student's t-distribution. In particular, the distribution arises in multivariate statistics in undertaking tests of the differences between the (multivariate) means of different populations, where tests for univariate problems would make use of a t-test. The distribution is named for Harold Hotelling, who developed it[1] as a generalization of Student's t-distribution. This distribution is commonly used to describe the sample Mahalanobis distance between two populations.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia "http://en.wikipedia.org/wiki/Hotelling's_T-squared_distribution" last polled: 2013-11-09

post-hoc analysis
type: Class
equivalent class: Restriction
  on property: preceded by
  some values from: ANOVA
subclass of: between group comparison statistical test
has curation status: ready for release
definition: A post-hoc analysis is a statistical test carried out following an analysis of variance which ruled out the null hypothesis of absence of difference between group which allows identifying which groups differ.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: a posteriori test
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Post-hoc_analysis last accessed: 2013-11-15

true negative rate
type: Class
subclass of: ratio
subclass of: Restriction
  on property: is about
  some values from: statistical test hypothesis
has curation status: ready for release
definition: specificity is a measurement datum qualifying a binary classification test and is computed by substracting the false positive rate to the integral numeral 1
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: specificity

strictly standardized mean difference
type: Class
subclass of: standardized mean difference
subclass of: Restriction
  on property: is about
  some values from: effect size estimate
subclass of: Restriction
  on property: is_specified_input_of
  some values from: hit selection
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/
has curation status: ready for release
definition: strictly standardized mean difference (SSMS) is a standardized mean difference which corresponds to the ratio of mean to the standard deviation of the difference between two groups. SSMD directly measures the magnitude of difference between two groups. SSMD is widely used in High Content Screen for hit selection and quality control. When the data is preprocessed using log-transformation as normally done in HTS experiments, SSMD is the mean of log fold change divided by the standard deviation of log fold change with respect to a negative reference. In other words, SSMD is the average fold change (on the log scale) penalized by the variability of fold change (on the log scale). For quality control, one index for the quality of an HTS assay is the magnitude of difference between a positive control and a negative reference in an assay plate. For hit selection, the size of effects of a compound (i.e., a small molecule or an siRNA) is represented by the magnitude of difference between the compound and a negative reference. SSMD directly measures the magnitude of difference between two groups. Therefore, SSMD can be used for both quality control and hit selection in HTS experiments.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/SSMD
definition source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/
STATO alternative term: SSMD

Tarone's test for homogeneity of odds ratio
type: Class
subclass of: data transformation
subclass of: odds ratio homogeneity test
subclass of: homogeneity test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: homogeneity test objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: odds ratio
has curation status: ready for release
definition: Tarone's test for homogeneity of odds ratio is a statistical test which evaluates the null hypothesis that odds ratio are homogeneous
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Tarone, R. E. ‘On heterogeneity tests based on efficient scores’, Biometrika, 72, 91-95 (1985).
R command: > library("metafor") > calcTaronesTest <- function(mylist,referencerow=2) http://a-little-book-of-r-for-biomedical-statistics.readthedocs.org/en/latest/src/biomedicalstats.html#calculating-the-mantel-haenszel-odds-ratio-when-there-is-a-stratifying-variable

homoskedasticity test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: equal variance testing objective
subclass of: statistical test hypothesis
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: variance
has curation status: ready for release
definition: an homoskedasticity test is a statistical test aiming at evaluate if the variances from several random samples are similar
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: equivariance test

2 by 2 contingency table
type: Class
subclass of: contingency table
subclass of: Class
  intersection of: Restriction
    on property: is about
    qualified cardinality: 1
    on class: dichotomous variable
  intersection of: Restriction
    on property: is about
    qualified cardinality: 1
    on class: Class
      intersection of: categorical variable
      intersection of: Restriction
        on property: specifies value of
        qualified cardinality: 2
        on class: data item
has curation status: ready for release
definition: a 2x2 contingency table is a contingency table build for 2 dichotomous variables (i.e. 2 categorical variables, each with only 2 possible outcomes). It is the simplest of contingency tables
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: 2x2 contingency table
R command: xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html

subject pairing
type: Class
subclass of: group assignment
subclass of: Restriction
  on property: has_specified_output
  some values from: matched pair of subjects
subclass of: Restriction
  on property: executes
  some values from: pairing rule
example of usage: pairing patients by age, pairing animals by body weight range
has curation status: ready for release
definition: a subject pairing is a planned process which executes a pairing rule and results in the creation of sets of 2 subjects meeting the pairing criteria
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

contingency table
type: Class
subclass of: matrix
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: categorical variable
has curation status: ready for release
definition: a contigency table is a data item which displays the (multivariate) frequency distribution of the possible values of categorical variables. The first row of the table corresponds to categories of one categorical variable, the first column of the table corresponds to categories of the other categorical variable, the cells corresponding to each combination of categories is filled with the observed occurences in the sample being considered. The table also contains marginal total (marginal sums) and grand total of the occurences The term contingency table was first used by Karl Pearson in "On the Theory of Contingency and Its Relation to Association and Normal Correlation", part of the Drapers' Company Research Memoirs Biometric Series I published in 1904.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Contingency_table)
R command: xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html

acute toxicity study
type: Class
subclass of: investigation
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: Class
      intersection of: q-value
      intersection of: Restriction
        on property: preceded by
        some values from: between group comparison statistical test
    union of: Class
      intersection of: p-value
      intersection of: Restriction
        on property: is_specified_output_of
        some values from: Class
subclass of: Restriction
  on property: executes
  some values from: Class
    intersection of: parallel group design
    intersection of: factorial design
definition: acute toxicity study is an investigation which use interventions organized according to a factorial design and a parallel group design to observe the effect of use of high dose xenobiotics in animal models or cellular models
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
STATO alternative term: acute toxicity study

correlation coefficient
type: Class
subclass of: effect size estimate
subclass of: measure of correlation
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
subclass of: Restriction
  on property: has numerator
  some values from: covariance
subclass of: Restriction
  on property: has denominator
  some values from: Restriction
    on property: is about
    qualified cardinality: 2
    on class: standard deviation
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: variable
subclass of: Restriction
  on property: has value
  some values from: Datatype
    intersection of: Datatype
      on datatype: real
      with restrictions:
        min inclusive: -1
    intersection of: Datatype
      on datatype: real
      with restrictions:
        max inclusive: 1
has curation status: ready for release
definition: The correlation coefficient of two variables in a data sample is their covariance divided by the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: r
STATO alternative term: r statistic

Bayesian model selection
type: Class
subclass of: statistical model selection
subclass of: Restriction
  on property: has part
  some values from: Bayes factor
subclass of: Restriction
  on property: has_specified_input
  some values from: data set
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: statistical model
has curation status: ready for release
definition: A Bayesian model selection is a data transformation which is based on Bayesian statistics to compute Bayes factor in order to evaluate which model best explains data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia

model parameter estimate
type: Class
subclass of: estimate
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: model parameter
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: model parameter estimation
subclass of: Restriction
  on property: estimate of
  some values from: model parameter
subclass of: Restriction
  on property: estimate of
  some values from: statistic
example of usage: for example , model parameter estimates could be produced using regression analysis (used in a model estimation process) , which attempts to express the response variable in terms of function of predictor variable and model parameters.
has curation status: pending final vetting
definition: a model parameter estimate is a data item which results from a model parameter estimation process and which provides a numerical value about a model parameter.
editor note: textual definition modified following contributiong by Thomas Nichols: https://github.com/ISA-tools/stato/issues/18
term editor: Alejandra Gonzalez Beltran
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

geometric distribution
type: Class
subclass of: negative binomial distribution
has curation status: ready for release
definition: the geometric distribution is a negative binomial distribution where r is 1. It is useful for modeling the runs of consecutive successes (or failures) in repeated independent trials of a system. The geometric distribution models the number of successes before one failure in an independent succession of tests where each test results in success or failure. The geometric distribution with prob = p has density p(x) = p (1-p)^x for x = 0, 1, 2, …, 0 < p ≤ 1. If an element of x is not integer, the result of dgeom is zero, with a warning. The quantile is defined as the smallest value x such that F(x) ≥ p, where F is the distribution function.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html
definition source: http://www.mathworks.co.uk/help/stats/geometric-distribution.html
R command: dgeom(x, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Geometric.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.geom.html#scipy.stats.geom

presence of between group difference hypothesis
type: Class
subclass of: hypothesis
has curation status: requires discussion
definition: a null hypothesis stating that there are differences observed between group of subjects
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

LD plot
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: centrally registered identifier
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: r2 measure of linkage desequilibrium
    intersection of: Restriction
      on property: is_specified_output_of
      all values from: test of association between categorical variables
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is_specified_output_of
      all values from: test of association between categorical variables
subclass of: Restriction
  on property: is about
  some values from: genome-wide association study
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: genome-wide association study
has curation status: ready for release
definition: Linkage Disequilibrium plot is a graph which represents pairwise linkage disequilibrium measures between SNP as a heatmap
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from R documentation (http://cran.r-project.org/web/packages/LDheatmap/index.html)
STATO alternative term: LD plot
STATO alternative term: Linkage Disequilibrium plot

Cochran-Armitage test for trend
type: Class
subclass of: data transformation
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Cochran-Armitage Chi-Square Statistic for Trend
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: 2 by n contingency table
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: polychotomous variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: dichotomous variable
has curation status: ready for release
definition: The Cochran-Armitage test is a statistical test used in categorical data analysis when the aim is to assess for the presence of an association between a dichotomous variable (variable with two categories) and a polychotomous variable (a variable with k categories). The two-level variable represents the response, and the other represents an explanatory variable with ordered levels. The null hypothesis is the hypothesis of no trend, which means that the binomial proportion is the same for all levels of the explanatory variable For example, doses of a treatment can be ordered as 'low', 'medium', and 'high', and we may suspect that the treatment benefit cannot become smaller as the dose increases. The trend test is often used as a genotype-based test for case-control genetic association studies.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: CATT
definition source: http://en.wikipedia.org/wiki/Cochran%E2%80%93Armitage_test_for_trend

binomial logistic regression for analysis of dichotomous dependent variable
type: Class
subclass of: regression analysis method
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design dependent variable
        intersection of: dichotomous variable
has curation status: requires discussion
definition: binomial logistic regression model is a model which attempts to explain data distribution associated with *dichotomous* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is logistic function.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Logistic_regression) polled in June 2013

minimum observed value
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: data set
has curation status: ready for release
definition: a minimum value is a data item which denotes the smallest value found in a dataset or resulting from a calculation.
term editor: Alejandra Gonzalez-Beltran
term editor: COKA group
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: minimum value
definition source: STATO

maximum observed value
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: data set
has curation status: ready for release
definition: maximum value is a data item which denotes the largest value found in a dataset or resulting from a calculation.
term editor: Alejandra Gonzalez-Beltran
term editor: COKA group
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: maximum value
definition source: STATO

quartile
type: Class
subclass of: quantile
has curation status: ready for release
definition: a quartile is a quantile which splits data into sections accrued of 25% of data, so the first quartile delineates 25% of the data, the second quartile delineates 50% of the data and the third quartile, 75 % of the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Quartile)

one sample Hotelling T2 test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Hotelling T2 distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      some values from: population
    intersection of: Restriction
      on property: is denoted by
      min qualified cardinality: 2
      on class: study design dependent variable
example of usage: http://arxiv.org/pdf/1007.1094.pdf
has curation status: ready for release
definition: The one-sample Hotelling’s T2 is the multivariate extension of the common one-sample or paired Student’s t-test. In a one-sample t-test, the mean response is compared against a specific value. Hotelling’s one-sample T2 is used when the number of response variables is two or more, although it can be used when there is only one response variable. T2 makes the usual assumption that the data are approximately multivariate normal. Randomization tests are provided that do not rely on this assumption. These randomization tests should be used whenever you want exact results that do not rely on several assumptions.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: https://ncss-wpengine.netdna-ssl.com/wp-content/themes/ncss/pdf/Procedures/NCSS/Hotellings_One-Sample_T2.pdf
R command: http://svitsrv25.epfl.ch/R-doc/library/rrcov/html/T2.test.html

violin plot
type: Class
subclass of: graph
has curation status: ready for release
definition: a violin plot is a plot combining the features of box plot and kernel density plot. The violin plot is therefore similar to box plot but it incorporated in the display the probability density of the data at different values. Typically violin plots will include a marker for the median of the data and a box indicating the interquartile range, as in standard box plots.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Violin_plot and Hintze, J. L. and R. D. Nelson (1998). Violin plots: a box plot-density trace synergism. The American Statistician, 52(2):181-4.
R command: http://www.inside-r.org/packages/cran/vioplot/docs/vioplot vioplot( x, ..., range=1.5, h, ylim, names, horizontal=FALSE, col="magenta", border="black", lty=1, lwd=1, rectCol="black", colMed="white", pchMed=19, at, add=FALSE, wex=1, drawRect=TRUE)

meta analysis
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: investigation
has curation status: ready for release
definition: meta-analysis is a data transformation which uses the effect size estimates from several independent quantitative scientific studies addressing the same question in order to assess finding consistency.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Metaanalysis last accessed: 2013-11-15

Scheffe test
type: Class
subclass of: data transformation
subclass of: post-hoc analysis
subclass of: Restriction
  on property: preceded by
  some values from: ANOVA
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: ready for release
definition: the Scheffe test is a data transformation which evaluates all possible contrasts and adjusting the levels significance by accounting for multiple comparison. The test is therefore conservative. Confidence intervals can be constructed for the corresponding linear regression. It was developped by American statistician Henry Scheffe in 1959.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Scheffé's_method)
R command: http://www.inside-r.org/packages/cran/agricolae/docs/scheffe.test

Least significance different test
type: Class
subclass of: data transformation
subclass of: post-hoc analysis
subclass of: Restriction
  on property: preceded by
  some values from: ANOVA
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: ready for release
definition: the LSD test is a statistical test for multiple comparisons of treatments by means of least significant difference following an ANOVA analysis
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: R
STATO alternative term: LSD test
R command: http://rss.acs.unt.edu/Rdoc/library/agricolae/html/LSD.test.html

presence of association hypothesis
type: Class
subclass of: hypothesis
has curation status: requires discussion
definition: a null hypothesis which states that a linkage exists between 2 categorical variables
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

stacked bar chart
type: Class
subclass of: bar chart
has curation status: ready for release
definition: Stacked bar chart is a bar which is used to compare overall quantities across items while showing the contribution of category to the total amount. Stacked bar chart can be used for highlighting the total as they visually aggregate all of the categories in a group while indicating a part to whole relationship. The downside is that it becomes harder to compare the sizes of the individual categories.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapter from http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts and http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/ [last accessed: 2014-03-04]
R command: barplot(height....) set argument " beside = FALSE " http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html

exponential distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 2
has curation status: ready for release
definition: The exponential distribution (a.k.a. negative exponential distribution) is the probability distribution that describes the time between events in a Poisson process, i.e. a process in which events occur continuously and independently at a constant average rate. It is the continuous analogue of the geometric distribution, and it has the key property of being memoryless.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Exponential.html dexp(x, rate = 1, log = FALSE) pexp(q, rate = 1, lower.tail = TRUE, log.p = FALSE) qexp(p, rate = 1, lower.tail = TRUE, log.p = FALSE) rexp(n, rate = 1)
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.expon.html#scipy.stats.expon

data distribution
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is denoted by
  some values from: measure of dispersion
subclass of: Restriction
  on property: is denoted by
  some values from: measure of central tendency
subclass of: Restriction
  on property: is denoted by
  some values from: statistic
has curation status: ready for release
definition: variable distribution is data item which denotes the spatial resolution of data point making up a variable. variable distribution may be compared to a known probability distribution using goodness of fit test or plotting a quantile-quantile plot for visual assessment of the fit.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: data distribution

experimental unit role
type: Class
subclass of: role
has curation status: requires discussion
definition: the role played by an entity part of study group as defined by an experimental design and realized in a data analysis and data interpretation
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

trimmed mean
type: Class
subclass of: measure of central tendency
has curation status: ready for release
definition: trimmed mean or truncated mean is a measure of central tendency which involves the calculation of the mean after discarding given parts of a probability distribution or sample at the high and low end, and typically discarding an equal amount of both
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia [last accessed 2014-03-04] http://en.wikipedia.org/wiki/Truncated_mean
STATO alternative term: truncated mean
Python command: scipy.stats.tmean(a, limits=None, inclusive=(True, True)) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.tmean.html#scipy.stats.tmean source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L684

inter quartile range
type: Class
subclass of: measure of dispersion
has curation status: ready for release
definition: The interquartile range is a data item which corresponds to the difference between the upper quartile (3rd quartile) and lower quartile (1st quartile). The interquartile range contains the second quartile or median. The interquartile range is a data item providing a measure of data dispersion.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO. adapted from wikipedia, wolfram alpha and oxford dictionary of statistics
R command: IQR(x, na.rm = FALSE, type = 7) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/IQR.html

pie chart
type: Class
subclass of: graph
has curation status: ready for release
definition: a pie chart is a graph in which a circular graph is divided into sector illustrating numerical proportion, meaning that the arc length of each sector (and consequently its central angle and area), is proportional to the quantity it represents.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia, last accessed [2014-03-05] http://en.wikipedia.org/wiki/Pie_chart
R command: pie(x, labels = names(x), edges = 200, radius = 0.8, clockwise = FALSE, init.angle = if(clockwise) 90 else 0, density = NULL, angle = 45, col = NULL, border = NULL, lty = NULL, main = NULL, ...) https://stat.ethz.ch/R-manual/R-devel/library/graphics/html/pie.html

bar chart
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: categorical label
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: data item
example of usage: A bar chart is appropriate to represent counts of data.
has curation status: ready for release
definition: the bart chart is a graph resulting from plotting rectangular bars with lengths proportional to the values that they represent.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia (http://en.wikipedia.org/wiki/Bar_chart) polled in June 2013
STATO alternative term: bar plot
R command: barplot(height, ...) http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html

first quartile
type: Class
subclass of: quartile
has curation status: ready for release
definition: the first quartile is a quartile which splits the lower 25 % of the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

real time quantitative pcr plot
type: Class
subclass of: line graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: number of PCR cycle
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: ΔRn
has curation status: pending final vetting
definition: a real time quantitative pcr plot is a line graph which plots the signal fluorescence intensity as a function of the number of PCR cycle
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

fold change
type: Class
subclass of: dimensionless ratio
has curation status: ready for release
definition: Fold change is a number describing how much a quantity changes going from an initial to a final value or one condition to another condition
editor note: 30/04/2014 - removed restriction: 'is about' exactly 2 'study group population' - need more discussion for the relationship of fold change to study group populations for particular examples.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Fold_change

third quartile
type: Class
subclass of: quartile
has curation status: ready for release
definition: the first quartile is a quartile which splits the 75 % of the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Spear box and whisker plot
type: Class
subclass of: box and whisker plot
has curation status: ready for release
definition: Spear Box and Whisker plot is a variation of Tukey Box and Whisker plot which use the criteria of Spear to create the 'whisker' of the plot.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Spear, M.E. Charting Statistics (McGraw-Hill, 1952)

FPKM-fragments per kilobase of transcript per million fragments mapped
type: Class
subclass of: count
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: gene expression
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: RNA-seq assay
      intersection of: Restriction
        on property: has_specified_input
        some values from: paired-end library
has curation status: pending final vetting
definition: FPKM, which is the expected fragments per kilobase of transcript per million fragments mapped is a metric used to report transcript expression event as generated by RNA-Seq using paired-end library. The calculated value results from 2 types of normalization, one to take into account the difference in reads counts associated with transcript length (at equal abundance, longer transcripts will have more reads than shorter transcripts) , (hence the 'per kilobase of transcript') and the other one to take into account different sequencing depth during distinct sequencing runs (hence the 'per millions mapped fragment'. The metric is specifically produced by cufflink software. Recommended use: -FPKM measure may be used for gene count comparisons within a sample. -FPKM measure is NOT suited for between sample comparisons. -FPKM measure is NOT suited for Differential Expression analysis.
editor note: The definition of FPKM has been modified in October 2019 to reflect the possible uses as detailed in https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html and distinguish more clearly FPKM from measures such as TPM
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: FPKM
definition source: adapted from: http://seqanswers.com/forums/showthread.php?t=3254 and from http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html and from https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html

homogeneity test objective
type: Class
subclass of: statistical hypothesis test objective
has curation status: ready for release
definition: homogeneity testing objective is the objective of a data transformation to test a null hypothesis that two or more sub-groups of a population share the same distribution of a single categorical variable. For example, do people of different countries have the same proportion of smokers to non-smokers
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Forest plot
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: effect size estimate
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: Restriction
      on property: preceded by
      some values from: meta analysis
has curation status: ready for release
definition: A forest plot is a graph designed to illustrate the relative strength of treatment effects in multiple quantitative scientific studies addressing the same question.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Forest_plot
R command: metaplot(mn, se, nn=NULL, labels=NULL, conf.level=0.95, xlab="Odds ratio", ylab="Study Reference",xlim=NULL, summn=NULL, sumse=NULL, sumnn=NULL, summlabel="Summary", logeffect=FALSE, lwd=2, boxsize=1, zero=as.numeric(logeffect), colors=meta.colors(), xaxt="s", logticks=TRUE, ...) http://rss.acs.unt.edu/Rdoc/library/rmeta/html/metaplot.html

confidence interval calculation
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: effect size estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
example of usage: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/confint.html
has curation status: ready for release
definition: confidence interval calculation is a data transformation which determines a confidence interval for a given statistical parameter
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

t-statistic
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Student's t-test
has curation status: ready for release
definition: t-statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a Student's t distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
preferred mathematical notation: T

beta distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution shape parameter
has curation status: ready for release
definition: the beta distribution is a continuous probability distributions defined on the interval [0, 1] parametrized by two positive shape parameters, denoted by α and β, that appear as exponents of the random variable and control the shape of the distribution
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Beta_distribution
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Beta.html dbeta(x, shape1, shape2, ncp = 0, log = FALSE) pbeta(q, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) qbeta(p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE) rbeta(n, shape1, shape2, ncp = 0)
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.beta.html#scipy.stats.beta

kurtosis
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: data set
    union of: probability distribution
has curation status: ready for release
definition: Kurtosis is a data item which denotes the degree of peakedness of a distribution. It is defined as a normalized form of the fourth central moment of a distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/Kurtosis.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kurtosis.html#scipy.stats.kurtosis

ANCOVA
type: Class
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    min qualified cardinality: 1
    on class: Class
      intersection of: study design independent variable
      intersection of: categorical variable
  intersection of: Restriction
    on property: has_specified_input
    min qualified cardinality: 1
    on class: Class
      intersection of: study design dependent variable
      intersection of: continuous variable
subclass of: Restriction
  on property: has_specified_input
  some values from: study design independent variable
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: ready for release
definition: ANCOVA or analysis of covariance is a data transformation which evaluates if population means of a dependent variable are equal across levels of a categorical independent variables while controlling for the effects of other continuous variable s, known as covariates. Therefore, when performing ANCOVA, we are adjusting the dependent variable means to what they would be if all groups were equal on the covariates. It augments the ANOVA model with one or more additional quantitative variables, called covariates, which are related to the response variable. The covariates are included to reduce the variance in the error terms and provide more precise measurement of the treatment effects. ANCOVA is used to test the main and interaction effects of the factors, while controlling for the effects of the covariate
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia

standard normal distribution
type: Class
subclass of: normal distribution
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: variance
    intersection of: Restriction
      on property: has value
      has value: 1
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: expected value
    intersection of: Restriction
      on property: has value
      has value: 0
has curation status: ready for release
definition: standard normal distribution is a normal distribution with variance = 1 and mean=0
editor note: we need to formally set value for mean and variance
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
R command: dnorm(x, mean = 0, sd = 1, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Normal.html

Hardy-Weinberg equilibrium testing
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: Likelihood-ratio test
    union of: Fisher's exact test
    union of: Pearson's Chi square test of independence between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: Hardy-Weinberg equilibrium test is a statistical test which aims to evaluate if a population's proportion of allele is stable or not. It is used as means of quality control to evaluate possibility of genotyping error or population structure.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO: adapted from wikipedia (http://en.wikipedia.org/wiki/Hardy–Weinberg_principle)
R command: > library(HardyWeinberg) > x <- c(298,489,213) > HW.test <- HWChisq(x,verbose=TRUE) http://cran.r-project.org/web/packages/HardyWeinberg/index.html

odds ratio
type: Class
subclass of: effect size estimate
subclass of: dimensionless ratio
subclass of: ratio-based measure of association
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    all values from: odds
  intersection of: Restriction
    on property: has denominator
    all values from: odds
subclass of: Restriction
  on property: is about
  some values from: disposition
subclass of: Restriction
  on property: is about
  some values from: genetic characteristics information
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
subclass of: Restriction
  on property: is_proxy_for
  some values from: measure of association
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: dichotomous variable
subclass of: Restriction
  on property: is about
  qualified cardinality: 4
  on class: study group population
has curation status: ready for release
definition: Odds ratio is a ratio that measures effect size, that is the strength of association between 2 dichotomous variables, one describing an exposure and one describing an outcome. It represents the odds that an outcome will occur given a particular exposure, compared to the odds of the outcome occurring in the absence of that exposure ( the probability of the event occuring divided by the probability of an event not occurring). The odds ratio is a ratio of describing the strength of association or non-independence between two binary data values by forming the ratio of the odds for the first group and the odds for the second group. Odds ratio are used when one wants to compare the odds of something occurring to two different groups.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2938757/ http://www.stats.org/stories/2008/odds_ratios_april4_2008.html
STATO alternative term: OR

sphericity testing objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: sphericity hypothesis
has curation status: ready for release
definition: sphericity testing objective is a statistical objective of a data transformation which aims to test a null hypothesis of sphericity holds.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: sphericity testing objective

ratio
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has numerator
    some values from: data item
  intersection of: Restriction
    on property: has denominator
    some values from: data item
subclass of: statistic
has curation status: pending final vetting
definition: A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s.
editor note: review formal definition as both numerator and denominator should be of the same type, not just some data item
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7

2 by n contingency table
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: is about
    min qualified cardinality: 1
    on class: Class
      intersection of: polychotomous variable
      intersection of: Restriction
        on property: specifies value of
        min qualified cardinality: 2
        on class: data item
  intersection of: Restriction
    on property: is about
    qualified cardinality: 1
    on class: dichotomous variable
subclass of: contingency table
has curation status: ready for release
definition: a 2 by n contingency table is a contingency table built for one dichotomous variable (a categorical variable with only 2 outcomes) and one polychotomous variable (a polychomotomous variable with at least 2 outcomes)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
R command: xtabs(formula = ~., data = parent.frame(), subset, sparse = FALSE, na.action, exclude = c(NA, NaN), drop.unused.levels = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/xtabs.html flat contingency tables: ftable(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ftable.html

Lineweaver-Burk plot
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: substrate concentration
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: reaction rate
subclass of: Restriction
  on property: is about
  some values from: Class
    intersection of: enzyme
    intersection of: Restriction
      on property: participates in
      some values from: catalytic activity
subclass of: Restriction
  on property: is_specified_output_of
  some values from: data visualization
has curation status: ready for release
definition: Lineweaver-Burk plot is a graph which is the graphical representation of the Lineweaver–Burk equation of enzyme kinetics, described by Hans Lineweaver and Dean Burk in 1934. The plot provides a useful graphical method for analysis of the Michaelis–Menten equation. It was widely used to determine important terms in enzymology and enzyme kinetics as the x-intercept of the graph represents −1/Km and the y-intercept of such a graph is equivalent to the inverse of Vmax
editor note: TODO: create 'inverse function' and replace 'data transformation' in the assertions.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
STATO alternative term: double reciprocal plot

Tukey HSD for Post-Hoc Analysis
type: Class
subclass of: data transformation
subclass of: post-hoc analysis
subclass of: Restriction
  on property: preceded by
  some values from: ANOVA
subclass of: Restriction
  on property: has_specified_input
  some values from: studentized range distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is about
      some values from: absence of between group difference hypothesis
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: expected value
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: study group population
has curation status: ready for release
definition: Tukey Honestly Significant Difference (HSD) test is a statistical test used following an ANOVA test yielding a statistically significant p-value in order to determine which means are different, to a given level of significance. The Tukey HSD test relies on the q-distribution. The procedure is conservative, meaning that if sample sizes (the sizes of different study groups) are equal, the risk of a Type I error is exactly α, and if sample sizes are unequal it’s less than α.
editor note: IMPORTANT: Do Not to confuse the Tukey HSD test with Tukey Mean Difference Test (Bland-Altman test)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.tc3.edu/instruct/sbrown/stat/anova1.htm#ANOVAprereq
STATO alternative term: Tukey's honestly significant difference
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/TukeyHSD.html

average log signal intensity
type: Class
subclass of: measurement datum
subclass of: normalized data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: logarithmic transformation
    intersection of: Restriction
      on property: has_specified_input
      some values from: fold change
has curation status: ready for release
definition: average log signal intensity is a data time which corresponds to the sum of 2 distinct logarithm base 2 transformed signal intensity, each corresponding to a distinct condition of signal acquisition, divided by 2.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/MA_plot last accessed: 2014-03-13
STATO alternative term: A-value

mixed effect model
type: Class
subclass of: statistical model
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: fixed effect model
    intersection of: random effect model
has curation status: requires discussion
definition: A mixed model is a statistical model containing both fixed effects and random effects. These models are useful in a wide variety of disciplines in the physical, biological and social sciences. They are particularly useful in settings where repeated measurements are made on the same statistical units (longitudinal study), or where measurements are made on clusters of related statistical units. Because of their advantage in dealing with missing values, mixed effects models are often preferred over more traditional approaches such as repeated measures ANOVA.
editor note: PRS: this is a stub and more work is needed to reconcile conflicting definitions
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia

threshold cycle
type: Class
subclass of: number of PCR cycle
has curation status: pending final vetting
definition: Threshold cycle (or Ct or Cq) is a count which is defined as the fractional PCR cycle number at which the reporter fluorescence is greater than the threshold in the context of the RT-qPCR assay. The Ct is a basic principle of real time PCR and is an essential component in producing accurate and reproducible data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Cq
alternative term: Ct
definition source: http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml

goodness of fit statistical test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: a goodness of fit statistical test is a statistical test which aim to evaluate if a sample distribution can be considered equivalent to a theoretical distribution used as input
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

cartesian product
type: Class
subclass of: data transformation
has curation status: ready for release
definition: a cartesian product is a data transformation which operates on a n Sets to produce a set of all possible ordered n-tuples where each element of the tuple comes from a Set
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: PERSON: Philippe Rocca-Serra
definition source: adapted from math wolfram (http://mathworld.wolfram.com/CartesianProduct.html)

study group population
type: Class
subclass of: population
has curation status: ready for release
definition: is a population whose individual members realize (may be expressed as) a combination of inclusion rule values specifications or resulting from a sampling process (e.g. recruitment followed by randomization to group) on which a number of measurements will be carried out, which may be used as input to statistical tests and statistical inference.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: statistical sample

cartesian product 2 sets
type: Class
subclass of: cartesian product
has curation status: ready for release
definition: self explanatory
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

number of factor level combinations
type: Class
subclass of: count
subclass of: Restriction
  on property: is about
  some values from: factor level combination
has curation status: ready for release
definition: A non-negative integer defining how many combination of factor levels (or treatments in the statistical sense) are to be used in a study.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

confidence interval
type: Class
subclass of: measure of dispersion
subclass of: Restriction
  on property: has part
  some values from: confidence level
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: upper confidence limit
    intersection of: lower confidence limit
subclass of: Restriction
  on property: is about
  some values from: effect size estimate
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: odds ratio
    union of: center value
subclass of: Restriction
  on property: is_specified_output_of
  some values from: confidence interval calculation
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
has curation status: ready for release
definition: A confidence interval is a data item which defines an range of values in which a measurement or trial falls corresponding to a given probability.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/ConfidenceInterval.html

genomic coordinate system
type: Class
subclass of: coordinate system
has curation status: pending final vetting
definition: a genomic coordinate system is a coordinate system to describe position of sequence on a genomic scaffold (assembly of chromosome, contig....)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: ensembl, ucsc

non-parametric test
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: ranking
  intersection of: Restriction
    on property: has_specified_output
    some values from: p-value
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: between group comparison objective
subclass of: statistical test hypothesis
subclass of: between group comparison statistical test
has curation status: requires discussion
definition: a statistical test which makes no assumption about the underlying data distribution
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Mauchly's test for sphericity
type: Class
subclass of: data transformation
subclass of: sphericity test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sphericity testing objective
has curation status: ready for release
definition: the Mauchly's test for sphericity is a statistical test which evaluates if the variance of the differences between all combinations of the groups are equal, a property known as 'sphericity' in the context of repeated measures. It is used for instance prior to repeated measure ANOVA. The test works by assessing if a Wishart-distributed covariance matrix (or transformation thereof) is proportional to a given matrix.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB-PRS, adapted from wikipedia (http://en.wikipedia.org/wiki/Mauchly's_sphericity_test) polled on june,10th, 2013 and from R manual: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html
STATO alternative term: Mauchly's test for sphericity
R command: mauchly.test(object, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/mauchly.test.html

statistical test power
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: statistical test hypothesis
has curation status: ready for release
definition: the statistical test power is data item which is about a statistical test and is obtained by subtracting the false negative rate (type II error rate) to 1. The power of a statistical test is the probability that it will correctly lead to the rejection of a false null hypothesis (Greene 2000). The statistical power is the ability of a test to detect an effect, if the effect actually exists (High 2000).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia (http://en.wikipedia.org/wiki/Statistical_power), polled June 10th, 2013

Spearman's rank correlation coefficient
type: Class
subclass of: correlation coefficient
subclass of: Restriction
  on property: is about
  some values from: effect size estimate
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: ordinal variable
has curation status: ready for release
definition: Spearman's rank correlation coefficient is a correlation coefficient which is a nonparametric measure of statistical dependence between two ranked variables. It assesses how well the relationship between two variables can be described using a monotonic function. If there are no repeated data values, a perfect Spearman correlation of +1 or −1 occurs when each of the variables is a perfect monotone function of the other. Spearman's coefficient may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables) but may require a ranking transformation of the variables
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Spearman's rho
definition source: http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
R command: cor(x, y = NULL, use = "everything",method = c("spearman"))
Python command: scipy.stats.spearmanr(a, b=None, axis=0) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.spearmanr.html#scipy.stats.spearmanr source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2643

within subject comparison statistical test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: within subject comparison objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: within subject comparison statistical test is a kind of statistical test which evaluates if a change occurs within one experimental unit over time following a treatment or an event
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

cohort
type: Class
subclass of: study group population
has curation status: ready for release
definition: a cohort is a study group population where the members are human beings which meet inclusion criteria and undergo a longitudinal design
editor note: possibly submit to 'Population and Community Ontology'
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

F-distribution
type: Class
subclass of: continuous probability distribution
has curation status: ready for release
definition: the F-distribution is a continuous probability distribution which arises in the testing of whether two observed samples have the same variance.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Fisher distribution
alternative term: Snedecor Fisher distribution
definition source: http://mathworld.wolfram.com/F-Distribution.html
R command: df(x, df1, df2, ncp, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Fdist.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.f.html#scipy.stats.f

RPKM-reads per kilobase of transcript per million fragments mapped
type: Class
subclass of: count
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: gene expression
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: Class
      intersection of: RNA-seq assay
      intersection of: Restriction
        on property: has_specified_input
        some values from: single fragment library
has curation status: pending final vetting
definition: RPKM is a kind of count which numbers the sequence reads found per kilobase of transcript reported to million of sequence reads. RPKM is a metric generated by ERANGE software tool as reported by Mortazi et al, in 2008. The metric has been enhanced and replaced by FPKM to better take into account splice variant. FKPM uses a statistical model to perform the computation. Recommended use: -RPKM measure may be used for gene count comparisons within a sample. -RPKM measure is NOT suited for between sample comparisons. -RPKM measure is NOT suited for Differential Expression analysis.
editor note: The definition of RPKM has been modified in October 2019 to reflect the possible uses as detailed in https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html and distinguish more clearly RPKM from measures such as TPM
term editor: Alejandra Gonzalez Beltran
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: RPKM
definition source: http://www.nature.com/nmeth/journal/v5/n7/full/nmeth.1226.html

specifying null and alternate hypothesis
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: null hypothesis
subclass of: Restriction
  on property: has_specified_output
  some values from: alternative hypothesis
has curation status: requires discussion
definition: a planned process which etablishes and states the different hypothesis to be evaluated during a null hypothesis statistical test
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

alternative hypothesis
type: Class
subclass of: hypothesis
has curation status: ready for release
definition: An alternative hypothesis is an hypothesis defined in a statistical test that is the opposite of the null hypothesis.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

area under curve
type: Class
subclass of: statistic
example of usage: PMID:12892658 "Two formulas for computation of the area under the curve represent measures of total hormone concentration versus time-dependent change."
has curation status: ready for release
definition: area under curve is a measurement datum which corresponds to the surface define by the x-axis and bound by the line graph represented in a 2 dimensional plot resulting from an integration or integrative calculus. The interpretation of this measurement datum depends on the variables plotted in the graph
editor note: PRS: submit 'integral calculus' as a kind of data transformation in OBI:DT branch
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

channel1/channel2 fluorescence intensity ratio
type: Class
subclass of: fold change
subclass of: Restriction
  on property: has numerator
  some values from: fluorescent reporter intensity
subclass of: Restriction
  on property: has denominator
  some values from: fluorescent reporter intensity
has curation status: ready for release
definition: is a data item formed by dividing the fluorescence intensity obtained in one channel to that obtained in the other channel, typically the case when considering 2-color microarray data when imaging is done for Cy3 and Cy5 dyes.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: channel1/channel2 fluorescence intensity ratio

odds ratio homogeneity hypothesis
type: Class
subclass of: hypothesis
has curation status: ready for release
definition: odds ratio homogeneity hypothesis is a null hypothesis stating that all odds ratio are homogenous, that is remain within the same range.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: odds ratio homogeneity hypothesis

tetrachoric correlation coefficient
type: Class
subclass of: polychoric correlation coefficient
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: dichotomous variable
has curation status: ready for release
definition: a tetrachoric correlation coefficient is a polychoric correlation coefficient for 2 dichotomous variables used as proxy for correlation between 2 continuous latent variables.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://www.rasch.org/rmt/rmt193c.htm and http://en.wikipedia.org/wiki/Polychoric_correlation

continuous variable discretization
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: continuous variable
subclass of: Restriction
  on property: executes
  some values from: rule
subclass of: Restriction
  on property: has_specified_output
  all values from: polychotomous variable
has curation status: ready for release
definition: discretization as a processing converting a continuous variable into a polychotomous variable by concretizing a set of discretization rules
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB,PRS adapted from wikipedia (http://en.wikipedia.org/wiki/Discretization)
R command: http://cran.r-project.org/web/packages/discretization/index.html

50% confidence interval
type: Class
subclass of: confidence interval
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: confidence level
    intersection of: Restriction
      on property: has specified value
      has value: 50
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
has curation status: ready for release
definition: a confidence interval which covers 50% of the sampling distribution, meaning that there is a 50% risk of false positive (type I error)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: confidence interval at 10% of type I error rate
definition source: STATO

ordered probit regression for analysis of ordinal dependent variable
type: Class
subclass of: regression analysis method
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design dependent variable
        intersection of: ordinal variable
has curation status: requires discussion
definition: probit regression model is a model which attempts to explain data distribution associated with *ordinal* response/dependent variable in terms of values assumed by the independent variable uses a function of predictor/independent variable(s): the function used in this instance of regression modeling is the ordered probit function.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Probit_model) polled in June 2013

stratum population
type: Class
subclass of: processed material
subclass of: population
subclass of: Restriction
  on property: is_specified_output_of
  some values from: population stratification prior to sampling
has curation status: requires discussion
definition: a stratum population is a population resulting from a population stratification prior to sampling process which aims to produce homogenous subpopulations from an heterogeneous population by applying one or more stratification criteria
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

sphericity hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: sphericity testing objective
has curation status: ready for release
definition: a null hypothesis which states that a given matrix is proportional to a Wishart-distributed covariance matrix
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: hypothesis of sphericity

model fitting
type: Class
subclass of: data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: data set
  intersection of: Restriction
    on property: has_specified_input
    some values from: statistical model
subclass of: Restriction
  on property: has part
  some values from: statistical test hypothesis
subclass of: Restriction
  on property: has part
  some values from: model parameter estimation
subclass of: Restriction
  on property: has part
  some values from: degree of freedom approximation
subclass of: Restriction
  on property: precedes
  some values from: Class
    union of: Bayesian model selection
    union of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study design independent variable
        intersection of: Restriction
has curation status: pending final vetting
definition: Model fitting is a data transformation process which evaluates if a model appropriately represents a dataset. A model fitting process tests the goodness of fit of the model to the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

RT-PCR standard curve
type: Class
subclass of: line graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: Class
        intersection of: mass measurement datum
        intersection of: Restriction
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: threshold cycle
has curation status: pending final vetting
definition: a real time pcr standard curve is a line graph which plots the fluorescence intensity signal as a function of the concentration of a sample used as reference and used to determine relative abundance of test samples
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/General_Information/qpcr_technical_guide.pdf and http://www.lifetechnologies.com/uk/en/home/life-science/pcr/real-time-pcr/qpcr-education/absolute-vs-relative-quantification-for-qpcr.html

false negative rate
type: Class
subclass of: proportion
subclass of: Restriction
  on property: is about
  some values from: statistical test hypothesis
has curation status: ready for release
definition: the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO, adapted from
STATO alternative term: type II error rate
STATO alternative term: β

random variable
type: Class
subclass of: variable
has curation status: ready for release
definition: a random variable (or aleatory variable or stochastic variable) in probability and statistics, is a variable whose value is subject to variations due to chance (i.e. randomness, in a mathematical sense)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: aleatory variable
alternative term: stochastic variable
definition source: wikipedia: http://en.wikipedia.org/wiki/Random_variable

graeco-latin square design
type: Class
subclass of: study design
subclass of: randomized complete block design
subclass of: Restriction
  on property: realized in
  some values from: complete randomization
subclass of: Restriction
  on property: declares
  qualified cardinality: 3
  on class: blocking variable
has curation status: pending final vetting
definition: graeco-latin square design is_a study design which allows in its simpler form controlling 3 levels of nuisance variables (also known as blocking variables). The 3 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

group assignment based on blocking variable specification
type: Class
subclass of: group assignment
subclass of: Restriction
  on property: has_specified_output
  some values from: population
has curation status: requires discussion
definition: group assignment based on blocking variable specification is a kind of group assignment process which takes into account the levels assumed by a blocking variable to allocate subjects or experimental units to a treatment group
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

goodness of fit testing objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: goodness of fit hypothesis
has curation status: ready for release
definition: A testing objective to ensure that the sample used in a statistical test actually follows a normal distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

probability distribution
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is denoted by
  some values from: statistic
subclass of: Restriction
  on property: is denoted by
  some values from: skewness
subclass of: Restriction
  on property: is denoted by
  some values from: variance
subclass of: Restriction
  on property: is denoted by
  some values from: kurtosis
subclass of: Restriction
  on property: is denoted by
  some values from: expected value
subclass of: Restriction
  on property: is denoted by
  some values from: standard deviation
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution shape parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution location parameter
has curation status: ready for release
definition: A probability distribution is a information content entity that specifies the probability of the value of a random variable. For a discrete random variable, a mathematical formula that gives the probability of each value of the variable. For a continuous random variable, a curve described by a mathematical formula which specifies, by way of areas under the curve, the probability that the variable falls within a particular interval.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

equal variance testing objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: homoskedasticity hypothesis
has curation status: ready for release
definition: It is a testing objective to ensure the variances of the different groups used in a statistical test are similar (i.e. not too different).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: homoschedacity testing objective
definition source: STATO

normal distribution
type: Class
subclass of: continuous probability distribution
subclass of: symmetric distribution
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 0
has curation status: ready for release
definition: a normal distribution is a continuous probability distribution described by a probability distribution function described here: http://mathworld.wolfram.com/NormalDistribution.html
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Gaussian distribution
definition source: http://mathworld.wolfram.com/NormalDistribution.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.norm.html#scipy.stats.norm

ordinal variable
type: Class
subclass of: categorical variable
subclass of: Restriction
  on property: is_specified_output_of
  some values from: ranking
has curation status: ready for release
definition: ordinal variable is a categorical variable where the discrete possible values are ordered or correspond to an implicit ranking
term editor: Alejandra Gonzalez-Beltan
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: ranked variable
definition source: http://udel.edu/~mcdonald/statvartypes.html

Chi-square probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: has part
  some values from: number of degrees of freedom
has curation status: ready for release
definition: Chi-square probability distribution with k degrees of freedom is a theoretical probability distribution which corresponds to the distribution of a sum of the squares of k independent standard normal random variables.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
R command: dchisq(x, df, ncp = 0, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Chisquare.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.chi2.html#scipy.stats.chi2

expected value
type: Class
subclass of: measure of central tendency
subclass of: Restriction
  on property: is about
  some values from: random variable
has curation status: ready for release
definition: the expected value (or expectation, mathematical expectation, EV, mean, or the first moment) of a random variable is a data item which corresponds to the weighted average of all possible values that this random variable can take on. The weights used in computing this average correspond to the probabilities in case of a discrete random variable, or densities in case of a continuous random variable. From a rigorous theoretical standpoint, the expected value is the integral of the random variable with respect to its probability measure.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: first moment
alternative term: mean
alternative term: μ
definition source: http://en.wikipedia.org/wiki/Expected_value

95% confidence interval
type: Class
subclass of: confidence interval
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: confidence level
    intersection of: Restriction
      on property: has specified value
      has value: 95
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2689604/
has curation status: ready for release
definition: a confidence interval which covers 95% of the sampling distribution, meaning that there is a 5% risk of false positive (type I error). If the number of observations made is large enough, the sampling distribution can be assumed to be normal, which entails that 95% of the sampling distributions falls within roughly2 (1.96) standard deviations from the mean.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: confidence interval at 5% of type I error rate
definition source: STATO

number of PCR cycle
type: Class
subclass of: count
has curation status: pending final vetting
definition: number of PCR cycle is a count which enumerates how many iterations of 'annealing, renaturation, amplification,' rounds (or cycles) are performed during a polymerase chain reaction (PCR) or an assay relying on PCR.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from various sources including: http://www.ncbi.nlm.nih.gov/genome/probe/doc/TechQPCR.shtml

true positive rate
type: Class
subclass of: ratio
subclass of: Restriction
  on property: is about
  some values from: statistical test hypothesis
has curation status: ready for release
definition: sensitivity is a measurement datum qualifying a binary classification test and is computed by substracting the false negative rate to the integral numeral 1
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: recall
alternative term: sensitivity
definition source: adapted from: http://en.wikipedia.org/wiki/Sensitivity_and_specificity and http://mathworld.wolfram.com/Sensitivity.html

residual
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: statistical error
has curation status: ready for release
definition: a residual is a data item which is the output of an error estimate or model fitting process and which is an observable estimate of the unobservable error
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

genetic association study
type: Class
subclass of: investigation
has curation status: metadata incomplete
definition: A genetic association study is a kind of study whose objective is to detect associations between phenotypes, between a phenotype and a genetic polymorphism or between two genetic polymorphisms.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Genetic_association

coefficient of variation
type: Class
subclass of: measure of dispersion
has curation status: ready for release
definition: the coefficient of variation is a normalized measure of dispersion of a probability distribution of frequency distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Coefficient_of_variation last accessed: 2013-10-18
Python command: scipy.stats.variation(a, axis=0) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.variation.html#scipy.stats.variation source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L951

standard deviation
type: Class
subclass of: measure of dispersion
has curation status: ready for release
definition: The standard deviation of a random variable, statistical population, data set, or probability distribution is a measure of variation which correspond to the average distance from the mean of the data set to any given point of that dataset. It also corresponds to the square root of its variance.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: σ
definition source: http://en.wikipedia.org/wiki/Standard_deviation
R command: sd(x, na.rm = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/sd.html

high-content screening
type: Class
subclass of: investigation
subclass of: high throughput screening
subclass of: Restriction
  on property: has part
  some values from: in live cell assay
subclass of: Restriction
  on property: has part
  some values from: normalization data transformation
subclass of: Restriction
  on property: has part
  some values from: hit selection
subclass of: Restriction
  on property: has part
  some values from: between group comparison statistical test
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: imaging assay
    union of: flow cytometry assay
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: cDNA library
    union of: screening library
has curation status: pending final vetting
definition: high content screening is a kind of investigation which uses a standardized cellular assays to test the effect of substances (RNAi or small molecules) held in libraries on a cellular phenotype. it relies on microscopy imaging and or flow-cytometry, robotic handling to ensure fast and high-throughput.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://en.wikipedia.org/wiki/High-content_screening

high throughput screening
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has part
    some values from: hit selection
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      union of: cDNA library
      union of: screening library
      union of: phage display library
subclass of: investigation
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: analyte assay
    union of: in live cell assay
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: Class
        union of: regression analysis method
        union of: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    union of: standardized mean difference
    union of: strictly standardized mean difference
has curation status: pending final vetting
definition: high throughput screening is a kind of investigation which uses a standardized assays (cell based, enzymatic or chemometric) to test the effect of substances (RNAi or small molecules) held in libraries on a very specific and measureable outcome (e.g fluorence intensity). it relies on robotic handling to ensure fast and high-throughput in assay performance, data acquisition and hit selection.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB,PRS

Kendall's correlation coefficient
type: Class
subclass of: correlation coefficient
subclass of: Restriction
  on property: is about
  some values from: effect size estimate
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: ordinal variable
has curation status: ready for release
definition: Kendall's correlation coefficient is a correlation coefficient between 2 ordinal variables (natively or following a ranking procedure) and may be used when the conditions for computing Pearson's correlation are not met (e.g linearity, normality of the 2 continuous variables)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Kendall rank correlation coefficient
alternative term: Kendall's tau (τ) coefficient
definition source: STATO, adapted from wikipedia (http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient), polled in june 2013 and from: http://stamash.org/pearsons-correlation-coefficient/ http://stamash.org/kendalls-tau-correlation/
R command: cor(x, y = NULL, use = "everything",method = c("kendall"))
Python command: scipy.stats.kendalltau(x, y, initial_lexsort=True) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.kendalltau.html#scipy.stats.kendalltau source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2827

Q-Q plot
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: Class
        intersection of: quantile
        intersection of: Restriction
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: Class
        intersection of: quantile
        intersection of: Restriction
subclass of: Restriction
  on property: is_specified_output_of
  some values from: data visualization
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: probability distribution
has curation status: ready for release
definition: Q-Q plot or quantile-quantile plot is the output of a graphical method for comparing two probability distributions by plotting their quantiles against each other
editor note: PRS,AGB: need to add the notion of quantile
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: quantile-quantile plot
R command: qqplot(x, y, plot.it = TRUE, xlab = deparse(substitute(x)), ylab = deparse(substitute(y)), ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/qqnorm.html

statistical error
type: Class
subclass of: statistic
has curation status: ready for release
definition: statistical error is an data item denoting the amount by which an observation differs from the expected value, being based on the whole statistical population from which the statistical unit was chosen randomly
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Errors_and_residuals_in_statistics last accessed: 18-11-2013
STATO alternative term: disturbance

box and whisker plot
type: Class
subclass of: graph
subclass of: Restriction
  on property: is about
  some values from: minimum observed value
subclass of: Restriction
  on property: is about
  some values from: maximum observed value
subclass of: Restriction
  on property: is about
  some values from: data distribution
subclass of: Restriction
  on property: is about
  some values from: first quartile
subclass of: Restriction
  on property: is about
  some values from: third quartile
subclass of: Restriction
  on property: is about
  some values from: center value
example of usage: A box and whisker plot is appropriate to represent the characteristics oc a distribution.
has curation status: ready for release
definition: a box plot is a graph which plots datasets relying on their quartiles and the interquartile range to create the box and the whiskers.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Tukey box and whisker plot
alternative term: box plot
definition source: Tukey, J. W. "Box-and-Whisker Plots." §2C in Exploratory Data Analysis. Reading, MA: Addison-Wesley, pp. 39-43, 1977.
STATO alternative term: boxplot
R command: boxplot(x, ...) http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/boxplot.html

ΔRn
type: Class
subclass of: data item
has curation status: pending final vetting
definition: (Rn +) − (Rn −), where Rn + = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR with template and Rn − = (emission intensity of reporter dye)/(emission intensity of passive reference dye) in PCR without template or early cycles of a real-time reaction. Ct = threshold cycle, i.e., cycle at which a statistically significant increase in ΔRn is first detected
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://jcm.asm.org/content/38/7/2516.figures-only

relative risk
type: Class
subclass of: effect size estimate
subclass of: risk
subclass of: Restriction
  on property: is about
  some values from: disposition
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
subclass of: Restriction
  on property: is about
  qualified cardinality: 4
  on class: study group population
definition: Relative risk is a measurement datum which denotes the risk of an 'event' relative to an 'exposure'. Relative risk is calculated by forming the ratio of the probability of the event occurring in the exposed group versus the probability of this event occurring in the non-exposed group.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: risk ratio
definition source: ready for release

Woolf's test
type: Class
subclass of: data transformation
subclass of: odds ratio homogeneity test
subclass of: homogeneity test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: homogeneity test objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: 2 by 2 contingency table
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: odds ratio
has curation status: ready for release
definition: Woolf's test is a statistical test which evaluates the null hypothesis that odds ratio are the same accross all strata of population under investigation
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://people.umass.edu/biep640w/pdf/4.%20%20Categorical%20Data%20Analysis%202012.pdf
R command: woolf_test(x) where x is 2 x 2 x k contingency table http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/vcd/html/woolf_test.html

odds ratio homogeneity test
type: Class
equivalent class: homogeneity test
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: homogeneity test objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: odds ratio homogeneity test is a statistical test which aims to evaluate that null the hypothesis of consistency odds ratio accross different strata of population is true or not
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

blocking variable
type: Class
subclass of: realizable entity
subclass of: variable
subclass of: Restriction
  on property: realized in
  some values from: group assignment based on blocking variable specification
example of usage: https://onlinecourses.science.psu.edu/stat503/node/19 Often in medical studies, the blocking factor used is the type of institution. This provides a very useful blocking factor, hopefully removing institutionally related factors such as size of the institution, types of populations served, hospitals versus clinics, etc., that would influence the overall results of the experiment.
has curation status: ready for release
definition: a blocking variable is a independent variable which is used in a blocking process part of an experiment with the purpose of maximizing the signal coming from the main variable.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: nuisance variable
definition source: https://onlinecourses.science.psu.edu/stat503/node/18

DNA microarray hybridization
type: Class
subclass of: assay
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: nucleic acid hybridization
  intersection of: Restriction
    on property: has_specified_input
    some values from: Class
      intersection of: labeled nucleic acid extract
      intersection of: DNA microarray
definition: a DNA microarray hybridization is an assay relying on nucleic acid hybridization , which uses a DNA microarray device and a nucleic acid as input. It precedes a data acquisition process
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

group comparison objective
type: Class
subclass of: data transformation objective
has curation status: metadata incomplete
definition: group comparison objective is a data transformation objective which aims to determine if 2 or more study group differ with respect to the signal of a response variable
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

continuous variable
type: Class
subclass of: variable
subclass of: Restriction
  on property: has part
  some values from: scalar measurement datum
disjoint with: categorical variable
example of usage: "Time to solve an anagram problem" is continuous since it could take 2 minutes, 2.13 minutes etc. to finish a problem
has curation status: ready for release
definition: A continuous variable is one for which, within the limits the variable ranges, any value is possible.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://davidmlane.com/hyperstat/A97418.html
definition source: http://udel.edu/~mcdonald/statvartypes.html

categorical variable
type: Class
subclass of: variable
subclass of: Restriction
  on property: has part
  all values from: categorical measurement datum
has curation status: ready for release
definition: a categorical variable is a variable which that can only assume a finite number of value and cast observation in a small number of categories
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: discrete variable
alternative term: nominal variable
alternative term: qualitative factor
definition source: http://udel.edu/~mcdonald/statvartypes.html
Source: https://onlinecourses.science.psu.edu/stat503/node/7

within subject comparison objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: absence of within subject difference hypothesis
has curation status: ready for release
definition: the objective of a data transformation to test a null hypothesis of absence of difference within subject holds.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

allele frequency
type: Class
subclass of: data item
subclass of: ratio
subclass of: Restriction
  on property: has numerator
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: population
        intersection of: allele information
subclass of: Restriction
  on property: has denominator
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: population
        intersection of: allele information
has curation status: ready for release
definition: The allele frequency is a data item which denotes the incidence of a gene variant in a population. It is calculated as a ratio, by dividing the number of copies of a particular allele by the number of copies of all alleles at the genetic place (locus) in a population.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.nature.com/scitable/definition/allele-frequency-298
STATO alternative term: gene frequency

between group comparison objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: absence of between group difference hypothesis
has curation status: ready for release
definition: the objective of a data transformation to test a null hypothesis of absence of difference withing subject holds.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

manhattan plot for gwas
type: Class
subclass of: scatter plot
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: genomic coordinate datum
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Class
      intersection of: Restriction
        on property: is about
        some values from: Class
      intersection of: Restriction
        on property: denotes
        some values from: Class
subclass of: Restriction
  on property: is about
  some values from: genome-wide association study
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: genome-wide association study
has curation status: ready for release
definition: a manhattan plot for gwas is a kind of scatter plot used to facilitate presentation of genome-wide association study (GWAS) data. Genomic coordinates are displayed along the X-axis, with the negative logarithm of the association P-value for each single nucleotide polymorphism displayed on the Y-axis.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Manhattan_plot
R command: plotGrandLinear(obj, ..., facets, space.skip = 0.01, geom = NULL, cutoff = NULL, cutoff.color = "red", cutoff.size = 1, legend = FALSE, xlim, ylim, xlab, ylab, main) http://www.tengfei.name/ggbio/docs/man/plotGrandLinear.html

family
type: Class
subclass of: population
definition: A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption.
editor note: import from Population and Community Ontology: http://www.ontobee.org/browser/rdf.php?o=PCO&iri=http://purl.obolibrary.org/obo/PCO_0000020
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://purl.obolibrary.org/obo/PCO_0000020

variable
type: Class
equivalent class: Class
  union of: study design independent variable
  union of: study design dependent variable
  union of: continuous variable
  union of: categorical variable
subclass of: data item
has curation status: ready for release
definition: a variable is a data item which can assume any of a set of values, either as determined by an agent or as randomly occuring through observation.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
definition source: adapted from wolfram-alpha (http://www.wolframalpha.com/input/?i=variable) definition 2. and from Oxford English Dictionary: http://www.oed.com/view/Entry/221514?redirectedFrom=variable#eid, definition B,1

repeated measure ANOVA
type: Class
subclass of: data transformation
subclass of: ANOVA
subclass of: within subject comparison statistical test
subclass of: Restriction
  on property: has part
  some values from: F-test
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: normal distribution hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: sphericity hypothesis
    intersection of: Restriction
      on property: has value
      has value: true
subclass of: Restriction
  on property: preceded by
  some values from: Mauchly's test for sphericity
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_output
  some values from: standardized mean difference
subclass of: Restriction
  on property: has_specified_output
  some values from: confidence interval
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: within subject comparison objective
    intersection of: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  all values from: balanced design
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design independent variable
    intersection of: categorical variable
    intersection of: Restriction
      on property: denotes
      some values from: time sampled measurement data set
has curation status: ready for release
definition: repeated measure ANOVA is a kind of ANOVA specifically developed for non-independent observations as found when repeated measurements on the sample experimental unit. repeated measure ANOVA is sensitive to departure from normality (evaluation using Bartlett's test), more so in the case of unbalanced groups (i.e. different sizes of sample populations). Departure from sphericity (evaluation using Mauchly'test) used to be an issue which is now handled robustly by modern tools such as R's lme4 or nlme, which accommodate dependence assumptions other than sphericity.
editor note: discussion in https://github.com/ISA-tools/stato/issues/28
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
alternative term: ANOVA for correlated samples
definition source: adapted from wikipedia and https://statistics.laerd.com/statistical-guides/repeated-measures-anova-statistical-guide-3.php
definition source: http://www.ats.ucla.edu/stat/sas/library/repeated_ut.htm
STATO alternative term: ANOVA for correlated samples
R command: http://cran.r-project.org/doc/contrib/Lemon-kickstart/kr_repms.html

Newman-Keuls test post-hoc analysis
type: Class
subclass of: data transformation
subclass of: post-hoc analysis
subclass of: Restriction
  on property: preceded by
  some values from: ANOVA
subclass of: Restriction
  on property: has_specified_input
  some values from: studentized range distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: Class
    intersection of: expected value
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: study group population
has curation status: ready for release
definition: The Newman–Keuls or Student–Newman–Keuls (SNK) method is a stepwise multiple comparisons procedure used to identify sample means that are significantly different from each other. It was named after Student (1927), D. Newman, and M. Keuls. This procedure is often used as a post-hoc test whenever a significant difference between three or more sample means has been revealed by an analysis of variance (ANOVA). The Newman–Keuls method is similar to Tukey's range test as both procedures use Studentized range statistics.Compared to Tukey's range test, the Newman–Keuls method is more powerful but less conservative.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: last accessed: 2013-11-15
R command: SNK.test(y, trt, DFerror, MSerror, alpha = 0.05, group=TRUE, main = NULL) http://artax.karlin.mff.cuni.cz/r-help/library/agricolae/html/SNK.test.html

Bernoulli distribution
type: Class
subclass of: binomial distribution
has curation status: ready for release
definition: Bernoulli distribution is a binomial distribution where the number of trials is equal to 1. notation: B(1,p) The mean is p The variance is p*q
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

Galbraith plot
type: Class
subclass of: scatter plot
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: standard error of the mean
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: effect size estimate
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: Restriction
      on property: preceded by
      some values from: meta analysis
has curation status: ready for release
definition: Galbraith (Radial) plot is a scatter plot which can be used in the meta-analytic context to examine the data for heterogeneity. For a fixed-effects model, the plot shows the inverse of the standard errors on the horizontal axis against the individual observed effect sizes or outcomes standardized by their corresponding standard errors on the vertical axis. Radial plots were introduced by Rex Galbraith (1988a, 1988b, 1994).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Galbraith, Rex (1988). "Graphical display of estimates having differing standard errors". Technometrics (Technometrics, Vol. 30, No. 3) 30 (3): 271–281. doi:10.2307/1270081. JSTOR 1270081
STATO alternative term: radial Galbraith plot
R command: http://www.inside-r.org/packages/cran/Luminescence/docs/plot_RadialPlot plot_RadialPlot(data, na.exclude = TRUE, negatives = "remove", log.z = TRUE, central.value, centrality = "mean.weighted", plot.ratio, bar.col, grid.col, legend.text, summary = FALSE, stats, line, line.col, line.label, output = FALSE, ...)
R command: http://www.metafor-project.org/doku.php/plots:radial_plot

factor level combination
type: Class
subclass of: data set
subclass of: Class
  intersection of: data set
  intersection of: Restriction
    on property: has part
    some values from: factor level
example of usage: http://isogenic.info/html/9__treatments.html#factorial
has curation status: ready for release
definition: a factor level combination is one a possible sets of factor levels resulting from the cartesian product of sets of factor and their levels as defined in a factorial design
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: treatment combination
definition source: STATO

factor level
type: Class
subclass of: data item
example of usage: http://isogenic.info/html/9__treatments.html#factorial
has curation status: ready for release
definition: A factor level is data item which corresponds to one of the value assumed by a factor or independent variable manipulated and set by the experimentalist. In the context of factorial design, a factor level is assumed to be or treated as a category in a categorical variable
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: treatment
definition source: AGB-PRS
definition source: https://onlinecourses.science.psu.edu/stat503/node/7

Bayes factor
type: Class
subclass of: ratio
subclass of: Restriction
  on property: is about
  some values from: statistical model
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Bayesian model selection
has curation status: ready for release
definition: Bayes factor is a ratio between 2 probabilities of observing data according 2 distinct models. It is used in Bayes model selection to evaluate which model best explains the data. if K<0, the model used in the denominator term is supported, if K>1, the model used in the numerator term is supported. The Bayes factor is about the plausibility of 2 different models
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia last accessed 2013-11-13

grouped bar chart
type: Class
subclass of: bar chart
has curation status: ready for release
definition: grouped bar chart is a kind of bar chart which juxtaposes the discrete values for each of the possible value of a given categorical variable, thus providing within group comparison. Grouped bar charts are good for comparing between each element in the categories, and comparing elements across categories. However, the grouping can make it harder to tell the difference between the total of each group.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from http://www2.le.ac.uk/offices/ld/resources/numeracy/bar-charts and http://blog.visual.ly/how-groups-stack-up-when-to-use-grouped-vs-stacked-column-charts/ [last accessed: 2014-03-04]
R command: barplot(height....) set argument " beside = TRUE " http://stat.ethz.ch/R-manual/R-patched/library/graphics/html/barplot.html

Gamma distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution shape parameter
has curation status: ready for release
definition: A gamma distribution is a general type of continous statistical distribution (related to the beta distribution) that arises naturally in processes for which the waiting times between Poisson distributed events are relevant. Gamma distributions have two free parameters shape k and scale denoted theta .
editor note: Alejandra Gonzalez-Beltran
editor note: Philippe Rocca-Serra
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/GammaDistribution.html
R command: dgamma(x, shape, rate = 1, scale = 1/rate, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.gamma.html#scipy.stats.gamma

polychoric correlation coefficient
type: Class
subclass of: correlation coefficient
subclass of: Class
  intersection of: Restriction
    on property: is_proxy_for
    some values from: Restriction
      on property: is about
      qualified cardinality: 2
      on class: Class
        intersection of: continuous variable
        intersection of: Restriction
  intersection of: Restriction
    on property: is about
    qualified cardinality: 2
    on class: polychotomous variable
has curation status: ready for release
definition: polychoric correlation coefficient is a correlation coefficient which is computed over 2 variables to characterise an association by proxy with 2 (latent) variables which are assumed to be continuous and normally distributed.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://www.rasch.org/rmt/rmt193c.htm and http://en.wikipedia.org/wiki/Polychoric_correlation
R command: http://cran.r-project.org/web/packages/polycor/ polychor(x, y, ML = FALSE, control = list(), std.err = FALSE, maxcor=.9999)

full factorial design
type: Class
equivalent class: Restriction
  on property: has part
  some values from: Class
    intersection of: number of factor level combinations
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: cartesian product
subclass of: factorial design
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: number of factor level combinations
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: cartesian product
subclass of: Restriction
  on property: declares
  min qualified cardinality: 1
  on class: study design independent variable
has curation status: ready for release
definition: a full factorial design is a factorial design which ensures that all possible factor level combinations are defined and used so all between group differences can be explored
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

permutation numbering
type: Class
subclass of: data transformation
has curation status: ready for release
definition: permutation numbering is a data tranformation allowing to count the number of possible permutations of elements in a set of size n, each element occurring exactly once. This number is factorial n.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

Michaelis-Menten constant
type: Class
subclass of: scalar measurement datum
has curation status: ready for release
definition: The Michaelis constant is the substrate concentration at which the reaction rate is at half-maximum, and is an inverse measure of the substrate's affinity for the enzyme—as a small indicates high affinity, meaning that the rate will approach more quickly.[5] The value of is dependent on both the enzyme and the substrate, as well as conditions such as temperature and pH.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Michaelis–Menten_constant last accessed: 22-11-2013
STATO alternative term: half maximal reaction rate substrate concentration (Km)

child-parents trio
type: Class
subclass of: family
definition: A population of two parents and a child.
editor note: possibly submit to 'Population and Community Ontology'
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
STATO alternative term: child-parent trio
STATO alternative term: parent-child trio
STATO alternative term: parents-child trio

receiver operational characteristics curve
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: true positive rate
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: true negative rate
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: assay
    union of: statistical test hypothesis
    union of: binary classification
subclass of: Restriction
  on property: is_specified_output_of
  some values from: data visualization
has curation status: ready for release
definition: receiver operational characteristics curve is a graphical plot which illustrates the performance of a binary classifier system as its discrimination threshold (aka cut-off point) is varied by plotting sensitivity vs (1 − specificity)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: ROC curve
definition source: http://en.wikipedia.org/wiki/Receiver_operating_characteristic
R command: roc.from.table(table, graph = TRUE, add = FALSE, title = FALSE, line.col = "red", auc.coords = NULL, ...) http://rss.acs.unt.edu/Rdoc/library/epicalc/html/roc.html

transmission disequilibrium test
type: Class
subclass of: data transformation
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study group population
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
has curation status: pending final vetting
definition: The transmission disequilibrium test is a statistical test for genetic linkage between genetic marker and a trait in families. The test is robust to population structure.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: TDT
definition source: STATO , adapted wikipedia (from http://en.wikipedia.org/wiki/Transmission_disequilibrium_test), polled on June,2013

binomial distribution
type: Class
subclass of: discrete probability distribution
has curation status: ready for release
definition: The binomial distribution is a discrete probability distribution which describes the probability of k successes in n draws with replacement from a finite population of size N. The binomial distribution is frequently used to model the number of successes in a sample of size n drawn with replacement from a population of size N. The binomial distribution gives the discrete probability distribution of obtaining exactly n successes out of N Bernoulli trials (where the result of each Bernoulli trial is true with probability p and false with probability q=1-p ) notation: B(n,p) The mean is N*p The variance is N*p*q
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Binomial_distribution
R command: dbinom(x, size, prob, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Binomial.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binom.html#scipy.stats.binom

hit selection
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: Class
      union of: z-score
      union of: strictly standardized mean difference
      union of: p-value
    intersection of: Restriction
      on property: is_specified_output_of
      some values from: between group comparison statistical test
subclass of: Restriction
  on property: executes
  some values from: Class
    intersection of: selection criterion
    intersection of: Restriction
      on property: is about
      some values from: effect size estimate
has curation status: pending final vetting
definition: hit selection is a planned process which in screening processes such as high-throughput screening, lead to the identification of perturbing agent which cause the typical signal generated by a standardized assay to significantly differ from the negative control. The selection hitself results from meeting or exceeding selection threshold (for instance 6 sigma from the mean or SSMD value beyond 5 when compared to positive controls or below -5 when compared to negative controls
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: AGB, PRS
definition source: adapted from: http://en.wikipedia.org/wiki/SSMD
definition source: adapted from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2789971/

pairing rule
type: Class
subclass of: rule
example of usage: age-matched participants
has curation status: ready for release
definition: pairing rule is a rule which specifies the criteria for deciding on how to associated any 2 entities.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

between group comparison statistical test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: between group comparison statistical test is a statistical test which aims to detect difference between the means computing for each of the study group populations
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

Pearson's correlation coefficient
type: Class
subclass of: correlation coefficient
subclass of: Restriction
  on property: is about
  some values from: effect size estimate
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: Class
    intersection of: continuous variable
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: normal distribution hypothesis
        intersection of: Restriction
has curation status: ready for release
definition: The Pearson's correlation coefficient is a correlation coefficient which evaluates two continuous variables for association strength in a data sample. It assumes that both variables are normally distributed and linearity exists. The coefficient is calculated by dividing their covariance with the product of their individual standard deviations. It is a normalized measurement of how the two are linearly related.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Pearson product-moment correlation coefficient
alternative term: Pearson's r
alternative term: r statistics
definition source: STATO, adapted from http://www.r-tutor.com/elementary-statistics/numerical-measures/correlation-coefficient and from: http://stamash.org/pearsons-correlation-coefficient/ http://stamash.org/kendalls-tau-correlation/
R command: cor(x, y = NULL, use = "everything",method = c("pearson"))
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html
Python command: scipy.stats.pearsonr(x, y) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.pearsonr.html#scipy.stats.pearsonr source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L2427

F-statistic
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_input_of
  some values from: F-test
has curation status: ready for release
definition: F statistic is a statistic computed from observations and used to produce a p-value in statistical test when compared to a F distribution. the F statistic is the ratio of two scaled sums of squares reflecting different sources of variability
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
preferred mathematical notation: F

negative binomial distribution
type: Class
subclass of: discrete probability distribution
has curation status: ready for release
definition: negative binomial probability distribution is a discrete probability distribution of the number of successes in a sequence of Bernoulli trials before a specified (non-random) number of failures (denoted r) occur. The negative binomial distribution, also known as the Pascal distribution or Pólya distribution, gives the probability of r-1 successes and x failures in x+r-1 trials, and success on the (x+r)th trial.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Pascal distribution
alternative term: Pólya distribution
definition source: http://mathworld.wolfram.com/NegativeBinomialDistribution.html
R command: dnbinom(x, size, prob, mu, log = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/NegBinomial.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.nbinom.html#scipy.stats.nbinom

Breusch-Pagan test
type: Class
subclass of: data transformation
subclass of: homoskedasticity test
subclass of: Restriction
  on property: has part
  some values from: linear regression for analysis of continuous dependent variable
subclass of: Restriction
  on property: has_specified_input
  some values from: statistical model
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: equal variance testing objective
has curation status: ready for release
definition: Breusch-Pagan test is a statistical test which computes a score test of the hypothesis of constant error variance against the alternative that the error variance changes with the level of the response (fitted values), or with a linear combination of predictors.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Breusch, T. S. and Pagan, A. R. (1979) A simple test for heteroscedasticity and random coefficient variation. Econometrica 47, 1287--1294. and adapted from: http://www.inside-r.org/packages/cran/car/docs/ncvTest last accessed [2014-03-15]
R command: http://hosho.ees.hokudai.ac.jp/~kubo/Rdoc/library/lmtest/html/bptest.html bptest(formula, varformula = NULL, studentize = TRUE, data = list()) or http://www.inside-r.org/packages/cran/car/docs/ncvTest

hypergeometric test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: two tailed test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: hypergeometric distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: statistical hypothesis test objective
    intersection of: Restriction
      on property: has part
      some values from: absence of enrichment hypothesis
    intersection of: Restriction
      on property: has part
      some values from: absence of depletion hypothesis
example of usage: http://www.ncbi.nlm.nih.gov/pubmed/?term=17182697 Bioinformatics. 2007 Feb 15;23(4):401-7. Enrichment or depletion of a GO category within a class of genes: which test? Rivals I1, Personnaz L, Taing L, Potier MC.
has curation status: ready for release
definition: hypergeometric test is a null hypothesis test which evaluates if a random variable follows a hypergeometric distribution. It is a test of goodness of fit to that distribution. The test is suited for situation aimed at assessing cases of sampling from a finite set without replacements. For instance, testing for enrichment or depletion of elements (e.g GO categories, genes)
editor note: Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
R command: phyper(q, m, n, k, lower.tail = TRUE, log.p = FALSE) lower.tail logical; if TRUE (default), probabilities are P[X ≤ x], otherwise, P[X > x]. http://stat.ethz.ch/R-manual/R-patched/library/stats/html/Hypergeometric.html

one tailed test
type: Class
subclass of: statistical test hypothesis
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: probability distribution
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: skewness
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: statistical hypothesis test objective
    intersection of: Class
      intersection of: Restriction
        on property: has part
        some values from: Class
      intersection of: Restriction
        on property: has part
        some values from: Class
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: statistical hypothesis test objective
    intersection of: Class
      union of: Restriction
        on property: has part
        some values from: Class
      union of: Restriction
        on property: has part
        some values from: Class
has curation status: ready for release
definition: a one-tailed test is a statistical test which, assuming an unskewed probability distribution, allocates all of the significance level to evaluate only one hypothesis to explain a difference. The one-tailed test provides more power to detect an effect in one direction by not testing the effect in the other direction. one-tailed test should be preceded by two-tailed test in order to avoid missing out on detecting alternate effect explaining an observed difference.
editor note: Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: one sided test
definition source: adapted from: http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm

two tailed test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: statistical hypothesis test objective
    intersection of: Class
      intersection of: Restriction
        on property: has part
        some values from: absence of negative difference hypothesis
      intersection of: Restriction
        on property: has part
        some values from: absence of positive difference hypothesis
subclass of: statistical test hypothesis
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: probability distribution
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: skewness
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
example of usage: For example, we may wish to compare the mean of a sample to a given value x using a t-test. Our null hypothesis is that the mean is equal to x. A two-tailed test will test both if the mean is significantly greater than x and if the mean significantly less than x. The mean is considered significantly different from x if the test statistic is in the top 2.5% or bottom 2.5% of its probability distribution, resulting in a p-value less than 0.05.
has curation status: ready for release
definition: a two tailed test is a statistical test which assess the null hypothesis of absence of difference assuming a symmetric (not skewed) underlying probability distribution by allocating half of the significance level selected to each of the direction of change which could explain a difference (for example, a difference can be an excess or a loss).
editor note: Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: two sided test
definition source: adapted from: http://www.ats.ucla.edu/stat/mult_pkg/faq/general/tail_tests.htm

absence of difference hypothesis
type: Class
subclass of: hypothesis
has curation status: ready for release
definition: A null hypothesis which states that no difference exists between 2 or more groups being considered.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

design matrix
type: Class
subclass of: data item
subclass of: matrix
subclass of: Restriction
  on property: part of
  some values from: statistical model
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: denotes
      some values from: study design independent variable
subclass of: Restriction
  on property: denotes
  some values from: study design
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: data transformation
    union of: model fitting
example of usage: let's consider an experiment evaluating 2 compounds (aspirin & ibuprofen) at 3 distinct dose levels (low, medium, high) and 4 time points post exposure (0h, 6h, 12h, 24h). Assuming the treatments are applied only once (no replication), the number of observation in a full factorial design is 2 x 3 x 4 = 24 so the design matrix would have 24 rows and 3 columns (1 per factor (independent variable).
has curation status: ready for release
definition: a design matrix is an information content entity which denotes a study design. The design matrix is a n by m matrix where n the number of rows, corresponds to the number of observations (4 rows if quadruplicates) and where m, the number of columns corresponds to the number of independent variables. Each element in the matrix correspond to a discretized value representing one of the factor levels for a given factor. A design matrix can be used as input to statistical modeling or statistical analysis. The design matrix contains data on the independent variables (also called explanatory variables) in statistical models which attempt to explain observed data on a response variable (often called a dependent variable) in terms of the explanatory variables. The theory relating to such models makes substantial use of matrix manipulations involving the design matrix: see for example linear regression. A notable feature of the concept of a design matrix is that it is able to represent a number of different experimental designs and statistical models, e.g., ANOVA, ANCOVA, and linear regression
editor note: Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/9
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: model matrix
definition source: adapted from: Design of Experiments: Principles and Applications edited by Lennart Eriksson, 1999-2008 Umetrics. ISBN-13:978-91-973730-4-3 and http://en.wikipedia.org/wiki/Design_matrix [last accessed: 22-05-2014]
R command: model.matrix(object, data = environment(object), contrasts.arg = NULL, xlev = NULL, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/model.matrix.html

contrast
type: Class
subclass of: data item
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: contrast weight matrix
    intersection of: average value
subclass of: Restriction
  on property: denotes
  some values from: Class
    intersection of: average value
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: study group population
        intersection of: Restriction
subclass of: Restriction
  on property: is_specified_input_of
  some values from: model fitting
has curation status: requires discussion
definition: A contrast is the weighted sum of group means, the c_j coefficients represent the assigned weights of the means (these must sum to 0 for orthogonal contrasts)
editor note: Term request by Nolan Nichols via https://github.com/ISA-tools/stato/issues/9
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://en.wikipedia.org/wiki/Contrast_%28statistics%29
R command: contrasts(x, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrasts.html

quantile
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: Class
    union of: data set
    union of: probability distribution
has curation status: ready for release
definition: a quantile is a data item which corresponds to specific elements x in the range of a variate X. the k-th n-tile P_k is that value of x, say x_k, which corresponds to a cumulative frequency of Nk/n (Kenney and Keeping 1962). If n=4, the quantity is called a quartile, and if n=100, it is called a percentile.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Evans, M.; Hastings, N.; and Peacock, B. Statistical Distributions, 3rd ed. New York: Wiley, 2000.
definition source: http://mathworld.wolfram.com/Quantile.html

decile
type: Class
subclass of: quantile
has curation status: ready for release
definition: a decile is a quantile where n=10 and which splits data into sections accrued of 10% of data, so the first decile delineates 10% of the data, the second decile delineates 20% of the data and the nineth decile, 90 % of the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

percentile
type: Class
subclass of: quantile
has curation status: ready for release
definition: a percentile is a quantile which splits data into sections accrued of 1% of data, so the first percentile delineates 1% of the data, the second quartile delineates 2% of the data and the 99th percentile, 99 % of the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

absence of negative difference hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: between group comparison objective
disjoint with: absence of positive difference hypothesis
has curation status: metadata incomplete
definition: absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly less than a threshold does not exist.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

absence of positive difference hypothesis
type: Class
subclass of: hypothesis
subclass of: Restriction
  on property: part of
  some values from: between group comparison objective
has curation status: metadata incomplete
definition: absence of negative difference hypothesis is a hypothesis which assumes that a difference significantly greater than a threshold does not exist.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

absence of enrichment hypothesis
type: Class
subclass of: absence of positive difference hypothesis
has curation status: metadata incomplete
definition: absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly greater than a threshold does not exist.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: absence of over representation hypothesis
definition source: STATO

absence of depletion hypothesis
type: Class
subclass of: absence of negative difference hypothesis
has curation status: metadata incomplete
definition: absence of depletion difference hypothesis is a hypothesis which assumes that the representation of an element significantly less than a threshold does not exist.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: absence of under representation hypothesis
definition source: STATO

exact binomial test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: binomial distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: a binomial test is a statistical hypothesis test which evaluates if the observations made about a Bernoulli experiment , that is an experiment which tests the statistical significance of deviations from a theoretically expected distribution (the binomial distribution) of observations into 2 categories. It is a goodness of fit test.
editor note: Added following a term request by Chris Mungall: https://github.com/ISA-tools/stato/issues/6
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://en.wikipedia.org/wiki/Binomial_test
STATO alternative term: binomial test
R command: binom.test(x, n, p = 0.5, alternative = c("two.sided", "less", "greater"), conf.level = 0.95) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/binom.test.html
comment: scipy.stats.binom_test(x, n=None, p=0.5) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binom_test.html#scipy.stats.binom_test source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/morestats.py#L1605

statistical inference
type: Class
subclass of: planned process
subclass of: drawing a conclusion
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: statistical test hypothesis
    intersection of: Restriction
      on property: precedes
      some values from: assess statistical evidence
subclass of: Restriction
  on property: has_specified_output
  some values from: conclusion textual entity
example of usage: Evaluation of statistical inference on empirical resting state fMRI. IEEE Trans Biomed Eng. 2014 Apr;61(4):1091-9. doi: 10.1109/TBME.2013.2294013. http://www.ncbi.nlm.nih.gov/pubmed/24658234
has curation status: ready for release
definition: Statistical inference is the process of deducing properties of an underlying probability distribution by analysis of data.
editor note: Added following a term request by Nolan Nichols: https://github.com/ISA-tools/stato/issues/12
editor note: Definition changed according to discussions in https://github.com/ISA-tools/stato/issues/55
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: The definition cited from Wikipedia is from: Upton, G., Cook, I. (2008) Oxford Dictionary of Statistics, OUP. ISBN 978-0-19-954145-4
definition source: https://en.wikipedia.org/wiki/Statistical_inference

dimensionless ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: A ratio where the numerator and denominator are expressed in the same unit.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: dimensionless ratio

covariance
type: Class
subclass of: measure of correlation
subclass of: Restriction
  on property: is about
  min qualified cardinality: 2
  on class: expected value
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: variable
has curation status: ready for release
definition: The covariance is a measurement data item about the strength of correlation between a set (2 or more) of random variables. The covariance is obtained by forming: cov(X,Y)=E([X-E(X)][Y-E(Y)] where E(X), E(Y) is the expected value (mean) of variable X and Y respectively. covariance is symmetric so cov(X,Y)=cov(Y,X). The covariance is usefull when looking at the variance of the sum of the 2 random variables since: var(X+Y) = var(X) +var(Y) +2cov(X,Y) The covariance cov(x,y) is used to obtain the coefficient of correlation cor(x,y) by normalizing (dividing) cov(x,y) but the product of the standard deviations of x and y.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://mathworld.wolfram.com/Covariance.html
STATO alternative term: covariance
R command: cov(x, y = NULL, use = "everything", method = c("pearson", "kendall", "spearman")) from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/cor.html

one sample t-test
type: Class
subclass of: Student's t-test
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: Student's t distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: t-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: ready for release
definition: one sample t-test is a kind of Student's t-test which evaluates if a given sample can be reasonably assumed to be taken from the population. The test compares the sample statistic (m) to the population parameter (M). The one sample t-test is the small sample analog of the z test, which is suitable for large samples.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from various sources, including: Practical Statistics for Medical Research by D.Altman. ISBN: 0-412-27630-5 http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tone.htm
STATO alternative term: one sample t-test
R command: t.test(x = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
Python command: scipy.stats.ttest_1samp(a, popmean, axis=0) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_1samp.html#scipy.stats.ttest_1samp source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3194

two sample t-test with equal variance
type: Class
subclass of: Student's t-test
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Student's t distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: t-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: normal distribution hypothesis
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: average value
    intersection of: Restriction
      on property: is about
      some values from: study group population
has curation status: ready for release
definition: two sample t-test is a null hypothesis statistical test which is used to reject or accept the hypothesis of absence of difference between the means over 2 randomly sampled populations. It uses a t-distribution for the test and assumes that the variables in the population are normally distributed and with equal variances.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: two sample t-test
definition source: adapted from: http://en.wikipedia.org/wiki/Student's_t-test#Independent_.28unpaired.29_samples and from: http://www.psychology.emory.edu/clinical/bliwise/Tutorials/TOM/meanstests/tind.htm
STATO alternative term: t-test for independent means assuming equal variance
R command: t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = TRUE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
Python command: scipy.stats.ttest_ind(a, b, axis=0, equal_var=True) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3271

two sample t-test with unequal variance
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: achieves_planned_objective
    some values from: between group comparison objective
  intersection of: Restriction
    on property: has_specified_input
    qualified cardinality: 2
    on class: Class
      intersection of: Class
        union of: trimmed mean
        union of: average value
      intersection of: Restriction
        on property: is about
        some values from: study group population
subclass of: Student's t-test
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Student's t distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: t-statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 1
  on class: Class
    intersection of: study design dependent variable
    intersection of: continuous variable
    intersection of: Restriction
      on property: is denoted by
      some values from: Class
        intersection of: normal distribution hypothesis
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: average value
    intersection of: Restriction
      on property: is about
      some values from: study group population
has curation status: ready for release
definition: Welch t-test is a two sample t-test used when the variances of the 2 populations/samples are thought to be unequal (homoskedasticity hypothesis not verified). In this version of the two-sample t-test, the denominator used to form the t-statistics, does not rely on a 'pooled variance' estimate.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Welsh t-test
definition source: Welch, B. L. (1947). "The generalization of "Student's" problem when several different population variances are involved". Biometrika 34 (1–2): 28–35. doi:10.1093/biomet/34.1-2.28
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Welch's_t_test last accessed: 2014-05-06
STATO alternative term: t-test for independent means assuming unequal variance
R command: t.test(x, y = NULL, alternative = c("two.sided", "less", "greater"), mu = 0, paired = FALSE, var.equal = FALSE, conf.level = 0.95, ...) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/t.test.html
Python command: scipy.stats.ttest_ind(a, b, axis=0, equal_var=False) http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.ttest_ind.html#scipy.stats.ttest_ind source: https://github.com/scipy/scipy/blob/v0.15.1/scipy/stats/stats.py#L3271

Helmert contrast
type: Class
subclass of: contrast
has curation status: requires discussion
definition: A Helmert contrast is a contrast in which the coefficients for the Helmert regressors compare each level with the average of the “preceding” ones
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.clayford.net/statistics/tag/helmert-contrasts/ An R and S-Plus Companion to Applied Regression. John Fox ISBN-13: 978-0761922803
R command: contr.helmert(n, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html

polynomial contrast
type: Class
subclass of: contrast
has curation status: requires discussion
definition: a polynomial contrast is a contrast which...
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
R command: contr.poly(n, scores = 1:n, contrasts = TRUE, sparse = FALSE) from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html

treatment contrast
type: Class
subclass of: contrast
has curation status: requires discussion
definition: treatment contrast is a contrast which allows to test how linear model coefficients of categorical variables are interpreted in case where the “first” level (aka, the baseline) is included into the intercept and all subsequent levels have a coefficient that represents their difference from the baseline.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from multiple sources: http://pic.dhe.ibm.com/infocenter/spssstat/v20r0m0/index.jsp?topic=%2Fcom.ibm.spss.statistics.help%2Fidh_idd_genlin_emmeans.htm http://www.clayford.net/statistics/tag/helmert-contrasts/ http://www.aliquote.org/articles/tech/contrasts.html
R command: contr.treatment(n, base = 1, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html

sum contrast
type: Class
subclass of: contrast
has curation status: requires discussion
definition: the sum contrast is a contrast in which each coefficient compares the corresponding level of the factor to the average of the other levels
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.clayford.net/statistics/tag/helmert-contrasts/ An R and S-Plus Companion to Applied Regression. John Fox ISBN-13: 978-0761922803
R command: contr.sum(n, contrasts = TRUE, sparse = FALSE) http://stat.ethz.ch/R-manual/R-patched/library/stats/html/contrast.html

Pearson's Chi square test of goodness of fit
type: Class
subclass of: chi square test
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_input
  some values from: contingency table
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
has curation status: ready for release
definition: Pearson's Chi-Squared test for goodnes of fit is a statistical null hypothesis test which is used to either evaluate goodness of fit of dataset to a Chi-Squared distribution
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Chi2 test for goodness of fit
definition source: adapted from: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html and http://en.wikipedia.org/wiki/Pearson's_chi-squared_test
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/chisq.test.html chisq.test(x = NULL, correct = FALSE, p = rep(1/length(x), length(x)), rescale.p = FALSE, simulate.p.value = FALSE, B = 2000)

Barnard's test
type: Class
subclass of: data transformation
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: hypergeometric distribution
    union of: multinomial distribution
    union of: binomial distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 1
  on class: 2 by 2 contingency table
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: categorical variable
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: data set
    intersection of: Restriction
      on property: is about
      some values from: study group population
has curation status: ready for release
definition: Barnard's test is an exact statistical test used to determine if there are non-random associations between two categorical variables. It was developed in 1949 by Barnard and is a test which is, most times, more powerful that the Fisher exact test
editor note: duplicate with OBI_0200176. so either MIREOT and add metadata and axioms or move from OBI
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Barnard's_test and G A Barnard (1945) "A New Test for 2X2 Tables", Nature, 156, 177 & 783.
STATO alternative term: Barnard's test
R command: barnardw.test(n1, n2, n3, n4, dp = 0.001, verbose = FALSE) from http://www.inside-r.org/packages/cran/Barnard/docs/barnardw.test

central composite design
type: Class
subclass of: study design
has curation status: ready for release
definition: a central composite design is a study design which contains an imbedded factorial or fractional factorial design with center points that is augmented with a group of so-called 'star points' that allow estimation of curvature. A CCD design with k factors has 2k star points.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3361.htm
STATO alternative term: Box-Wilson Central Composite Design
R command: cd(basis, generators, blocks = "Block", n0 = 4, alpha = "orthogonal", wbreps = 1, bbreps = 1, randomize = TRUE, inscribed = FALSE, coding) http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/ccd.html

Box–Behnkens design
type: Class
subclass of: study design
has curation status: ready for release
definition: The Box-Behnken design is an independent quadratic design in that it does not contain an embedded factorial or fractional factorial design. In this design the treatment combinations are at the midpoints of edges of the process space and at the center. These designs are rotatable (or near rotatable) and require 3 levels of each factor. The designs have limited capability for orthogonal blocking compared to the central composite designs.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3362.htm
R command: bbd(k, n0 = 4, block = (k == 4 | k == 5), randomize = TRUE, coding) from: http://artax.karlin.mff.cuni.cz/r-help/library/rsm/html/bbd.html

Plackett-Burman design
type: Class
subclass of: study design
has curation status: pending final vetting
definition: Plackett-Burman design is a type of study design optimizing multifactorial experiments characterized by their parsimony and economy with the run number a multiple of 4 (rather than a power of 2). Plackett-Burman design is often used for screening experiments where the main effect is often heavily confounded with two-factor interactions. This type of design is very useful for economically detecting large main effects, assuming all interactions are negligible when compared with the few important main effects.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.itl.nist.gov/div898/handbook/pri/section3/pri335.htm
R command: pb(nruns, nfactors = nruns - 1, factor.names = if (nfactors <= 50) Letters[1:nfactors] else paste("F", 1:nfactors, sep = ""), default.levels = c(-1, 1), ncenter=0, center.distribute=NULL, boxtyssedal = TRUE, n12.taguchi = FALSE, replications = 1, repeat.only = FALSE, randomize = TRUE, seed = NULL, oldver = FALSE, ...) from: http://www.inside-r.org/packages/cran/FrF2/docs/pb

upper confidence limit
type: Class
subclass of: cutoff
subclass of: Restriction
  on property: part of
  some values from: confidence interval
has curation status: pending final vetting
definition: upper confidence limit is a data item which is a largest value bounding a confidence interval
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

lower confidence limit
type: Class
subclass of: cutoff
subclass of: Restriction
  on property: part of
  some values from: confidence interval
has curation status: ready for release
definition: lower confidence limit is a data item which is a lowest value bounding a confidence interval
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

root-mean-square standardized effect
type: Class
subclass of: statistic
subclass of: effect size estimate
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
has curation status: pending final vetting
definition: root-mean-square standardized effect is a statistic which denotes effect size in the context of analysis of variance and corresponds to the square root of the arithmetic average of p standardized effects (effects normalized to be expressed in standard deviation units).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: Ψ
definition source: http://www.statpower.net/Steiger%20Biblio/Steiger04.pdf
STATO alternative term: RMSSE

eta-squared
type: Class
subclass of: effect size estimate
subclass of: estimate
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
has curation status: pending final vetting
definition: Eta-squared is a biased estimator of the variance explained by the model in the population (it estimates only the effect size in the sample). Eta-squared describes the ratio of variance explained in the dependent variable by a predictor while controlling for other predictors, making it analogous to the r2. This estimate shares the weakness with r2 that each additional variable will automatically increase the value of η2. In addition, it measures the variance explained of the sample, not the population, meaning that it will always overestimate the effect size, although the bias grows smaller as the sample grows larger.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Effect_size#Eta-squared.2C_.CE.B72
STATO alternative term: η2

omega-squared
type: Class
subclass of: effect size estimate
subclass of: estimate
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
has curation status: ready for release
definition: omega-squared is a effect size estimate for variance explained which is less biased than the eta-squared coefficient.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://en.wikipedia.org/wiki/Effect_size#Omega-squared.2C_.CF.892
STATO alternative term: ω2

Hedges's g
type: Class
subclass of: standardized mean difference
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
has curation status: ready for release
definition: Hedges's g is an estimator of effect size, which is similar to Cohen's d and is a measure based on a standardized difference. However, the denominator, corresponding to a pooled standard deviation, is computed differently from Cohen's d coefficient, by applying a correction factor (which involves a Gamma function).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from : http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d and http://blog.stata.com/tag/cohens-d/

Glass's delta
type: Class
subclass of: standardized mean difference
subclass of: Restriction
  on property: is_specified_input_of
  some values from: confidence interval calculation
has curation status: ready for release
definition: Glass's delta is an estimator of effect size which is similar to Cohen's d but where the denominator corresponds only to the standard deviation of the control group (or second group). It is considered less biais than the Cohen's d for estimating effect sizes based on means and distances between means.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from : http://en.wikipedia.org/wiki/Effect_size#Cohen.27s_d and http://blog.stata.com/tag/cohens-d/

non-parametric distribution
type: Class
subclass of: probability distribution
subclass of: symmetric distribution
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 0
has curation status: metadata incomplete
definition: Probability distribution estimated empirically on the data without assumptions on the shape of the probability distribution.
term editor: Camille Maumet
term editor: Karl Helmer
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
comment: Initially discussed at https://github.com/incf-nidash/nidm/pull/191

contrast weight
type: Class
subclass of: data item
example of usage: http://artax.karlin.mff.cuni.cz/r-help/library/nparcomp/html/weight.matrix.html
has curation status: ready for release
definition: a contrast weight is a coefficient which multiplies a group mean, part of a linear combinaison defining a constrast as a weighted sum of group means, giving a 'weight' to a specific group mean hence the name.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: adapted from wikipedia: http://en.wikipedia.org/wiki/Contrast_%28statistics%29
STATO alternative term: contrast coefficient

contrast weight matrix
type: Class
subclass of: matrix
subclass of: Restriction
  on property: has part
  some values from: contrast weight
subclass of: Restriction
  on property: is about
  some values from: contrast
example of usage: [1,0,0]
definition: a contrast weight matrix is a information content entity which holds a set of contrast weight, coefficient used in a weighting sum of means defining a contrast
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: STATO
STATO alternative term: contrast weights

contrast weight estimate
type: Class
subclass of: model parameter estimate
subclass of: Restriction
  on property: is about
  some values from: contrast weight
subclass of: Restriction
  on property: estimate of
  some values from: statistic
has curation status: ready for release
definition: contrast weight estimate is a model parameter estimate which results from the computation from the data and that is used as input to a model fitting process
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: STATO

Akaike information criterion
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: statistical model
subclass of: Restriction
  on property: is_specified_input_of
  some values from: statistical model selection
example of usage: http://www.ncbi.nlm.nih.gov/pubmed/7791040
has curation status: ready for release
definition: The Akaike information criterion (AIC) is a measure of the relative quality of a statistical model for a given set of data. As such, AIC provides a means for model selection. AIC is defined as: AIC = 2K - 2log(L) where K is the number of predictors and L is the maximized likelihood value. AIC deals with the trade-off between the goodness of fit of the model and the complexity of the model. It is founded on information theory: it offers a relative estimate of the information lost when a given model is used to represent the process that generates the data. AIC does not provide a test of a model in the sense of testing a null hypothesis; i.e. AIC can tell nothing about the quality of the model in an absolute sense. If all the candidate models fit poorly, AIC will not give any warning of that.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Akaike_information_criterion and http://users.ecs.soton.ac.uk/jn2/teaching/aic.pdf
STATO alternative term: AIC
R command: AIC(object, ..., k = 2) from: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/AIC.html

corrected Akaike information criterion
type: Class
subclass of: Akaike information criterion
example of usage: http://www.ncbi.nlm.nih.gov/pubmed/19761098
has curation status: metadata complete
definition: corrected Akaike information criteria is a modified version of the Akaike information criterion.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
STATO alternative term: CAIC

Bayesian information criterion
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: statistical model
subclass of: Restriction
  on property: is_specified_input_of
  some values from: statistical model selection
example of usage: http://www.ncbi.nlm.nih.gov/pubmed/7791040
has curation status: metadata incomplete
definition: Bayesian information criterion or Schwartz's Bayesian information criterion is a criterion for model selection among a finite set of models. It is based, in part, on the likelihood function and it is closely related to the Akaike information criterion (AIC). Given any two estimated models, the model with the lower value of BIC is the one to be preferred. The BIC is an increasing function of sigma_e^2 and an increasing function of k. That is, unexplained variation in the dependent variable and the number of explanatory variables increase the value of BIC. Hence, lower BIC implies either fewer explanatory variables, better fit, or both.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Schwarz, Gideon E. (1978). "Estimating the dimension of a model". Annals of Statistics 6 (2): 461–464. doi:10.1214/aos/1176344136.
definition source: http://en.wikipedia.org/wiki/Bayesian_information_criterion
STATO alternative term: BIC
STATO alternative term: SBIC
STATO alternative term: Schwartz's Baeysian information criterion

statistical model selection
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: data set
subclass of: Restriction
  on property: has_specified_input
  min qualified cardinality: 2
  on class: statistical model
has curation status: metadata complete
definition: A statistical model selection is a data transformation which is based on computing a relative quality value in order to evaluate and select which model best explains data.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO

symmetric distribution
type: Class
equivalent class: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 0
subclass of: probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 0
has curation status: metadata complete
definition: Probability distribution which has no skew so its skewness=0
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: STATO

empirical distribution
type: Class
subclass of: probability distribution
has curation status: metadata incomplete
definition: Probability distribution estimated empirically from all acquired data
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://reference.wolfram.com/language/ref/EmpiricalDistribution.html

histogram distribution
type: Class
subclass of: probability distribution
has curation status: metadata incomplete
definition: Probability distribution estimated empirically on the data following a binning process
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols

smooth kernel distribution
type: Class
subclass of: probability distribution
has curation status: metadata incomplete
definition: Probability distribution estimated using a smooth kernel function to avoid making assumptions about the distribution of the data. The kernel density estimator is the estimated probability density function (pdf) of the random variable.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://uk.mathworks.com/help/stats/kernel-distribution.html and http://reference.wolfram.com/language/ref/SmoothKernelDistribution.html

kernel mixture distribution
type: Class
subclass of: probability distribution
has curation status: requires discussion
definition: kernel density estimation (KDE) is a non-parametric way to estimate the probability density function of a random variable
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: https://en.wikipedia.org/wiki/Kernel_density_estimation
definition source: https://reference.wolfram.com/language/ref/KernelMixtureDistribution.html

mixture distribution
type: Class
subclass of: probability distribution
has curation status: metadata incomplete
definition: Mixture distribution is the probability distribution of a random variable that is derived from a collection of other random variables as follows: first, a random variable is selected by chance from the collection according to given probabilities of selection, and then the value of the selected random variable is realized.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://en.wikipedia.org/wiki/Mixture_distribution

survival distribution
type: Class
subclass of: empirical distribution
has curation status: metadata incomplete
definition: Probability distribution estimated empirically from a censored lifetime data
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://reference.wolfram.com/language/ref/SurvivalDistribution.html

best linear unbiased predictor
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: best linear unbiased prediction is a data transformation which predicts <TDB> under the assumption that the variable(s) under consideration have a random effect
term editor: Philippe Rocca-Serra
definition source: Henderson C. R., 1984 Applications of Linear Models in Animal Breeding. University of Guelph, Guelph, Ontario, Canada. ftp://tech.obihiro.ac.jp/suzuki/Henderson.pdf
STATO alternative term: BLUP
STATO alternative term: best linear unbiased predictor of the random effect
STATO alternative term: conditional mode of the random effect

breeding value estimation
type: Class
equivalent class: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: data transformation
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: best linear unbiased predictor
    union of: ridge regression best linear unbiaised predictor
    union of: trait-specific relationship matrix best linear unbiaised prediction
    union of: Bayes A
    union of: Bayes B
    union of: Bayesian least absolute shrinkage and selection operator
    union of: Bayes C pi
    union of: reproducing kernel Hilbert space procedure
    union of: Bayes R
    union of: best linear unbiased estimator
subclass of: Restriction
  on property: has_specified_input
  some values from: statistical model
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: genotype data set
    union of: pedigree data set
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
has curation status: ready for release
definition: breeding value estimation is a data transformation process aiming at computing breeding value estimates of an organism given a set of genomic (SNP) observations, pedigree information and/or phenotypic observations.
term editor: Philippe Rocca-Serra

breeding value estimation using genotype data
type: Class
subclass of: breeding value estimation
subclass of: Restriction
  on property: has part
  some values from: best linear unbiased estimator
subclass of: Restriction
  on property: has_specified_input
  some values from: genotype data set
subclass of: Restriction
  on property: has_specified_input
  some values from: genetic inheritance model
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
has curation status: ready for release
definition: breeding value estimation is a data transformation process aiming at computing breeding value estimates of an organism given a set of genomic (SNP) observations.
term editor: Philippe Rocca-Serra

breeding value estimation using pedigree data
type: Class
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: pedigree data set
has curation status: ready for release
definition: breeding value estimation is a data transformation process aiming at computing breeding value estimates of an organism given a set of pedigree information.
term editor: Philippe Rocca-Serra

breeding value estimation using phenotypic data
type: Class
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: data set
has curation status: ready for release
definition: breeding value estimation is a data transformation process aiming at computing breeding value estimates of an organism given a set of phenotypic observations.
term editor: Philippe Rocca-Serra

genomic selection objective
type: Class
subclass of: data transformation objective
has curation status: metadata incomplete
definition: genomic selection objective is a data transformation objective which is a special case of marker-assisted selection in which genetic markers covering the whole genome are used so that all quantitative trait loci (QTL) are in linkage disequilibrium with at least one marker.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: http://genomics.cimmyt.org/
definition source: https://doi.org/10.1016/j.tplants.2017.08.011
definition source: https://www.ncbi.nlm.nih.gov/pubmed/18076469

genotype data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: genotype information
has curation status: metadata incomplete
definition: a dataset which is made up of genotypic information, that is presenting allele information at specific loci in a set of individuals of an organism.
term editor: Philippe Rocca-Serra

covariance structure
type: Class
subclass of: data item
subclass of: statistical model
subclass of: Restriction
  on property: part of
  some values from: regression model
subclass of: Restriction
  on property: is about
  some values from: covariance matrix
subclass of: Restriction
  on property: is model for
  some values from: covariance
has curation status: metadata complete
definition: a covariance structure is a data item which is part of a regression model and which indicates a pattern in the covariance matrix. The nature of covariance structure is specified before the regression analysis and various covariance structure may be tested and evaluated using information criteria to help choose the most suiteable model
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://www3.nd.edu/~kyuan/courses/sem/readpapers/benter.pdf

Matern function anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: Given two sets of locations computes the Matern cross covariance matrix for covariances among all pairings.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: Matern covariance function
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
definition source: https://www.rdocumentation.org/packages/fields/versions/2.3/topics/matern.cov
R command: matern.cov

rational quadratic anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: The rational quadratic covariance function is used in spatial statistics, geostatistics, machine learning, image analysis, and other fields where multivariate statistical analysis is conducted on metric spaces. It is commonly used to define the statistical covariance between measurements made at two points that are d units distant from each other. Since the covariance only depends on distances between points, it is stationary. If the distance is Euclidean distance, the rational quadratic covariance function is also isotropic.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
definition source: https://en.wikipedia.org/wiki/Rational_quadratic_covariance_function
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corRatio.html

spatial linear geometric anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: spatial linear geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give linear features.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: SP(LINGA)
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corLin.html

spatial spherical geometric anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: spatial spherical geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give spherical features.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: SP(SPHGA)
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corSpher.html

spatial gaussian geometric anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: spatial gaussian geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give gaussian features.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: SP(GAUGA)
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corGaus.html

spatial exponential geometric anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: spatial exponential geometric anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give exponential features.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: SP(EXPGA)
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm

spatial exponential anisotropic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: spatial exponential anisotropic covariance structure is a type of covariance structure characterized by its anisotropy, i.e., the variation of properties can be different in directions x and y, which is this case give exponential features.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: SP(EXPA)(c-list)
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm Sacks et al. (1989)
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corExp.html

banded heterogeneous Toeplitz covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: the banded heterogeneous Toeplitz covariance structure is a type of coviance structure which is often used to analyzed and intepret repeated measure design.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: TOEPH(q)

heterogeneous Toeplitz covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: This covariance structure has heterogenous variances and heterogenous correlations between elements. The correlation between adjacent elements is homogenous across pairs of adjacent elements. The correlation between elements separated by a third is again homogenous, and so on.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: TOEPH
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm as well as: https://www.ibm.com/support/knowledgecenter/en/SSLVMB_23.0.0/spss/advanced/covariance_structures.html

banded Toeplitz covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: A banded Toeplitz structure, defined by parameter q, can be viewed as a moving-average structure with order q-1.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: TOEP(q)

Toeplitz covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: The Toeplitz covariance structure has homogenous variances and heterogenous correlations between elements. The correlation between adjacent elements is homogenous across pairs of adjacent elements. The correlation between elements separated by a third is again homogenous, and so on.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
definition source: https://www.ibm.com/support/knowledgecenter/en/SSLVMB_23.0.0/spss/advanced/covariance_structures.html
STATO alternative term: TOEP

Huynh-Feldt covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: a form of covariance structure used to provide analysis ground s in the context of repeated measures datasets (longitudinal, time series)
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: HF
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm Huynh and Feldt 1970

equal diagonal Factor Analytic covariance structure
type: Class
subclass of: Factor Analytic covariance structure
has curation status: metadata complete
definition: factor-analytic structure is a covariance structure which is specified for q factors equal diagonal factor-analytic covariance structure is a type of factor analytic covariance structure specified for q factors, which includes a diagonal component for repeated measures.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: FA1(q)

no diagonal Factor Analytic covariance structure
type: Class
subclass of: Factor Analytic covariance structure
has curation status: metadata complete
definition: no diagonal factor-analytic covariance structure is a type of factor analytic covariance structure specified for q factors, which does not include a diagonal component for repeated measures.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: FA0(q)

Factor Analytic covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: factor-analytic structure is a type of heterogeneous covariance structure which is specified for q factors
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: adapted from: Heterogeneous Variance: Covariance Structures for Repeated Measures Russell D. Wolfinger. Journal of Agricultural, Biological, and Environmental Statistics Vol. 1, No. 2 (Jun., 1996), pp. 205-230. https://doi.org/10.2307/1400366 and http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm Jennrich and Schluchter 1986
STATO alternative term: FA(q)

compound symmetry covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: compound symmetry covariance structure is a covariance structure which means that all the variances are equal and all the covariances are equal.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: CS
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corCompSymm.html

heterogeneous compound symmetry covariance structure
type: Class
subclass of: compound symmetry covariance structure
has curation status: metadata complete
definition: heterogenous compound symmetry structure is a compound symmetry covariance structure which has a different variance parameter for each diagonal element, and it uses the square roots of these parameters in the off-diagonal entries.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: CSH

first order autoregressive moving average covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: first order autoregressive moving average covariance structure is a type of covariance structure which is used in the context of time series analysis
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
alternative term: ARMA(1,1)
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corARMA.html

first order autoregressive covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: first order autoregressive covariance structure is a covariance structure where correlations among errors decline exponentially with distance
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: AR(1)
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/corAR1.html

heterogeneous first-order autoregressive covariance structure
type: Class
subclass of: first order autoregressive covariance structure
has curation status: metadata complete
definition: This is an homogeneous structure, i.e. the variance along the main diagonal is constant. The covariances decline exponentially. It has only 2 parameters.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: ARH(1)

Ante-dependence covariance structure
type: Class
subclass of: covariance structure
has curation status: metadata complete
definition: Ante-dependence covariance structure is a covariance structure which specifies that the covariance between two time points is a function of the product of variances at both points (hence allowing hetrogenity of error variance across measures to affect the correlation) and the product of the correlations at the distances up to the one chosen.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm
STATO alternative term: ANTE(1)

Mallows' Cp
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: statistical model
subclass of: Restriction
  on property: is_specified_input_of
  some values from: statistical model selection
has curation status: ready for release
definition: Mallows' Cp is a data item which compares the precision and bias of the full model to models with a subset of the predictors thus helping to choose between multiple regression models. the mallows cp is a function of the number of parameter used in the model relying on the residuals sum of squares to compute a score. the smaller Cp is, the better the model fit is.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://support.minitab.com/en-us/minitab/17/topic-library/modeling-statistics/regression-and-correlation/goodness-of-fit-statistics/what-is-mallows-cp/
R command: http://ugrad.stat.ubc.ca/R/library/locfit/html/cp.html

repeated measure analysis
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: statistical model
    intersection of: Restriction
      on property: has part
      some values from: covariance structure
has curation status: pending final vetting
definition: repeated measure analysis is a kind of data transformation which deals with signals measured in the same experimental units at different times and, possibly, under different conditions over a period of time. Data produced by longitudinal studies qualify for such analysis. Since measurements are made on the same experimental units a number of times, they are likely to be correlated. Repeated measure analysis usually takes into consideration the possibility of correlation with time. It does so by specifying covariance structure in the analysis
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from https://ciser.cornell.edu/sasdoc/saspdf/analyst/chap16.pdf
STATO alternative term: repeated measure analysis

ordinary least squares estimation
type: Class
subclass of: model parameter estimation
subclass of: Restriction
  on property: part of
  some values from: linear regression for analysis of continuous dependent variable
has curation status: metadata complete
definition: the ordinary least squares estimation is a model parameter estimation for a linear regression model when the errors are uncorrelated and equal in variance. Is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://en.wikipedia.org/wiki/Ordinary_least_squares and Tom Nichols
STATO alternative term: OLS estimation
R command: https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html

weighted least squares estimation
type: Class
subclass of: model parameter estimation
subclass of: Restriction
  on property: part of
  some values from: linear regression for analysis of continuous dependent variable
has curation status: metadata complete
definition: the weighted least squares estimation is a model parameter estimation for a linear regression model with errors that independent but have heterogeneous variance. Difficult to use use in practice, as weights must be set based on the variance which is usually unknown. If true variance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://en.wikipedia.org/wiki/Least_squares#Weighted_least_squares and Tom Nichols
STATO alternative term: WLS estimation
R command: https://stat.ethz.ch/R-manual/R-patched/library/stats/html/lm.html

generalized least squares estimation
type: Class
subclass of: model parameter estimation
subclass of: Restriction
  on property: part of
  some values from: linear regression for analysis of continuous dependent variable
has curation status: metadata complete
definition: the generalized least squares estimation is a model parameter estimation for a linear regression model with errors that are dependent and (possibly) have heterogeneous variance. Difficult to use use in practice, as covariance matrix of the errors must known to "whiten" data and model. If true covariance is known, it is the Best Linear Unbiased Estimation (BLUE) method under these assumptions, Uniformly Minimum-Variance Unbiased Estimator (UMVUE) with addition of a Gaussian assumption.
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: http://en.wikipedia.org/wiki/Generalized_least_squares and Tom Nichols
STATO alternative term: GLS estimation
R command: http://stat.ethz.ch/R-manual/R-devel/library/nlme/html/gls.html

iteratively reweighted least squares estimation
type: Class
subclass of: model parameter estimation
subclass of: Restriction
  on property: part of
  some values from: linear regression for analysis of continuous dependent variable
has curation status: metadata complete
definition: the iteratively reweighted least squares estimation is a model parameter estimation which is a practical implementation of Weighted Least Squares, where the heterogeneous variances of the errors are estimated from the residuals of the regression model, providing an estimate for the weights. Each successive estimate of the weights improves the estimation of the regression parameters, which in turn are used to compute residuals and update the weights
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: Tom Nichols

feasible generalized least squares estimation
type: Class
subclass of: generalized least squares estimation
subclass of: Restriction
  on property: part of
  some values from: linear regression for analysis of continuous dependent variable
has curation status: metadata complete
definition: the feasible generalized least squares estimation is a model parameter estimation which is a practical implementation of Generalised Least Squares, where the covariance of the errors is estimated from the residuals of the regression model, providing the information needed to whiten the data and model. Each successive estimate of the whitening matrix improves the estimation of the regression parameters, which in turn are used to compute residuals and update the whitening matrix.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: Tom Nichols

residual mean square
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: residual
example of usage: used as an unbiased estimator of the variance for a regression model
has curation status: ready for release
definition: a residual mean square is a data item which is obtained by dividing the sum of squared residuals (SSR) by the number of degrees of freedom
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://en.wikipedia.org/wiki/Mean_squared_error#Regression
definition source: http://support.minitab.com/en-us/minitab/17/topic-library/modeling-statistics/anova/anova-statistics/understanding-mean-squares/
definition source: https://github.com/ISA-tools/stato/issues/35
STATO alternative term: MSE
STATO alternative term: error mean square

Z-statistic
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Z-test
has curation status: metadata complete
definition: Z-statistic is a statistic computed from observations and used to produce a p-value when compared to a Standard Normal Distribution in a statistical test called the Z-test.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maument
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://en.wikipedia.org/wiki/Z-test

deviance
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is about
  some values from: statistical model
has curation status: ready for release
definition: Deviance is an indicator of fit and can be estimated by computing -2 times the log-likelihood ratio of the fitted model compared to a saturated(full) model. It is a generalization of the idea of using the sum of squares of residuals in ordinary least squares to cases where model-fitting is achieved by maximum likelihood.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Deviance_%28statistics%29
STATO alternative term: deviance
R command: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/deviance.html

deviance information criterion
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: statistical model
subclass of: Restriction
  on property: is_specified_input_of
  some values from: statistical model selection
example of usage: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682718/
has curation status: ready for release
definition: The deviance information criterion (DIC) is a hierarchical modeling generalization of the AIC (Akaike information criterion) and BIC (Bayesian information criterion, also known as the Schwarz criterion). It is particularly useful in Bayesian model selection problems where the posterior distributions of the models have been obtained by Markov chain Monte Carlo (MCMC) simulation. Like AIC and BIC it is an asymptotic approximation as the sample size becomes large. It is only valid when the posterior distribution is approximately multivariate normal. The deviance information criterion was published in 2002 by Spiegelhalter et al. Spiegelhalter, D. J., N. G. Best, B. P. Carlin, and A. van der Linde, 2002. Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society, B, 64, 583-639.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://en.wikipedia.org/wiki/Deviance_information_criterion
STATO alternative term: DIC
R command: http://artax.karlin.mff.cuni.cz/r-help/library/SpatialExtremes/html/DIC.html

focused information criterion
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: is about
  some values from: statistical model
subclass of: Restriction
  on property: is_specified_input_of
  some values from: statistical model selection
has curation status: metadata complete
definition: The focused information criterion is a measurement data item which aims at facilitating model selection. It was published in 2003 by Claeskens, G. and Hjort, N.L. (2003). "The focused information criterion".
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Journal of the American Statistical Association, volume 98, pp. 879–899. doi:10.1198/016214503000000819
STATO alternative term: FIC

contrast estimation
type: Class
subclass of: data transformation
subclass of: Class
  intersection of: Restriction
    on property: has_specified_input
    some values from: contrast weight
  intersection of: Restriction
    on property: has_specified_output
    some values from: contrast estimate
  intersection of: Restriction
    on property: has_specified_output
    some values from: standard error of a contrast estimate
has curation status: ready for release
definition: a data transformation that finds a contrast value (the contrast estimate) by computing the weighted sum of model parameter estimates using a set of contrast weights.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: https://github.com/ISA-tools/stato/pull/37

contrast estimate
type: Class
subclass of: estimate
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: contrast
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: contrast estimation
has curation status: ready for release
definition: estimate of a contrast obtained by computing the weighted sum of model parameter estimates using a set of contrast weights.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: https://github.com/ISA-tools/stato/pull/37

standard error of a contrast estimate
type: Class
subclass of: standard error of estimate
subclass of: Class
  intersection of: Restriction
    on property: is about
    some values from: contrast estimate
  intersection of: Restriction
    on property: is_specified_output_of
    some values from: contrast estimation
subclass of: Restriction
  on property: estimate of
  some values from: statistic
has curation status: ready for release
definition: an estimate of the standard deviation of a contrast estimate sampling distribution.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: https://github.com/ISA-tools/stato/pull/37

scree plot
type: Class
subclass of: graph
has curation status: ready for release
definition: A scree plot is a graphical display of the variance of each component in the dataset which is used to determine how many components should be retained in order to explain a high percentage of the variation in the data
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: http://www.stats.gla.ac.uk/glossary/
STATO alternative term: Cattell scree test plot
R command: screeplot(x, npcs = min(10, length(x$sdev)), type = c("barplot", "lines"), main = deparse(substitute(x)), ...) from: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/screeplot.html

scatterplot matrix
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: scatter plot
has curation status: ready for release
definition: A scatterplot matrix contains all the pairwise scatter plots of a set of variables on a single page in a matrix format.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: Adapted from http://itl.nist.gov/div898/handbook/eda/section3/eda33qb.htm

alpha distribution
type: Class
subclass of: continuous probability distribution
has curation status: metadata incomplete
definition: The alpha distribution is a continuous probability distribution whose density function is as defined at: https://docs.scipy.org/doc/scipy-1.0.0/reference/tutorial/stats/continuous_alpha.html
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://docs.scipy.org/doc/scipy-1.0.0/reference/tutorial/stats/continuous_alpha.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.alpha.html#scipy.stats.alpha

power law distribution
type: Class
subclass of: probability distribution
has curation status: ready for release
definition: a power-law probability distribution is a probability distribution whose density function (or mass function in the discrete case) has the form p(x) = L(x) . x^{-alpha} where alpha is a parameter >1 and L(x) is a slowly varying function.
definition source: adapted from wikipedia and wolfram alpha: https://en.wikipedia.org/wiki/Power_law#Power-law_probability_distributions last accessed: 2015-11-03
R command: https://cran.r-project.org/web/packages/poweRlaw/index.html
Python command: http://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.powerlaw.html#scipy.stats.powerlaw

regression model
type: Class
subclass of: statistical model
has curation status: metadata incomplete
definition: A regression model is a statistical model used in a type of analysis knowns as regression analysis, whereby a function is used to determine the relation between a response variable and an independent variable , with a set of unknown parameters.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Regression_analysis#Regression_models last accessed: 2015-11-03

Pareto type-I probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
has curation status: ready for release
definition: The Pareto distribution is a continuous probability distribution, which is defined by the follwoing probability density (1) function and distribution function (2) (1): P(x)=(ab^a)/(x^(a+1)) (2): D(x)=1-(b/x)^a defined over the interval x>=b.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapter from: http://mathworld.wolfram.com/ParetoDistribution.html last accessed: 2015-11-04
R command: http://artax.karlin.mff.cuni.cz/r-help/library/LaplacesDemon/html/dist.Pareto.html last accessed: 2015-11-04 Usage >dpareto(x, alpha, log=FALSE) >ppareto(q, alpha) >qpareto(p, alpha) >rpareto(n, alpha) Arguments x,q These are each a vector of quantiles. p This is a vector of probabilities. n This is the number of observations, which must be a positive integer that has length 1. alpha This is the shape parameter alpha, which must be positive. log Logical. If log=TRUE, then the logarithm of the density or result is returned.

Pareto type-II probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
has curation status: ready for release
definition: the Pareto type-II probability distribution is a continuous probability distribution which is defined by a probability density function characterized by 2 parameters, alpha and lambda, 2 real, strictly positive numbers. alpha is known as the shape parameter while lambda is known as the scale parameter. the function defines the probably of a continous random variable according to the following: p(x) = {\alpha \over \lambda} \left[{1+ {x \over \lambda}}\right]^{-(\alpha+1)}, \qquad x \geq 0,
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Lomax_distribution
STATO alternative term: Lomax distribution
R command: http://www.inside-r.org/packages/cran/actuar/docs/Pareto dpareto(x, shape, scale, log = FALSE)

Pareto type-III probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
has curation status: ready for release
definition: The Pareto(III) distribution is a continous probability distribution which is described with a cumulative distribution function of the following form: F(x) = 1 − [1 + ((x − mu)/sigma)1/gamma]−1 for x > mu, sigma > 0, gamma > 0 and s =1. a is the location parameter, b is the scale parameter, g is the inequality parameter s is the shape parameter of value 1 The Pareto III distribution corresponds to a Pareto Type IV distribution where the shape parameter has a value of 1.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Pareto_distribution#Pareto_types_I.E2.80.93IV last accessed: 2015-11-04

Pareto type-IV probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
has curation status: ready for release
definition: The Pareto(IV) distribution is a continous probability distribution which is described with a cumulative distribution function of the following form: F(y) = 1 − [1 + ((y − a)/b)1/g]−s for y > a, b > 0, g > 0 and s > 0. a is the location parameter, b is the scale parameter, g is the inequality parameter s is the shape parameter The distribution is used in actuarial science, economics, finance and telecommunications, but not restricted to those fields.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://cran.r-project.org/web/packages/VGAM/VGAM.pdf page 517
R command: dparetoIV(x, location = 0, scale = 1, inequality = 1, shape = 1, log = FALSE) https://cran.r-project.org/web/packages/VGAM/VGAM.pdf

geometric mean
type: Class
subclass of: measure of central tendency
example of usage: The geometric mean of two numbers, say 2 and 8, is just the square root of their product; that is sqrt(2 x 8)=4.
has curation status: ready for release
definition: The geometric mean is defined as the nth root of the product of n numbers, i.e., for a set of numbers \{x_i\}_{i=1}^N, the geometric mean is defined as \left(\prod_{i=1}^N x_i\right)^{1/N}.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: https://en.wikipedia.org/wiki/Mean#Geometric_mean_.28GM.29 https://en.wikipedia.org/wiki/Geometric_mean
R command: http://personality-project.org/r/html/geometric.mean.html Usage: >geometric.mean(x,na.rm=TRUE) Arguments: x , a vector or data.frame
Python command: http://docs.scipy.org/doc/scipy-0.13.0/reference/generated/scipy.stats.mstats.gmean.html

harmonic mean
type: Class
subclass of: measure of central tendency
definition: The harmonic mean is a kind of mean which is calculated by dividing the total number of observations by the reciprocal of each number in a series. Harmonic Mean = N/(1/a1+1/a2+1/a3+1/a4+.......+1/aN) where a(i)= Individual score and N = Sample size (Number of scores)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia and https://www.easycalculation.com/statistics/learn-harmonic-mean.php last accessed: 2015-11-04
definition source: https://en.wikipedia.org/wiki/Harmonic_mean
definition source: https://en.wikipedia.org/wiki/Mean#Harmonic_mean_.28HM.29
R command: http://personality-project.org/r/html/harmonic.mean.html Usage: > harmonic.mean(x,na.rm=TRUE) Arguments: x, a vector, matrix, or data.frame na.rm, na.rm=TRUE remove NA values before processing.
Python command: http://docs.scipy.org/doc/scipy-0.13.0/reference/generated/scipy.stats.mstats.hmean.html

weighted arithmetic mean
type: Class
subclass of: measure of central tendency
has curation status: ready for release
definition: The weighted arithmetic mean is a measure of central tendency that is the sum of the products of each observed value and their respective non-negative weights, divided by the sum of the weights, such that the contribution of each observed value to the mean may defer according to its respective weight. It is defined by the formula: A = sum(vi*wi)/sum(wi), where 'i' ranges from 1 to n, 'vi' is the value of each observation, and 'wi' is the value of the respective weight for each observed value. The weighted arithmetic mean is a kind of mean similar to an ordinary arithmetic mean (the most common type of average), except that instead of each of the data points contributing equally to the final average, some data points are weighted, meaning they contribute more than others. The weighted arithmetic mean is often used if one wants to combine average values from samples of the same population with different sample sizes.
term editor: Alejandra Gonzalez-Beltran
term editor: Matthew Diller
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Weighted_arithmetic_mean
STATO alternative term: weighted average
R command: weighted.mean(x, w, ...) https://stat.ethz.ch/R-manual/R-devel/library/stats/html/weighted.mean.html
Python command: From numpy https://docs.scipy.org/doc/numpy/reference/generated/numpy.average.html np.average(range(1,11), weights=range(10,0,-1))
bug-database: https://github.com/ISA-tools/stato/issues/59

interquartile mean
type: Class
subclass of: trimmed mean
has curation status: metadata incomplete
definition: The interquartile mean (IQM) (or midmean) is a statistical measure of central tendency based on the truncated mean of the interquartile range. In the calculation of the IQM, only the data in the second and third quartiles is used (as in the interquartile range), and the lowest 25% and the highest 25% of the scores are discarded. These points are called the first and third quartiles, hence the name of the IQM.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: IQM
definition source: https://en.wikipedia.org/wiki/Mean#Interquartile_mean

quadratic mean
type: Class
subclass of: measure of central tendency
has curation status: ready for release
definition: The root mean square (abbreviated RMS or rms), also known as the quadratic mean, in statistics is a statistical measure of central tendency defined as the square root of the mean of the squares of a sample. ( To find the root mean square of a set of numbers, square all the numbers in the set and then find the arithmetic mean of the squares. Take the square root of the result. This is the root mean square.)
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: RMS
alternative term: root mean square
definition source: https://en.wikipedia.org/wiki/Root_mean_square and http://www.mathwords.com/r/root_mean_square.htm last accessed: 2015-11-04

sample mean
type: Class
subclass of: average value
subclass of: estimate
subclass of: Restriction
  on property: denotes
  some values from: statistical sample
subclass of: Restriction
  on property: estimate of
  some values from: population mean
has curation status: metadata incomplete
definition: the sample mean of sample of size n with n observations is an arithmetic mean computed over n number of observations on a statistical sample. The sample mean, denoted x¯ and read “x-bar,” is simply the average of the n data points x1, x2, ..., xn: x¯=x1+x2+⋯+xnn=1n∑i=1nxi The sample mean summarizes the "location" or "center" of the data. the sample mean is a measure of dispersion of the observations made on the sample and provides an unbias estimate of the population mean
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: https://onlinecourses.science.psu.edu/stat414/node/66 and http://mathworld.wolfram.com/SampleMean.html last accessed: 2015-11-05

population mean
type: Class
subclass of: measure of central tendency
has curation status: metadata incomplete
definition: the population mean or distribution mean is a parameter of a probability distribution or population indicative of the data dispersion. For continous probabibility distribution, the population mean is computed using the probability density function, for discrete probability distributions, a mass density function is used instead. A population mean can be estimated by computing a sample mean
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
alternative term: distribution mean
definition source: adapted from: http://mathworld.wolfram.com/PopulationMean.html last accessed: 2015-11-05

unstructured covariance structure
type: Class
subclass of: covariance structure
has curation status: ready for release
definition: A covariance structure where no restrictions are made on the covariance between any pair of measurements.
term editor: Alejandra Gonzalez-Beltran
term editor: Camille Maumet
term editor: Philippe Rocca-Serra
term editor: Thomas Nichols
definition source: http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#statug_mixed_sect019.htm#statug.mixed.mixedcovstruct

Yuen t-Test with trimmed means
type: Class
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
subclass of: Restriction
  on property: has_specified_input
  qualified cardinality: 2
  on class: Class
    intersection of: trimmed mean
    intersection of: Restriction
      on property: is about
      some values from: study group population
has curation status: ready for release
definition: The Yuen's t-test is a two sample t-test with populations of unequal variance which provides a more robust t-test procedure under normal distribution and long tailed distributions. The test computes a t statistics not using 'arithmetic means' but using 'trimmed means' instead as well as winsorized variances.
term editor: Philippe Rocca-Serra
alternative term: Yuen-Welch's t-test
definition source: Biometrika (1974) 61 (1): 165-170 10.1093/biomet/61.1.165
R command: http://finzi.psych.upenn.edu/library/DescTools/html/YuenTTest.html

Fagan nomogram
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: axis
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: axis
    intersection of: Restriction
      on property: denotes
      some values from: likelihood ratio
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: axis
    intersection of: Restriction
      on property: denotes
      some values from: pretest probability
has curation status: ready for release
definition: Fagan nomogram is a graph plotting pre-test probabilities, likelyhood ratios and post-test probabilities on 3 parallel axis. The plot was first proposed by Fagan in 1975 as a way to visualize Baye's Theorem data where P(D) is the probability that the patient has the disease before the test. P(D|T) is the probability that the patient has the disease after the test result. P(T|D) is the probability of the test result if the patient has the disease, and P(T|D̄) is the probability of the test result if the patient does not have the disease. With this terminology the usefulness of both positive and negative test results can be assessed. A line drawn from P(D) on the right through the ratio of P(T|D) to P(T|D̄) gives P(D|T) on the left of the nomogram.
term editor: Philippe Rocca-Serra
definition source: http://www.ncbi.nlm.nih.gov/pubmed/1143310 N Engl J Med 1975; 293:257July 31, 1975 DOI: 10.1056/NEJM197507312930513

2 step Fagan nomogram
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: axis
    intersection of: Restriction
      on property: denotes
      some values from: true negative rate
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: axis
    intersection of: Restriction
      on property: denotes
      some values from: true positive rate
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: axis
    intersection of: Restriction
      on property: denotes
      some values from: likelihood ratio
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: axis
    intersection of: Restriction
      on property: denotes
      some values from: pretest probability
has curation status: ready for release
definition: Two-Step Fagan Nomogram, which adds two extra axis between the LR axis that represents sensibility and specificity to calculate negative and positive likelihood ratios in the same nomogram
term editor: Philippe Rocca-Serra
definition source: http://www.ncbi.nlm.nih.gov/pubmed/23468201

likelihood ratio
type: Class
subclass of: ratio
subclass of: ratio-based measure of association
subclass of: Restriction
  on property: is_proxy_for
  some values from: measure of association
has curation status: ready for release
definition: the likelihood ratio is a ratio which is formed by dividing the post-test odds with the pre-test odds in the context of a Bayesian formulation
term editor: Philippe Rocca-Serra

negative likelihood ratio
type: Class
subclass of: likelihood ratio
has curation status: ready for release
definition: the likelihood ratio of negative results is a ratio which is formed by dividing the difference between 1 and sensitivity of the test by the specificity value of a test. This can be expressed also as dividing the probability of a person who has the disease testing negative by the probability of a person who does not have the disease testing negative.
term editor: Philippe Rocca-Serra
alternative term: likelihood ratio for negative results
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing last accessed: May 2016

positive likelihood ratio
type: Class
subclass of: likelihood ratio
has curation status: ready for release
definition: the likelihood ratio of positive results is a ratio which is form by dividing the sensitivity value of a test by the difference between 1 and specificity of the test. This can be expressed also as dividing the probability of the test giving a positive result when testing an affected subject versus the probability of the test giving a positive result when a subject is not affected.
term editor: Philippe Rocca-Serra
alternative term: likelihood ratio for positive results
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Likelihood_ratios_in_diagnostic_testing last accessed: May 2016

prevalence
type: Class
subclass of: proportion
example of usage: disease prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size.
has curation status: ready for release
definition: A proportion in which the numerator represents all events of interest (for example, both new and preexisting cases of a disease) in the population, which is represented by the denominator.
term editor: Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Janice Tufte, Kenneth Wilkins, Harold Lehmann
term editor: Philippe Rocca-Serra
definition source: adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm

incidence
type: Class
subclass of: proportion
example of usage: For instance, Disease Incidence is the ratio of the number of new cases of a disease divided by the number of persons at risk for the disease.
has curation status: ready for release
definition: A proportion in which the numerator represents new events.
editor note: Expert Working Group Agreement: 2022-01-12 vote 6-0 by Harold Lehman, Mario Tristan, janice tufte, Andrew Beck, Robin Ann Yurk, Paul Harris
term editor: Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Janice Tufte
term editor: Philippe Rocca-Serra
alternative term: cumulative incidence
alternative term: incidence proportion
definition source: adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm

mortality
type: Class
subclass of: ratio
has curation status: ready for release
definition: mortality is a ratio formed by the number of deaths due to a disease divided by the total population size.
term editor: Philippe Rocca-Serra
definition source: adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm

accuracy
type: Class
subclass of: percentage
has curation status: ready for release
definition: in the context of binary classification, accuracy is defined as the proportion of true results (both true positives and true negatives) to the total number of cases examined (the sum of true positive, true negative, false positive and false negative). It can be understood as a measure of the proximity of measurement results to the true value. Accuracy is a metric used in the context of classification tasks to evaluate the proportion of correctly predicted instances among the total instances. Key Points: Use Case: Classification performance evaluation. Metric: Measures the proportion of correct predictions. Interpretation: Higher values indicate better classification performance.
editor note: In the context of unsupervised learning, such as in clustering, the same formula is used to calculate the Rand Index or Rand accuracy. The Rand Index is primarily used to measure the similarity between two data clusterings. It is commonly employed in clustering validation to compare the similarity between a predicted clustering and a ground truth clustering. Key Points: Use Case: Clustering validation. Metric: Measures pairwise agreement between two clusterings. Interpretation: Higher values indicate more similar clusterings
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016 adapted from ChatGPT using the following prompt: [what is the difference between "Rand Index" and "Accuracy" in statistics] last accessed: July 2024
STATO alternative term: Rand index
R command: Accuracy(y_pred, y_true) from: https://www.rdocumentation.org/packages/MLmetrics/versions/1.1.1/topics/Accuracy

precision
type: Class
subclass of: proportion
has curation status: ready for release
definition: precision or positive predictive value is defined as the proportion of the true positives against all the positive results (both true positives and false positives) A proportion in which the numerator represents the correctly detected items within the denominator that represents all items detected.
term editor: Philippe Rocca-Serra
alternative term: positive predictive value
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016

pretest probability
type: Class
subclass of: ratio
has curation status: ready for release
definition: The probability of a patient having the target disorder before a diagnostic test result is known
term editor: Philippe Rocca-Serra
definition source: http://www.cebm.net/pre-test-probability/

measure of heterogeneity
type: Class
subclass of: measure of dispersion
has curation status: ready for release
definition: a measure of heterogeneity in meta-analysis is a data item which aims to describe the variation in study outcomes between studies.
term editor: Philippe Rocca-Serra
definition source: adapted from http://www.statsdirect.com/help/default.htm#meta_analysis/heterogeneity.htm last accessed: May 2016

Cochran's Q statistic
type: Class
subclass of: measure of heterogeneity
has curation status: ready for release
definition: The Cochran's Q statistic is a measure of heterogeneity accros study computed by summing the squared deviations of each study's estimate from the overall meta-analytic estimate, weighting each study's contribution in the same manner as in the meta-analysis.
term editor: Philippe Rocca-Serra
definition source: Cochran WG. The combination of estimates from different experiments. Biometrics 1954;10: 101-29. https://doi.org/10.2307/3001666
R command: http://www.inside-r.org/packages/cran/RVAideMemoire/docs/cochran.qtest

I-squared
type: Class
subclass of: measure of heterogeneity
has curation status: ready for release
definition: The quantity called I2, describes the percentage of total variation across studies that is due to heterogeneity rather than chance. I2 can be readily calculated from basic results obtained from a typical meta-analysis as I2 = 100%×(Q - df)/Q, where Q is Cochran's heterogeneity statistic and df the degrees of freedom. Negative values of I2 are put equal to zero so that I2 lies between 0% and 100%. A value of 0% indicates no observed heterogeneity, and larger values show increasing heterogeneity. Unlike Cochran's Q, it does not inherently depend upon the number of studies considered. A confidence interval for I² is constructed using either i) the iterative non-central chi-squared distribution method of Hedges and Piggott (2001); or ii) the test-based method of Higgins and Thompson (2002). The non-central chi-square method is currently the method of choice (Higgins, personal communication, 2006) – it is computed if the 'exact' option is selected.
term editor: Philippe Rocca-Serra
alternative term: I2
definition source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC192859/ and http://www.statsdirect.com/help/default.htm#meta_analysis/heterogeneity.htm

Tau squared
type: Class
subclass of: measure of heterogeneity
has curation status: ready for release
definition: Tau-squared is an estimate of the between-study variance in a random-effects meta-analysis. The square root of this number (i.e. tau) is the estimated standard deviation of underlying effects across studies.
term editor: Philippe Rocca-Serra
definition source: http://handbook.cochrane.org/chapter_9/9_5_4_incorporating_heterogeneity_into_random_effects_models.htm
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor

L'Abbe plot
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: observed risk
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: observed risk
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: data visualization
    intersection of: Restriction
      on property: preceded by
      some values from: meta analysis
has curation status: ready for release
definition: The L’Abbé plot was introduced in 1987 in the context of meta-analyses of clinical trials with dichotomous (binary) outcomes, as a plot of observed risks in the treatment group against observed risks in the control group. Another formulation is that it plots the event rate in the experimental (intervention) group against the event rate in the control group, as an aid to exploring the heterogeneity of effect estimates within a meta-analysis. It is diagram used in meta-analysis that compares the risks observed in the experimental and control arms of clinical trials. Each trial is located in the space of a diagram where the sizes of the circles indicate the sizes of the trials. Trials in which the experimental treatment had a higher risk than the control will be in the upper left of the plot. If risk in the both groups is the same the circle will fall on the line of equality. If the control treatment has a higher risk than the experimental treatment then the point will be in the lower right of the plot. It is often used as an indicator of heterogeneity and hence as an indicator of the likelihood that results from different trials can be validly combined. Named after Kristin L'Abbé.
term editor: Philippe Rocca-Serra
definition source: 10.1002/jrsm.6 Graphical displays for meta-analysis: An overview with suggestions for practice
definition source: http://www.ncbi.nlm.nih.gov/pubmed/3300460 and http://www.dictionarycentral.com/definition/l-abb-plot.html
R command: http://www.inside-r.org/packages/cran/meta/docs/labbe.metabin

observed risk
type: Class
subclass of: risk
has curation status: ready for release
definition: the proportion of individuals in a population with the outcome of interest
term editor: Philippe Rocca-Serra
definition source: adapted from: http://handbook.cochrane.org/chapter_9/9_2_2_4_measure_of_absolute_effect_the_risk_difference.htm

risk difference
type: Class
subclass of: absolute difference
has curation status: ready for release
definition: The risk difference is the difference between the observed risks (proportions of individuals with the outcome of interest) in the two groups. The risk difference is straightforward to interpret: it describes the actual difference in the observed risk of events between experimental and control interventions.
term editor: Alejandra Gonzalez-Beltran
term editor: Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel, Harold Lehmann, Janice Tufte
term editor: Philippe Rocca-Serra
alternative term: ARD
alternative term: RD
alternative term: absolute risk difference
definition source: http://handbook.cochrane.org/chapter_9/9_2_2_4_measure_of_absolute_effect_the_risk_difference.htm

Sidik-Jonkman estimator
type: Class
subclass of: estimate
subclass of: Restriction
  on property: estimate of
  some values from: Tau squared
has curation status: ready for release
definition: Sidik-Jonkman estimator is a data item computed to estimate heterogeneity parameter (estimate of between-study variance) in a random effect model for meta analysis.
term editor: Philippe Rocca-Serra
definition source: http://www.ncbi.nlm.nih.gov/pubmed/16955539
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor metacor(cor, n, studlab, data=NULL, subset=NULL, sm=.settings$smcor, level=.settings$level, level.comb=.settings$level.comb, comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random, hakn="FALSE", method.tau="SJ", tau.common=.settings$tau.common, prediction=.settings$prediction, level.predict=.settings$level.predict, method.bias=.settings$method.bias, backtransf=.settings$backtransf, title=.settings$title, complab=.settings$complab, outclab="", byvar, bylab, print.byvar=.settings$print.byvar, keepdata=.settings$keepdata )

Hunter-Schmidt estimator
type: Class
subclass of: estimate
subclass of: Restriction
  on property: estimate of
  some values from: statistic
subclass of: Restriction
  on property: estimate of
  some values from: Tau squared
has curation status: ready for release
definition: Hunter-Schmidt estimator is a data item computed to estimate heterogeneity parameter (estimate of between-study variance) in a random effect model for meta analysis.
term editor: Philippe Rocca-Serra
definition source: Methods of Meta-Analysis: Correcting Error and Bias in Research Findings. by John E. Hunter, Frank L. Schmidt doi:10.2307/2289738
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor metacor(cor, n, studlab, data=NULL, subset=NULL, sm=.settings$smcor, level=.settings$level, level.comb=.settings$level.comb, comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random, hakn="FALSE", method.tau="HS", tau.common=.settings$tau.common, prediction=.settings$prediction, level.predict=.settings$level.predict, method.bias=.settings$method.bias, backtransf=.settings$backtransf, title=.settings$title, complab=.settings$complab, outclab="", byvar, bylab, print.byvar=.settings$print.byvar, keepdata=.settings$keepdata )

restricted maximum likelihood estimation
type: Class
subclass of: maximum likelihood estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: model parameter estimate
    intersection of: Restriction
      on property: is about
      some values from: Class
        intersection of: random effect model
        intersection of: variance
has curation status: ready for release
definition: restricted maximum likelihood estimation is a kind of maximum likelihood estimation data transformation which estimates the variance components of random-effects in univariate and multivariate meta-analysis. in contrast to 'maximum likelihood estimation', reml can produce unbiased estimates of variance and covariance parameters.
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1093/biomet/58.3.545
STATO alternative term: REML
R command: reml(y, v, x, data, RE.constraints = NULL, RE.startvalues = 0.1, RE.lbound = 1e-10, intervals.type = c("z", "LB"), model.name="Variance component with REML", suppressWarnings = TRUE, silent = TRUE, run = TRUE, ...) https://www.rdocumentation.org/packages/metaSEM/versions/1.0.0/topics/reml

maximum likelihood estimation
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
has curation status: ready for release
definition: maximum likelihood estimation (MLE) is a method of estimating the parameters of a statistical model, given observations. MLE attempts to find the parameter values that maximize the likelihood function, given the observations. The method of maximum likelihood is based on the likelihood function, {\displaystyle {\mathcal {L}}(\theta \,;x)} {\displaystyle {\mathcal {L}}(\theta \,;x)}. We are given a statistical model, i.e. a family of distributions {\displaystyle \{f(\cdot \,;\theta )\mid \theta \in \Theta \}} {\displaystyle \{f(\cdot \,;\theta )\mid \theta \in \Theta \}}, where {\displaystyle \theta } \theta denotes the (possibly multi-dimensional) parameter for the model. The method of maximum likelihood finds the values of the model parameter, {\displaystyle \theta } \theta , that maximize the likelihood function, {\displaystyle {\mathcal {L}}(\theta \,;x)} {\displaystyle {\mathcal {L}}(\theta \,;x)}. I
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Maximum_likelihood_estimation
R command: http://stat.ethz.ch/R-manual/R-devel/library/stats4/html/mle.html

DerSimonian-Laird estimator
type: Class
subclass of: estimate
subclass of: Restriction
  on property: estimate of
  some values from: statistic
subclass of: Restriction
  on property: estimate of
  some values from: Tau squared
has curation status: ready for release
definition: DerSimonian-Laird estimator s a data item computed to estimate heterogeneity parameter (estimate of between-study variance) in a random effect model for meta analysis. The estimator is used in simple noniterative procedure for characterizing the distribution of treatment effects in a series of studies
term editor: Philippe Rocca-Serra
definition source: doi:10.1016/j.cct.2006.04.004
definition source: http://www.ncbi.nlm.nih.gov/pubmed/3802833 doi:10.1016/0197-2456(86)90046-2
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor metacor(cor, n, studlab, data=NULL, subset=NULL, sm=.settings$smcor, level=.settings$level, level.comb=.settings$level.comb, comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random, hakn="FALSE", method.tau="DL", tau.common=.settings$tau.common, prediction=.settings$prediction, level.predict=.settings$level.predict, method.bias=.settings$method.bias, backtransf=.settings$backtransf, title=.settings$title, complab=.settings$complab, outclab="", byvar, bylab, print.byvar=.settings$print.byvar, keepdata=.settings$keepdata )

meta analysis by Hartung-Knapp-Sidik-Jonkman method
type: Class
subclass of: meta analysis
subclass of: Restriction
  on property: has_specified_input
  some values from: random effect model
subclass of: Restriction
  on property: has_specified_input
  some values from: Sidik-Jonkman estimator
has curation status: metadata incomplete
definition: a random effect meta analysis procedure defined by Hartung and Knapp and by Sidik and Jonkman which performs better than DerSimonian and Laird approach, especially when there is heterogeneity and the number of studies in the meta-analysis is small.
term editor: Philippe Rocca-Serra
alternative term: HKSJ method
definition source: doi:10.1186/1471-2288-14-25
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor metacor(cor, n, studlab, data=NULL, subset=NULL, sm=.settings$smcor, level=.settings$level, level.comb=.settings$level.comb, comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random, hakn="TRUE", method.tau="HS", tau.common=.settings$tau.common, prediction=.settings$prediction, level.predict=.settings$level.predict, method.bias=.settings$method.bias, backtransf=.settings$backtransf, title=.settings$title, complab=.settings$complab, outclab="", byvar, bylab, print.byvar=.settings$print.byvar, keepdata=.settings$keepdata )

meta analysis by DerSimonian and Leard method
type: Class
subclass of: meta analysis
subclass of: Restriction
  on property: has_specified_input
  some values from: random effect model
subclass of: Restriction
  on property: has_specified_input
  some values from: DerSimonian-Laird estimator
has curation status: metadata incomplete
definition: a meta analysis which relies on the computation of the DerSimonian and Leard estimator as a measure of heterogeneity over a set of studies.
term editor: Philippe Rocca-Serra
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor metacor(cor, n, studlab, data=NULL, subset=NULL, sm=.settings$smcor, level=.settings$level, level.comb=.settings$level.comb, comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random, hakn="FALSE", method.tau="DL", tau.common=.settings$tau.common, prediction=.settings$prediction, level.predict=.settings$level.predict, method.bias=.settings$method.bias, backtransf=.settings$backtransf, title=.settings$title, complab=.settings$complab, outclab="", byvar, bylab, print.byvar=.settings$print.byvar, keepdata=.settings$keepdata )

meta analysis by Hunter-Schmidt method
type: Class
subclass of: meta analysis
subclass of: Restriction
  on property: has_specified_input
  some values from: random effect model
subclass of: Restriction
  on property: has_specified_input
  some values from: Hunter-Schmidt estimator
has curation status: metadata incomplete
definition: a meta analysis which relies on the computation of the Hunter and Schmidt estimator as a measure of heterogeneity over a set of studies by considering the weighted mean of the raw correlation coefficient. Hunter and Schmidt developed what is commonly termed validity generalization procedures (Schmidt and Hunter, 1977). These involve correcting the effect sizes in the meta-analysis for sampling, and measurement error and range restriction.
term editor: Philippe Rocca-Serra
definition source: Hunter JE, Schmidt FL. Methods of Meta-analysis: correcting error and bias in research findings. Newbury Park, CA: Sage 1990.
R command: http://www.inside-r.org/packages/cran/meta/docs/metacor metacor(cor, n, studlab, data=NULL, subset=NULL, sm=.settings$smcor, level=.settings$level, level.comb=.settings$level.comb, comb.fixed=.settings$comb.fixed, comb.random=.settings$comb.random, hakn="FALSE", method.tau="HS", tau.common=.settings$tau.common, prediction=.settings$prediction, level.predict=.settings$level.predict, method.bias=.settings$method.bias, backtransf=.settings$backtransf, title=.settings$title, complab=.settings$complab, outclab="", byvar, bylab, print.byvar=.settings$print.byvar, keepdata=.settings$keepdata )

McNemar test
type: Class
subclass of: study design execution
subclass of: statistical test hypothesis
subclass of: data transformation
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: matched pairs design
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
has curation status: ready for release
definition: McNemar's test is a statistical test used on paired nominal data. It is applied to 2 × 2 contingency tables with a dichotomous trait, with matched pairs of subjects, to determine whether the row and column marginal frequencies are equal (that is, whether there is "marginal homogeneity"). It is named after Quinn McNemar, who introduced it in 1947. An application of the test in genetics is the transmission disequilibrium test for detecting linkage disequilibrium
term editor: Philippe Rocca-Serra
alternative term: McNemar's Chi-squared Test for Count Data
alternative term: test of the marginal homogeneity of a contingency table
alternative term: within-subjects chi-squared test
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/McNemar%27s_test last accessed: May 2016
definition source: https://www.ncbi.nlm.nih.gov/pubmed/20254758
R command: mcnemar.test(x, y = NULL, correct = TRUE) from: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/mcnemar.test.html

Cochran's q test for heterogeneity
type: Class
subclass of: data transformation
subclass of: test of association between categorical variables
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: Cochran's Q statistic
    intersection of: Restriction
      on property: is about
      some values from: randomized complete block design
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: association between categorical variables testing objective
has curation status: ready for release
definition: Cochran's Q test is a statistical test used for unreplicated randomized block design experiments with a binary response variable and paired data. In the analysis of two-way randomized block designs where the response variable can take only two possible outcomes (coded as 0 and 1), Cochran's Q test is a non-parametric statistical test to verify whether k treatments have identical effects.
term editor: Philippe Rocca-Serra
definition source: adapted from: http://www.inside-r.org/packages/cran/CVST/docs/cochranq.test and https://en.wikipedia.org/wiki/Cochran%27s_Q_test last accessed: May 2016
R command: cochran.qtest(formula, data, alpha = 0.05, p.method = "fdr") from: http://www.inside-r.org/packages/cran/RVAideMemoire/docs/cochran.qtest

probability distribution scale parameter
type: Class
subclass of: measure of dispersion
subclass of: Restriction
  on property: denotes
  some values from: probability distribution
has curation status: ready for release
definition: a probability distribution scale parameter is a measure of variation which is set by the operator when selecting a parametric probability distribution and which defines how spread the distribution is. The larger the value of the scale parameter is, the more spread out the distribution.
editor note: user request: https://github.com/ISA-tools/stato/issues/47
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Scale_parameter. last accessed: 2016/11/11
STATO alternative term: scale
STATO alternative term: statistical dispersion

probability distribution shape parameter
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: probability distribution
has curation status: ready for release
definition: a probability distribution shape parameter is a data item which is set by the operator when selecting a parametric probability distribution and which dictates the way the profile but not the location or size of the distribution plot looks like.
editor note: user request: https://github.com/ISA-tools/stato/issues/47
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Shape_parameter last accessed: 2016-11-11
STATO alternative term: shape
R command: http://stat.ethz.ch/R-manual/R-patched/library/stats/html/GammaDist.html

scale estimator
type: Class
subclass of: estimate
subclass of: Restriction
  on property: is about
  some values from: probability distribution scale parameter
subclass of: Restriction
  on property: estimate of
  some values from: probability distribution scale parameter
has curation status: ready for release
definition: a scale estimator is a measurement datum (a statistic) which is calculated to approach the actual scale parameter of a probability distribution from observed data.
editor note: user request: https://github.com/ISA-tools/stato/issues/47
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Scale_parameter last accessed: 2016/11/11
R command: https://stat.ethz.ch/R-manual/R-devel/library/mgcv/html/gam.scale.html

log normal distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution location parameter
has curation status: ready for release
definition: a log-normal (or lognormal) distribution is a continuous probability distribution of a random variable whose logarithm is normally distributed. Thus, if the random variable {\displaystyle X} X is log-normally distributed, then {\displaystyle Y=\ln(X)} Y=\ln(X) has a normal distribution. Likewise, if {\displaystyle Y} Y has a normal distribution, then {\displaystyle X=\exp(Y)} X=\exp(Y) has a log-normal distribution. A random variable which is log-normally distributed takes only positive real values. The distribution is occasionally referred to as the Galton distribution or Galton's distribution, after Francis Galton.
editor note: user request: https://github.com/ISA-tools/stato/issues/47
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Log-normal_distribution last accessed: 2016/11/11
R command: dlnorm(x, meanlog = 0, sdlog = 1, log = FALSE) plnorm(q, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE) qlnorm(p, meanlog = 0, sdlog = 1, lower.tail = TRUE, log.p = FALSE) rlnorm(n, meanlog = 0, sdlog = 1) https://stat.ethz.ch/R-manual/R-devel/library/stats/html/Lognormal.html

outlier detection testing objective
type: Class
subclass of: statistical hypothesis test objective
has curation status: ready for release
definition: outlier detection testing objective is a statistical objective of a data transformation which aims to test a null hypothesis that an observation is not an outlier.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: outlier detection testing objective

Dixon Q test
type: Class
subclass of: data transformation
subclass of: generalized extreme studentized deviate test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: outlier detection testing objective
has curation status: ready for release
definition: Dixon test is a statistical test used to detect outliers in a univariate data set assumed to come from a normally distributed population.
editor note: Le test de Dixon est un test statistique destiné à identifier des données abérrantes dans un jeu de données associées à une variable aléatoire univariée dont la distribution sous-jacente est supposée normale. @fr
term editor: Philippe Rocca-Serra
alternative term: Dixon test
alternative term: Q test
definition source: Robert B. Dean and Wilfrid J. Dixon (1951) "Simplified Statistics for Small Numbers of Observations". Anal. Chem., 1951, 23 (4), 636–638.
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Dixon%27s_Q_test last accessed: 2016-11-19
R command: dixon.outliers(data) from: http://finzi.psych.upenn.edu/library/referenceIntervals/html/dixon.outliers.html

Grubbs' test
type: Class
subclass of: data transformation
subclass of: generalized extreme studentized deviate test
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: Shapiro-Wilk test
    union of: Kolmogorov-Smirnov test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: Class
    intersection of: p-value
    intersection of: Restriction
      on property: is about
      qualified cardinality: 1
      on class: outlier
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: outlier detection testing objective
has curation status: ready for release
definition: Grubbs' test is a statistical test used to detect one outlier in a univariate data set assumed to come from a normally distributed population.
editor note: Le test de Grubb est un test statistique destiné à identifier une (et une seule) abérration dans un jeu de données associées à une variable aléatoire univariée dont la distribution sous-jacente est supposée normale. @fr
term editor: Philippe Rocca-Serra
alternative term: maximum normed residual test
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Grubbs'_test_for_outliers last accessed: 2016-11-19
R command: rgrubbs.test(x, alpha = 0.05) from: http://finzi.psych.upenn.edu/library/OutlierDM/html/rgrubbs.test.html

Tietjen-Moore test for outliers
type: Class
subclass of: data transformation
subclass of: generalized extreme studentized deviate test
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: Shapiro-Wilk test
    union of: Kolmogorov-Smirnov test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is about
      some values from: outlier
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: outlier detection testing objective
has curation status: ready for release
definition: Tietjen-Moore test for outlier is a statistical test used to detect outliers and corresponds to a generalization of the Grubb's test, thus allowing detection of more than one outlier in a univariate data set assumed to come from a normally distributed population. If testing for a single outlier, the Tietjen-Moore test is equivalent to the Grubbs' test.
editor note: Le test de Tietjen-Moore est un test statistique destiné à identifier des données abérrantes dans un jeu de données associées à une variable aléatoire univariée dont la distribution sous-jacente est supposée normale. Ce test est une généralisation du test de Grubb dans le sens où il permet de tester pour la présence de plus d'une seule et unique abérration. @fr
term editor: Philippe Rocca-Serra
alternative term: Tietjen-Moore test
definition source: adapted from NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda35h2.htm last accessed: 2016-11-19
R command: FindOutliersTietjenMooreTest(dataSeries,k,alpha=0.05) from: https://rdrr.io/rforge/climtrends/man/findOutliers.Tietjen.Moore.test.html

generalized extreme studentized deviate test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: outlier detection testing objective
subclass of: statistical test hypothesis
subclass of: data transformation
subclass of: Restriction
  on property: has part
  some values from: multiple testing correction method
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: upper confidence limit
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: outlier detection testing objective
has curation status: ready for release
definition: The Extreme Studentized Deviate Test is a statistical test used to detect outliers in a univariate data set assumed to come from a normally distributed population. The ESD Test differs from the Grubbs' test and the Tietjen-Moore test in the sense that it contains built-in correction for multiple testing.
term editor: Philippe Rocca-Serra
alternative term: ESD test for outliers
alternative term: generalized ESD test for outliers
definition source: Rosner, Bernard (May 1983), Percentage Points for a Generalized ESD Many-Outlier Procedure,Technometrics, 25(2), pp. 165-172.
definition source: STATO
definition source: adapted from NIST: http://www.itl.nist.gov/div898/handbook/eda/section3/eda35h3.htm last accessed: 2016-11-19
R command: rgrubbs.test(x, alpha = 0.05) from: http://finzi.psych.upenn.edu/library/OutlierDM/html/rgrubbs.test.html

split-plot design
type: Class
equivalent class: Restriction
  on property: declares
  some values from: Class
    intersection of: whole plot number
    intersection of: sub-plot number
subclass of: study design
subclass of: restricted randomized design
subclass of: Restriction
  on property: realized in
  some values from: restricted randomization
subclass of: Restriction
  on property: declares
  some values from: blocking variable
subclass of: Restriction
  on property: declares
  some values from: Class
    intersection of: whole plot number
    intersection of: sub-plot number
subclass of: Restriction
  on property: declares
  min qualified cardinality: 2
  on class: study design independent variable
has curation status: metadata complete
definition: a split-plot design is kind of factorial design which is used when running a full factorial completely randomized design is inpractical, either for cost or practicalities (e.g. equipment, fields), in other words, when a restricted randomization has to be applied. A split-plot design is used whenever practioners fix the level of 'hard to change factor' and run all the combinations of the other factors. The hard to change factor is also refered to as the 'whole plot' factor, while the remainders of the factors are refered to as 'split plot factor'. Performing a split-plot design therefore means fixing one factor level, and then applying the treatments formed by the cartesian products of the levels for the other factors. A mininum of 2 factors are required and one being applied before the other(s).
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from: http://www.minitab.com/uploadedFiles/Content/News/Published_Articles/recognize_split_plot_experiment.pdf adapted from wikipedia: https://en.wikipedia.org/wiki/Restricted_randomization last accessed: 14.12.2016
definition source: https://pdfs.semanticscholar.org/bb4b/d979610388c76bb81568f14a886304ce4662.pdf

split split plot design
type: Class
subclass of: study design
subclass of: split-plot design
subclass of: Restriction
  on property: realized in
  some values from: restricted randomization
subclass of: Restriction
  on property: declares
  some values from: blocking variable
subclass of: Restriction
  on property: declares
  some values from: Class
    intersection of: whole plot number
    intersection of: sub-plot number
    intersection of: sub sub-plot number
subclass of: Restriction
  on property: declares
  min qualified cardinality: 3
  on class: study design independent variable
has curation status: metadata complete
definition: a split split plot design is a study design where restricted randomization affect 2 study factors (and not 1 as in split-plot design). Such design is only possible if at least 3 independent variables are present.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: adapted from https://onlinecourses.science.psu.edu/stat503/node/72 last accessed 2016/12/15

restricted randomization
type: Class
subclass of: group randomization
disjoint with: complete randomization
has curation status: metadata complete
definition: Restricted randomization is a kind of randomization which is used or occured when hard to change factors exist in a study design. In other words, when complete randomization is not possible, a case of restricted randomization exists, for instance in the case of split-plot design. Restricted randomization allows intuitively poor allocations of treatments to experimental units to be avoided, while retaining the theoretical benefits of randomization. Restricted randomization can also result from an unplanned event and is then something that should be avoided. RandomizeR R package can be used to detect such events and assess the quality of randomization process.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: Adapted from Wikipedia: https://en.wikipedia.org/wiki/Restricted_randomization last accessed: 2016/12/15

whole plot number
type: Class
subclass of: data item
has curation status: pending final vetting
definition: a 'whole plot number' is a data item used to count and identify the actual piece of land (in the case of real field based trials) used in a split plot design experiment and receiving treatments corresponding to the levels of a factor whose randomization is restricted (these factors are known as 'hard to change' factors). In the case of non-field based trials, the 'whole plot' is a metaphor.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO adapted from http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/PDFbigbook-R/R-part012.pdf last accessed: 2016/12/15

sub-plot number
type: Class
subclass of: data item
has curation status: pending final vetting
definition: a 'sub plot number' is a data item used to count and identify the actual piece of land located within a 'whole plot', in the case of real field based trials using a split-plot design, and received completely randomized treatments corresponding to the factor levels combinations of the remainder factors declared in the experiment. in the case of 'split-split plot design', sub-plots also receive treatments corresponding to a factor whose randomization is restriction. In such configuration, each 'sub-plot' is itself divided into 'sub sub-plot', which then received the remainder of the treatments in completely randomized fashion. In the case of non-field based trials, the notion 'sub-plot' is a metaphor.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO adapted from http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/PDFbigbook-R/R-part012.pdf last accessed: 2016/12/15

sub sub-plot number
type: Class
subclass of: data item
has curation status: pending final vetting
definition: a 'sub sub-plot number' is a data item used to count and identify the actual piece of land located within a 'sub plot', in the case of real field based trials using a split-split-plot design, and received completely randomized treatments corresponding to the factor levels combinations of the remainder factors declared in the experiment. in the case of 'split-split plot design', sub-plots also receive treatments corresponding to a factor whose randomization is restriction. In such configuration, each 'sub-plot' is itself divided into 'sub sub-plot', which then received the remainder of the treatments in completely randomized fashion. In the case of non-field based trials, the notion 'sub sub-plot' is a metaphor.
term editor: Alejandra Gonzalez-Beltran
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra
definition source: STATO adapted from http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/PDFbigbook-R/R-part012.pdf last accessed: 2016/12/15

Wilk's Lambda
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_output_of
  some values from: multivariate analysis of variance
has curation status: ready for release
definition: "Wilks' lambda is a test statistic used in multivariate analysis of variance (MANOVA) to test whether there are differences between the means of identified groups of subjects on a combination of dependent variables."
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: http://www.blackwellpublishing.com/specialarticles/jcn_9_381.pdf
R command: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/summary.manova.html ## S3 method for class 'manova' summary(object, test = c("Pillai", "Wilks", "Hotelling-Lawley", "Roy"), intercept = FALSE, tol = 1e-7, ...)
Python command: https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.mstats.f_value_wilks_lambda.html#scipy.stats.mstats.f_value_wilks_lambda scipy.stats.mstats.f_value_wilks_lambda(ER, EF, dfnum, dfden, a, b)

Pillai's trace
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_output_of
  some values from: multivariate analysis of variance
has curation status: ready for release
definition: Pillai trace is a statistic used for the following three tests during a multivariate analysis of variance: (a) equality of mean vectors of lp‐variate normal distributions with the common but unknown covariance matrix, (b) independence between two sets of variates distributed jointly as a normal distribution with unknown mean vector, and (c) equality of covariance matrices of two p‐variate normal distributions with unknown mean vectors.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1002/0470011815.b2a13067

Hotelling-Lawley trace
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_output_of
  some values from: multivariate analysis of variance
has curation status: ready for release
definition: "The Lawley–Hotelling trace is used to test the equality of mean vectors of k p‐variate normal distributions with common but unknown covariance matrix. The explicit form of the null distribution of T$_{0}^{2}$equation image is the F distribution. The asymptotic null distribution is the chi‐square distribution. The power function of the test is described and its power is compared with the likelihood ratio test. "
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1002/0470011815.b2a13035
STATO alternative term: Lawley–Hotelling Trace

Roy’s Maximum Root
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_output_of
  some values from: multivariate analysis of variance
has curation status: ready for release
definition: Roy's maximum root is a statistic used in multivariate analysis of variance to find the maximum characteristic root or eigenvalue statistic for testing equality of k p-variate normal distributions with same covariance matrix, independence between two sets of variables jointly distributed as a normal distribution, equality of covariance matrices of two p-variate normal distributions, whether the covariance matrix of a p-variabte normal distribution with unknown mean vector equals a specified matrix.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: Oxford Dictionary of Statistical Terms
definition source: https://onlinecourses.science.psu.edu/stat505/node/163

multivariate analysis of variance
type: Class
subclass of: data transformation
subclass of: ANOVA
subclass of: Restriction
  on property: has part
  some values from: F-test
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: ready for release
definition: "The multivariate analysis of variance, or MANOVA, is a procedure for comparing multivariate sample means. As a multivariate procedure, it is used when there are two or more dependent variables, and is typically followed by significance tests involving individual dependent variables separately. It helps to answer: 1. Do changes in the independent variable(s) have significant effects on the dependent variables? 2. What are the relationships among the dependent variables? 3. What are the relationships among the independent variables?"
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Multivariate_analysis_of_variance
STATO alternative term: MANOVA
R command: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/manova.html

credible interval
type: Class
subclass of: measure of dispersion
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: upper confidence limit
    intersection of: lower confidence limit
subclass of: Restriction
  on property: is about
  some values from: model parameter estimate
has curation status: ready for release
definition: In Bayesian statistics context, a credible interval is an interval of a posterior distribution which is such that the density at any point inside the interval is greater than the density at any point outside and that the area under the curve for that interval is equal to a prespecified probability level. For any probability level there is generally only one such interval, which is also often known as the highest posterior density region. Unlike the usual confidence interval associated with frequentist inference, here the intervals specify the range within which parameters lie with a certain probability. The Bayesian counterparts of the confidence interval used in Frequentists Statistics.
term editor: Philippe Rocca-Serra
alternative term: Bayesian credibility interval
definition source: Adapted from Wikipedia: https://en.wikipedia.org/wiki/Credible_interval and from the Cambridge Dictionary of Statistics, fourth edition, ISBN-13 978-0-511-78827-7 last accessed: 2017-07-01
STATO alternative term: HPD
STATO alternative term: region of highest posterior density

95% credible interval
type: Class
subclass of: credible interval
has curation status: ready for release
definition: In Bayesian statistics context, a 95% credible interval is a credible interval which,given the data, includes the true parameter with probability of 95%.
term editor: Philippe Rocca-Serra
alternative term: Bayesian credibility interval at 95%
definition source: Wikipedia: https://en.wikipedia.org/wiki/Credible_interval last accessed: 2017-07-01

mean difference
type: Class
subclass of: absolute difference
example of usage: " In clinical trials, it gives you an idea of how much difference there is between the averages of the experimental group and control groups."
has curation status: ready for release
definition: The mean difference, or difference in means, measures the absolute difference between the mean value in two different groups. The mean difference is a subtraction of one mean from another. The primary use of this term is in analyzing between-group differences
editor note: Expert Working Group Agreement: 2021-12-01 vote 6-0 by Philippe Rocca-Serra, Paola Rosati, Robin Ann Yurk, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte
term editor: Alejandra Gonzalez-Beltran
term editor: Harold Lehmann, Brian S. Alper, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra, Kenneth Wilkins, Joanne Dehnbostel, Janice Tufte
term editor: Philippe Rocca-Serra
definition source: http://www.statisticshowto.com/mean-difference/
STATO alternative term: MD
STATO alternative term: difference in means

99% credible interval
type: Class
subclass of: credible interval
has curation status: ready for release
definition: In Bayesian statistics context, a 99% credible interval is a credible interval which, given the data, includes the true parameter with probability of 99%.
term editor: Philippe Rocca-Serra
alternative term: Bayesian credible interval at 99%
definition source: Wikipedia: https://en.wikipedia.org/wiki/Credible_interval last accessed: 2017-07-01

group sequential design
type: Class
subclass of: study design
has curation status: ready for release
definition: group sequential design is a study design used in clinical trial settings in which interim analyses of the data are conducted after groups of patients are recruited. After each interim analysis, the trial may stop early if the evidence so far shows the new treatment is particularly effective or ineffective. Such designs are ethical and cost-effective, and so are of great interest in practice.
term editor: Philippe Rocca-Serra
definition source: adapted from https://www.jstatsoft.org/article/view/v066i02/v66i02.pdf
R command: https://cran.r-project.org/web/packages/gsDesign/index.html

interim analysis
type: Class
subclass of: data transformation
has curation status: ready for release
definition: interim analysis is a data transformation used to analyzed studies implementing a group-sequential design, to evaluate and interpret the accumulating information during a clinical trial. It means that the analysis of data that is conducted before full data collection has been completed. Clinical trials are unusual in that enrollment of patients is a continual process staggered in time. This means that if a treatment is particularly beneficial or harmful compared to the concurrent placebo group while the study is on-going, the investigators are ethically obliged to assess that difference using the data at hand and to make a deliberate consideration of terminating the study earlier than planned.
term editor: Philippe Rocca-Serra
definition source: adapted from https://onlinecourses.science.psu.edu/stat509/node/75 and from wikipedia: https://en.wikipedia.org/wiki/Interim_analysis last accessed: 2017-10-9

O'brien-Flemming boundary analysis
type: Class
subclass of: interim analysis
subclass of: Restriction
  on property: has part
  some values from: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: count
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: the O'brien-Flemming boundary analysis is a kind of interim-analysis method implemented by O'brien and Flemming to account for the As all frequentist methods of the same type, it focuses on controlling the type I error rate as the repeated hypothesis testing of accumulating data increases the type I error rate of a clinical trial.

Pocock boundary analysis
type: Class
subclass of: interim analysis
subclass of: Restriction
  on property: has part
  some values from: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: count
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
example of usage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3856440/
has curation status: ready for release
definition: The Pocock boundary analysis gives a p-value threshold for each interim analysis which guides the data monitoring committee on whether to stop the trial. The boundary used depends on the number of interim analyses. The Pocock boundary is simple to use in that the p-value threshold is the same at each interim analysis. The disadvantages are that the number of interim analyses must be fixed at the start and it is not possible under this scheme to add analyses after the trial has started. Another disadvantage is that investigators and readers frequently do not understand how the p-values are reported: for example, if there are five interim analyses planned, but the trial is stopped after the third interim analysis because the p-value was 0.01, then the overall p-value for the trial is still reported as <0.05 and not as 0.01. As all frequentist methods of the same type, it focuses on controlling the type I error rate as the repeated hypothesis testing of accumulating data increases the type I error rate of a clinical trial.
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1093%2Fbiomet%2F64.2.191 and Wikipedia: https://en.wikipedia.org/wiki/Pocock_boundary

Haybittle-Peto boundary analysis
type: Class
subclass of: interim analysis
subclass of: Restriction
  on property: has part
  some values from: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_input
  some values from: count
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: The Haybittle–Peto boundary analysis is an interim analysis where a rule for deciding when to stop a clinical trial prematurely is defined. It is named for John Haybittle and Richard Peto. The Haybittle–Peto boundary is one such stopping rule, and it states that if an interim analysis shows a probability of equal to, or less than 0.001 that a difference as extreme or more between the treatments is found, given that the null hypothesis is true, then the trial should be stopped early. The final analysis is still evaluated at the normal level of significance (usually 0.05).[3][4] The main advantage of the Haybittle–Peto boundary is that the same threshold is used at every interim analysis, unlike the O'Brien–Fleming boundary, which changes at every analysis. Also, using the Haybittle–Peto boundary means that the final analysis is performed using a 0.05 level of significance as normal, which makes it easier for investigators and readers to understand. The main argument against the Haybittle–Peto boundary is that some investigators believe that the Haybittle–Peto boundary is too conservative and makes it too difficult to stop a trial. As all frequentist methods of the same type, it focuses on controlling the type I error rate as the repeated hypothesis testing of accumulating data increases the type I error rate of a clinical trial.
term editor: Philippe Rocca-Serra
definition source: 10.1259/0007-1285-44-526-793 and adapted from Wikipedia: https://en.wikipedia.org/wiki/Haybittle%E2%80%93Peto_boundary

linear mixed model
type: Class
subclass of: mixed effect model
has curation status: metadata complete
definition: A lnear mixed model is a mixed model containing both fixed effects and random effects and in which factors and covariates are assumed to have a linear relationship to the dependent variable. These models are useful in a wide variety of disciplines in the physical, biological and social sciences. They are particularly useful in settings where repeated measurements are made on the same statistical units (longitudinal study), or where measurements are made on clusters of related statistical units. Because of their advantage in dealing with missing values, mixed effects models are often preferred over more traditional approaches such as repeated measures ANOVA. Fixed-effects factors are generally considered to be the variables whose values of interest are all represented in the data file. Random-effects factors are variables whose values correspond to unwanted variation. They are useful when trying to understand variability in the dependent variable which was not anticipated and exceeds what was expected. Linear mixed models also allow to specify specific interactions between factors, and allow the evaluation of the various linear effect that a particular combination of factor levels may have on a response variable. Finally, linear mixed models allow to specify variance components in order to describe the relation between various random effects levels.
term editor: Hanna Cwiek
term editor: Pawel Krajewski
term editor: Philippe Rocca-Serra
alternative term: LMM
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Mixed_model

empirical measure
type: Class
subclass of: data item
has curation status: ready for release
definition: An empirical measure is a random measure arising from a particular realization of a (usually finite) sequence of random variables.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Empirical_measure

model term
type: Class
subclass of: data item
subclass of: Restriction
  on property: has part
  some values from: model parameter
subclass of: Restriction
  on property: is declared by
  some values from: statistical model
has curation status: requires discussion
definition: A model term is a data item set in statistical model formula to apportion source of variation.
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: statistical model term

model random effect term
type: Class
subclass of: study design dependent variable
subclass of: model term
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Class
    union of: best linear unbiased predictor
    union of: restricted maximum likelihood estimation
subclass of: Restriction
  on property: is declared by
  some values from: Class
    union of: random effect model
    union of: linear mixed model
subclass of: Restriction
  on property: has order in sequence
  some values from: count
subclass of: Restriction
  on property: is modeled by
  some values from: covariance structure
has curation status: requires discussion
definition: the model random effect term is model term which aims to account for the unwanted variability in the data associated with a range of independent variables which are not the primary interest in the dataset. It is there also known as the variance component of the model
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
alternative term: variance component

model fixed effect term
type: Class
subclass of: model term
subclass of: Restriction
  on property: is_specified_input_of
  some values from: best linear unbiased estimator
subclass of: Restriction
  on property: is declared by
  some values from: Class
    union of: fixed effect model
    union of: linear mixed model
subclass of: Restriction
  on property: has order in sequence
  some values from: count
has curation status: requires discussion
definition: a model fixed effect term is a model term which accounts for variation explained by an independent variable and its levels.
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra

model interaction effect term
type: Class
subclass of: model term
subclass of: Restriction
  on property: is declared by
  some values from: Class
    union of: random effect model
    union of: linear mixed model
subclass of: Restriction
  on property: has order in sequence
  some values from: count
has curation status: requires discussion
definition: a model interaction effect term is a model term which accounts for variation explained by the combined effects of the factor levels of more than one (usually 2) independent variables.
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra

model error term
type: Class
subclass of: study design dependent variable
subclass of: model term
subclass of: Restriction
  on property: is declared by
  some values from: statistical model
subclass of: Restriction
  on property: has order in sequence
  some values from: count
subclass of: Restriction
  on property: is modeled by
  some values from: covariance structure
has curation status: requires discussion
definition: a model error term is a model term which accounts for residual variation not explained by the other components (fixed and random effect terms)
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra

estimate
type: Class
equivalent class: Restriction
  on property: estimate of
  some values from: statistic
subclass of: statistic
subclass of: Restriction
  on property: estimate of
  some values from: statistic
has curation status: ready for release
definition: a estimate is a data item which is computed from a dataset to provide an approximated value (an estimator) for a 'statistical parameter' (a 'characteristics/parameter' of the true underlying distribution) of a real population.
editor note: Hanna Cwiek
editor note: Tom Nichols
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: STATO
term tracker item: https://github.com/ISA-tools/stato/issues/74

degree of freedom approximation
type: Class
subclass of: data transformation
has curation status: ready for release
definition: An estimate of the number of degrees of freedom.
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
definition source: STATO

Kenward-Roger degree of freedom approximation
type: Class
subclass of: degree of freedom approximation
has curation status: ready for release
definition: The Kenward-Roger method's fundamental idea is to calculate the approximate mean and variance of their statistic and then match moments with an F distribution to obtain the denominator degrees of freedom.
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
definition source: https://support.sas.com/documentation/cdl/en/statug/68162/HTML/default/viewer.htm#statug_glimmix_details40.htm
definition source: https://www.jstatsoft.org/article/view/v059i09
definition source: https://www.ncbi.nlm.nih.gov/pubmed/9333350
STATO alternative term: Kenward-Roger
R command: https://www.rdocumentation.org/packages/lmerTest/versions/2.0-36/topics/anova-methods ibrary(lme4) library(pbkrtest) fm1 <- lmer(Reaction ~ Days + (Days| Subject), sleepstudy) get_Lb_ddf(fm1, lme4::fixef(fm1))

Satterthwaite degree of freedom approximation
type: Class
subclass of: degree of freedom approximation
has curation status: ready for release
definition: Satterthwaite degree of freedom approximation is a type of degree of freedom approximation which is used to estimate an “effective degrees of freedom” for a probability distribution formed from several independent normal distributions where only estimates of the variance are known. It was originally developed by statistician Franklin E. Satterthwaite.
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
alternative term: satterthwaite
definition source: Satterthwaite, F. E. (1946), "An Approximate Distribution of Estimates of Variance Components.", Biometrics Bulletin, 2: 110–114, doi:10.2307/3002019
STATO alternative term: Welch-Satterthwaite
R command: https://www.rdocumentation.org/packages/metRology/versions/0.9-23-2/topics/welch.satterthwaite

between-within denominator degrees of freedom approximation
type: Class
subclass of: degree of freedom approximation
has curation status: ready for release
definition: a data transformation to determine the number of degree of freedom
term editor: Alejandra Gonzalez-Beltran
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
alternative term: between-within
definition source: https://www.ncbi.nlm.nih.gov/pubmed/25899170

partial least square weight
type: Class
subclass of: data item
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Partial Least Square Discriminant Analysis
has curation status: ready for release
definition: PLS weight (or Partial Least Square weight) is a information content entity which is generated when performing a Partial Least Square analysis
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: PLS weight

pedigree data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: is about
  some values from: family
has curation status: metadata incomplete
definition: a dataset which is made up of pedigree information, that is presenting ancestry or lineage information in a set of individuals of an organism.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra

ridge regression best linear unbiaised predictor
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: RR-BLUP is a data transformation used in the context of estimating breeding value using a Bayesian ridge regression. It can be obtained from Bayes B procedure by setting pi parameter to zero ( ) and assuming that all the markers have the same variance.
editor note: term request by Guillaume Bauchet, cassavabase.org, Cornell University
term editor: Philippe Rocca-Serra
definition source: Comparison Between Linear and Non-parametric Regression Models for Genome-Enabled Prediction in Wheat Paulino Pérez-Rodríguez, Daniel Gianola, Juan Manuel González-Camacho, José Crossa, Yann Manès and Susanne Dreisigacker G3: GENES, GENOMES, GENETICS December 1, 2012 vol. 2 no. 12 1595-1605; https://doi.org/10.1534/g3.112.003665
STATO alternative term: RRBLUP

genomic best linear unbiased prediction
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: a data transformation which calculate predictions of breeding values using an animal model and a relationship matrix calculated from the genomic/genetic markers (G Matrix), in constrast to using Pedigree information as in BLUP, also known as ABLUP
term editor: Philippe Rocca-Serra
definition source: adapted from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3382275/ and from: https://www.rdocumentation.org/packages/pedigree/versions/1.4/topics/gblup and from
STATO alternative term: GBLUP
R command: gblup(formula, data, M, lambda) where: formula: formula of the model, do not include the random effect due to animal (generally ID). data: data.frame with columns corresponding to ID and the columns mentioned in the formula. M: Matrix of marker genotypes, usually the count of one of the two SNP alleles at each markers (0, 1, or 2). lambda : Variance ratio (σ2e/σ2a) https://www.rdocumentation.org/packages/pedigree/versions/1.4/topics/gblup

trait-specific relationship matrix best linear unbiaised prediction
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: a data transformation which calculate estimates of genomic estimated breeding values (GEBVs) on an animal or plant model utilizing trait-specific marker information.
term editor: Philippe Rocca-Serra
definition source: from: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012648
STATO alternative term: TABLUP

Bayes A
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: scaled t distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: Bayes A is a data transformation used in the context of estimating breeding value, which relies on a Bayesian model and treats the prior probability π that a SNP has zero effect as unknown (i.e π=0)
term editor: Philippe Rocca-Serra
definition source: A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637029/ doi: 10.1186/1297-9686-41-2. and: Prediction of total genetic value using genome-wide dense marker maps. Meuwissen TH, Hayes BJ, Goddard ME. Genetics. 2001 Apr;157(4):1819-29. PMID: 11290733

Bayes B
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: mixture distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: Bayes B is a data transformation used in the context of estimating breeding value, which relies on a Bayesian model, treats the prior probability π that a SNP has zero effect to a set value (i.e π >0) and uses a mixture distribution.
term editor: Philippe Rocca-Serra
definition source: A fast algorithm for BayesB type of prediction of genome-wide estimates of genetic value. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2637029/ doi: 10.1186/1297-9686-41-2. and: Prediction of total genetic value using genome-wide dense marker maps. Meuwissen TH, Hayes BJ, Goddard ME. Genetics. 2001 Apr;157(4):1819-29. PMID: 11290733

estimated breeding value
type: Class
subclass of: estimate
subclass of: Restriction
  on property: is_specified_output_of
  some values from: breeding value estimation
has curation status: ready for release
definition: the estimated breeding value of an organism is a data item computed to estimate the true breeding value defined as genetic merit of an organism, half of which will be passed on to its progeny. While the exact breeding value can not been known, for performance traits it is possible to make good estimates. These estimates are called Estimated Breeding Values (EBVs). EBVs are expressed in the units of measurement for each particular trait. These estimates are output of various estimation methods which differ depending on the underlying assumptions (equal variance of marker effect, all markers contributing to the trait) , the mathemical methods used (bayesian or non-bayesians) and the genetic inheritance models being considered (additive, dominant, epistatic) selected by the analysts.
term editor: Philippe Rocca-Serra
definition source: adapted from: http://abri.une.edu.au/online/pages/understanding_ebvs_char.htm
STATO alternative term: EBV

additive genetic inheritance model
type: Class
subclass of: genetic inheritance model
has curation status: ready for release
definition: an additive genetic model is a data item which refers to the contributions to the final phenotype from more than one gene, or from alleles of a single gene (in heterozygotes), that combine in such a way that the sum of their effects in unison is equal to the sum of their effects individually.
term editor: Philippe Rocca-Serra

additive dominant genetic inheritance model
type: Class
subclass of: genetic inheritance model
has curation status: ready for release
definition: an additive genetic model is a data item which refer to the contributions to the final phenotype from more than one gene, or from alleles of a single gene (in heterozygotes), that combine in such a way that the sum of their effects in unison is equal to the sum of their individual effects and their dominance effect (of alleles at a single locus).
term editor: Philippe Rocca-Serra

additive dominant genetic and epistatic inheritance model
type: Class
subclass of: genetic inheritance model
has curation status: ready for release
definition: an additive genetic model is a data item which refer to the contributions to the final phenotype from more than one gene, or from alleles of a single gene (in heterozygotes), that combine in such a way that the sum of their effects in unison is equal to the sum of their individual effect, their additive dominant (effect (of alleles at a single locus) and their epistasic effect (of alleles at more different loci).
term editor: Philippe Rocca-Serra

Dunn’s multiple comparison test
type: Class
subclass of: data transformation
subclass of: multiple testing correction method
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: preceded by
  some values from: Class
    union of: ANOVA
    union of: Kruskal Wallis test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: multiple testing correction objective
    intersection of: between group comparison objective
has curation status: ready for release
definition: Dunn’s Multiple Comparison Test is a post hoc (i.e. it’s run after an ANOVA) non parametric test (a “distribution free” test that doesn’t assume your data comes from a particular distribution). It is one of the least powerful of the multiple comparisons tests and can be a very conservative test–especially for larger numbers of comparisons. The Dunn is an alternative to the Tukey test when you only want to test for differences in a small subset of all possible pairs; For larger numbers of pairwise comparisons, use Tukey’s instead. Use Dunn’s when you choose to test a specific number of comparisons before you run the ANOVA and when you are not comparing to controls. If you are comparing to a control group, use the Dunnett test instead.
term editor: Philippe Rocca-Serra
definition source: Dunn, O.J. (1961) Multiple comparisons among means. JASA, 56: 54-64 Dunn, Olive Jean (1964). "Multiple comparisons using rank sums". Technometrics. 6 (3): 241–252. doi:10.2307/1266041 and adapted from: http://www.statisticshowto.com/dunns-test/
STATO alternative term: Dunn's test
R command: ## Default S3 method: dunnTest(x, g, method = dunn.test::p.adjustment.methods[c(4, 2:3, 5:8, 1)], two.sided = TRUE, altp = two.sided, ...) from: http://www.rforge.net/doc/packages/FSA/dunnTest.html

Conover-Iman test of multiple comparisons using rank sums
type: Class
subclass of: data transformation
subclass of: multiple testing correction method
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: preceded by
  some values from: Kruskal Wallis test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: Class
    intersection of: multiple testing correction objective
    intersection of: between group comparison objective
has curation status: ready for release
definition: Conover-Iman test for stochastic dominance is a stastical test for multiple group comparisons and reports the results among multiple pairwise comparisons after a Kruskal-Wallis test for stochastic dominance among k groups (Kruskal and Wallis, 1952). The interpretation of stochastic dominance requires an assumption that the CDF of one group does not cross the CDF of the other. The null hypothesis for each pairwise comparison is that the probability of observing a randomly selected value from the first group that is larger than a randomly selected value from the second group equals one half; this null hypothesis corresponds to that of the Wilcoxon-Mann-Whitney rank-sum test. Like the rank-sum test, if the data can be assumed to be continuous, and the distributions are assumed identical except for a difference in location, Conover-Iman test may be understood as a test for median difference. conover.test accounts for tied ranks. The Conover-Iman test is strictly valid if and only if the corresponding Kruskal-Wallis null hypothesis is rejected.
term editor: Philippe Rocca-Serra
definition source: Conover, W. J. and Iman, R. L. (1979). On multiple-comparisons procedures. Technical Report LA-7677-MS, Los Alamos Scientific Laboratory.
R command: posthoc.kruskal.conover.test(x, …) # S3 method for default posthoc.kruskal.conover.test( x, g, p.adjust.method = p.adjust.methods, …) # S3 method for formula posthoc.kruskal.conover.test(formula, data, subset, na.action, p.adjust.method = p.adjust.methods, …) https://www.rdocumentation.org/packages/PMCMR/versions/4.2/topics/posthoc.kruskal.conover.test conover.test makes k(k-1)/2 multiple pairwise comparisons based on Conover-Iman t-test-statistic of the rank differences.

Bayesian least absolute shrinkage and selection operator
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: Laplace probability distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
example of usage: application to breeding value estimation and genomic selection https://www.ncbi.nlm.nih.gov/pubmed/20122298
has curation status: ready for release
definition: Bayesian LASSO is a data transformation where the regression parameters have independent Laplace (i.e., double-exponential) priors and are used to interprete Lasso estimate for linear regression parameters as Bayesian posterior mode estimates in accordance to a Bayesian framework.
term editor: Philippe Rocca-Serra
definition source: https://www.tandfonline.com/doi/abs/10.1198/016214508000000337
STATO alternative term: Bayes LASSO

genotype matrix
type: Class
subclass of: matrix
subclass of: Restriction
  on property: is about
  some values from: genotype information
has curation status: ready for release
definition: a genotype matrix is a kind of genomic relationship matrix in the rawest of form and which simply corresponds to a matrix of individuals genotype for a given set of markers or genomic positions. Columns are snps or markers, Rows are individuals. Each column/row cell contains a genotype expressed as, in the genome is diploid, as a pair of characters chosen from ATGC where the dominant variant is uppercased and the recessive variant is lower cased.
term editor: Philippe Rocca-Serra
definition source: http://articles.extension.org/pages/68019/genomic-relationships-and-gblup

MAF matrix
type: Class
subclass of: matrix
subclass of: Restriction
  on property: is about
  some values from: genotype information
subclass of: Restriction
  on property: is about
  some values from: genomic coordinate datum
subclass of: Restriction
  on property: computed from
  some values from: genotype matrix
has curation status: ready for release
definition: the MAF matrix is a genomic relationship matrix which is obtained from the genotype matrix by counting the number of minor alleles at each locus
term editor: Philippe Rocca-Serra
definition source: http://articles.extension.org/pages/68019/genomic-relationships-and-gblup
STATO alternative term: MAF matrix
STATO alternative term: gene content matrix
STATO alternative term: matrix of minor allele count

M matrix
type: Class
subclass of: matrix
subclass of: Restriction
  on property: computed from
  some values from: MAF matrix
has curation status: ready for release
definition: the M matrix is a genomic relationship matrix which is obtained by subtracting 1 to every value of the MAF matrix (gene content matrix). The values of the M matrix are only -1, 0 or 1 and makes computation easier. M = MAF-1
term editor: Philippe Rocca-Serra
definition source: http://articles.extension.org/pages/68019/genomic-relationships-and-gblup Efficient Methods to Compute Genomic Predictions. J. Dairy Sci. 91:4414-4423. 2008 P. M. VanRaden. 10.31 68/jds.2007-0980
STATO alternative term: deviation of 1 from the gene content matrix
R command: >M = MAF-1

P matrix
type: Class
subclass of: matrix
subclass of: Restriction
  on property: computed from
  some values from: MAF matrix
has curation status: ready for release
definition: P matrix is a kind of genomic relationship matrix which contains allele frequencies expressed as a difference from 0.5 and multiplied by 2.
term editor: Philippe Rocca-Serra
definition source: http://articles.extension.org/pages/68019/genomic-relationships-and-gblup Efficient Methods to Compute Genomic Predictions. J. Dairy Sci. 91:4414-4423. 2008 P. M. VanRaden. 10.31 68/jds.2007-0980

Z matrix
type: Class
subclass of: matrix
has curation status: ready for release
definition: the Z-matrix is a genomic relationship matrix which is obtained by substracted the M matrix with the P matrix. It is also known as the incidence matrix for the markers.
term editor: Philippe Rocca-Serra
definition source: http://articles.extension.org/pages/68019/genomic-relationships-and-gblup Efficient Methods to Compute Genomic Predictions. J. Dairy Sci. 91:4414-4423. 2008 P. M. VanRaden. 10.31 68/jds.2007-0980
STATO alternative term: incidence matrix for genotyping markers

numerator degrees of freedom
type: Class
subclass of: number of degrees of freedom
subclass of: Restriction
  on property: is_specified_input_of
  some values from: ANOVA
has curation status: ready for release
definition: The degree of freedom numerator is the number of degrees of freedom that the estimate of variance used in the numerator is based on. It is one of the parameters for the F-distribution used to compute probabilities in analysis of variance.
editor note: term request: https://github.com/ISA-tools/stato/issues/71
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
STATO alternative term: df1
STATO alternative term: num df

augmented experimental design
type: Class
subclass of: study design
has curation status: ready for release
definition: augmented design is a kind of experimental design where the goal is to compare existing (control) treatments with new treatments that have an experimental constraint of "limited replication". To understand limited replication, consider about experiments that may only allow a single representation of the new treatment, this limitation may be many times due to the cost associated with the experiment, limited resources, or limited number of new units that can be used in the experiment. In contrast, the existing treatments are referred as checks and are generally replicated multiple times. With augmented design one can estimate the following: a) Differences between checks and new treatments, b) Differences among new treatments, c) Differences among check treatments, and d) Differences among new and check treatments combined.
term editor: Philippe Rocca-Serra
definition source: Federer, W.T. 1956. Augmented (or hoonuiaku) designs. Hawaiian Planters’ Record LV(2): 191–208) http://rna.genomics.purdue.edu/
R command: an example of dataset representing an augmented design: https://www.rdocumentation.org/packages/sommer/versions/3.2/topics/augment

probability distribution location parameter
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: probability distribution
has curation status: ready for release
definition: a probability distribution location parameter is a data item which is set by the operator when selecting a parametric probability distribution and which dictates the way the location but not the profile or size of the distribution plot looks like.
editor note: https://github.com/ISA-tools/stato/issues/50
term editor: Philippe Rocca-Serra
definition source: adapted from: https://docs.scipy.org/doc/scipy/reference/tutorial/stats.html#shifting-and-scaling
Python command: norm.stats(loc=3, scale=4, moments="mv"), where loc is the location parameter indicated how much shift is given

Weibull probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution scale parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution shape parameter
subclass of: Restriction
  on property: is denoted by
  some values from: probability distribution location parameter
has curation status: ready for release
definition: the Weibull probability distribution is continuous probabibility distribution which is used to model time to fail, time to repair and material strength in material science. In biomedicine, the Weibull probability is used to in determining 'hazard functions'. The 'location parameter' of the Weibull probability distribution can be used to define a failure-free zone. If the quantity X is a "time-to-failure", the Weibull distribution gives a distribution for which the failure rate is proportional to a power of time. The shape parameter, k, is that power plus one, and so this parameter can be interpreted directly as follows: A value of {\displaystyle k<1\,} {\displaystyle k<1\,} indicates that the failure rate decreases over time. This happens if there is significant "infant mortality", or defective items failing early and the failure rate decreasing over time as the defective items are weeded out of the population. In the context of the diffusion of innovations, this means negative word of mouth: the hazard function is a monotonically decreasing function of the proportion of adopters; A value of {\displaystyle k=1\,} {\displaystyle k=1\,} indicates that the failure rate is constant over time. This might suggest random external events are causing mortality, or failure. The Weibull distribution reduces to an exponential distribution; A value of {\displaystyle k>1\,} {\displaystyle k>1\,} indicates that the failure rate increases with time. This happens if there is an "aging" process, or parts that are more likely to fail as time goes on. In the context of the diffusion of innovations, this means positive word of mouth: the hazard function is a monotonically increasing function of the proportion of adopters. The function is first concave, then convex with an inflexion point at {\displaystyle (e^{1/k}-1)/e^{1/k},k>1\,} {\displaystyle (e^{1/k}-1)/e^{1/k},k>1\,}.
term editor: Philippe Rocca-Serra
alternative term: Weibull distribution
definition source: adapted from : https://en.wikipedia.org/wiki/Weibull_distribution and from http://www.engineeredsoftware.com/nasa/weibull.htm
STATO alternative term: Weibull probability distribution
R command: pweibull(q, shape, scale = 1, lower.tail = TRUE, log.p = FALSE) from: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/Weibull.html
Python command: scipy.stats.weibull_min from: https://docs.scipy.org/doc/scipy-0.14.0/reference/generated/scipy.stats.weibull_min.html#scipy.stats.weibull_min

statistical sampling
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: study group population
subclass of: Restriction
  on property: has_specified_output
  some values from: statistical sample
has curation status: ready for release
definition: statistical sampling is a planned process which aims at assembling a population of observation units (samples) in as an unbiaised manner as possible in order to obtain or infer information about the actual population these samples have been drawn.
term editor: Philippe Rocca-Serra
definition source: STATO

simple random sampling
type: Class
subclass of: statistical sampling
disjoint with: systematic sampling
has curation status: ready for release
definition: Simple random sampling is a statistical sampling process which creates a sample of a size n entirely by chance. In such process, each unit has the same probability of being selected. Depending on the size of the population being sampled, the sampling process may be done with or without replacement
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Simple_random_sample
STATO alternative term: random sampling
R command: srswor(n,N) from https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/srswor [simple random sampling without replacement] Sampling R package
R command: srswr(n,N) from: https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/srswr [simple random sampling with replacement] Sampling R package

line intercept sampling
type: Class
subclass of: systematic sampling
example of usage: It is a sampling process used, among other things, in ecological studies when studying how things change in an given environment
has curation status: ready for release
definition: line intercept sampling is a sampling process by which an element in a spatial region is included in a sample if it is intersected by a line chosen by the operator.
term editor: Philippe Rocca-Serra
alternative term: LIS
alternative term: LIS sampling
definition source: Lee Kaiser, Biometrics, Vol. 39, No. 4 (Dec., 1983), pp. 965-976 http://www.jstor.org/stable/2531331
STATO alternative term: line intercept sampling

quadrat sampling
type: Class
subclass of: systematic sampling
has curation status: ready for release
definition: Quadrat sampling is a classic tool for the study of ecology, especially biodiversity. In general, a series of squares (quadrats) of a set size are placed in a habitat of interest and the species within those quadrats are identified and recorded. Passive quadrat sampling (done without removing the organisms found within the quadrat) can be either done by hand, with researchers carefully sorting through each individual quadrat or, more efficiently, can be done by taking a photograph of the quadrat for future analysis.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: http://www.coml.org/investigating/observing/quadrat_sampling.html

cluster sampling
type: Class
subclass of: systematic sampling
has curation status: ready for release
definition: Cluster sampling is a sampling plan used when mutually homogeneous yet internally heterogeneous groupings are evident in a statistical population.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Cluster_sampling
R command: cluster(data, clustername, size, method=c("srswor","srswr","poisson", "systematic"),pik,description=FALSE) from: https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/cluster Sampling R package

probability-proportional-to-size sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: Probability proportional to size ('PPS') sampling is a sampling method in which the selection probability for each element is set to be proportional to its size measure, up to a maximum of 1. In a simple PPS design, these selection probabilities can then be used as the basis for Poisson sampling. However, this has the drawback of variable sample size, and different portions of the population may still be over- or under-represented due to chance variation in selections.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Sampling_(statistics)#Probability-proportional-to-size_sampling
STATO alternative term: PPS sampling

stratified sampling
type: Class
subclass of: statistical sampling
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: simple random sampling
    union of: systematic sampling
subclass of: Restriction
  on property: preceded by
  some values from: population stratification prior to sampling
has curation status: ready for release
definition: stratified sampling is a statistical sampling method which divides the population into homogenous subpopulations, which are then sampled using random or systematic sampling methods
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Stratified_sampling
STATO alternative term: stratified sampling
R command: strata(data, stratanames=NULL, size, method=c("srswor","srswr","poisson", "systematic"), pik,description=FALSE) From: https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/strata R Sampling Package

systematic sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: systematic sampling is a process for collecting samples and assembling a statistical sample using a system or method (.e.g unequal probabilities, without replacement, fixed sample size), as opposed to a random sampling.
term editor: Philippe Rocca-Serra
definition source: Madow, W.G. (1949), On the theory of systematic sampling, II, Annals of Mathematical Statistics, 20, 333-354.
R command: from: https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/UPsystematic Sampling R package

quota sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: Quota sampling is a method for selecting survey participants that is a non-probabilistic version of stratified sampling. In quota sampling, a population is first segmented into mutually exclusive sub-groups, just as in stratified sampling. Then judgment is used to select the subjects or units from each segment based on a specified proportion. For example, an interviewer may be told to sample 200 females and 300 males between the age of 45 and 60. This means that individuals can put a demand on who they want to sample (targeting).
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Quota_sampling

panel sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: Panel sampling is the method of first selecting a group of participants through a random sampling method and then asking that group for (potentially the same) information several times over a period of time. Therefore, each participant is interviewed at two or more time points; each period of data collection is called a "wave". The method was developed by sociologist Paul Lazarsfeld in 1938 as a means of studying political campaigns.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Sampling_(statistics)#Panel_sampling

chain-referral sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: Snowball sampling (or chain sampling, chain-referral sampling, referral sampling) is a non-probability sampling technique where existing study subjects recruit future subjects from among their acquaintances. Thus the sample group is said to grow like a rolling snowball.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: from: https://en.wikipedia.org/wiki/Snowball_sampling
STATO alternative term: chain sampling
STATO alternative term: referral sampling
STATO alternative term: snowball sampling

voluntary sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: The voluntary sampling method is a type of non-probability sampling. A voluntary sample is made up of people who self-select into the survey. Often, these subjects have a strong interest in the main topic of the survey. Volunteers may be invited through advertisements on Social Media Sites
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Sampling_(statistics)#Voluntary_Sampling

convenience sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: Convenience sampling (also known as grab sampling, accidental sampling, or opportunity sampling) is a type of non-probability sampling that involves the sample being drawn from that part of the population that is close to hand. This type of sampling is most useful for pilot testing.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: from wikipedia: https://en.wikipedia.org/wiki/Convenience_sampling
STATO alternative term: accidental sampling
STATO alternative term: grab sampling
STATO alternative term: opportunity sampling

Brewer sampling
type: Class
subclass of: systematic sampling
has curation status: ready for release
definition: Brewer's sampling is a statistical sampling method which was proposed by Brewer in 1975 and uses unequal probabibility sampling technique
term editor: Philippe Rocca-Serra
definition source: Brewer, Kenneth RW (1975). A Simple Procedure For Sampling πpswor1. Australian Journal of Statistics, 17(3), 166-172.
R command: UPbrewer(pik,eps=1e-06) from: https://www.rdocumentation.org/packages/sampling/versions/2.8/topics/UPbrewer Sampling R package

minimax sampling
type: Class
subclass of: statistical sampling
has curation status: ready for release
definition: In imbalanced datasets, where the sampling ratio does not follow the population statistics, one can resample the dataset in a conservative manner called minimax sampling. The minimax sampling has its origin in Anderson minimax ratio whose value is proved to be 0.5: in a binary classification, the class-sample sizes should be chosen equally. This ratio can be proved to be minimax ratio only under the assumption of LDA classifier with Gaussian distributions. The notion of minimax sampling is recently developed for a general class of classification rules, called class-wise smart classifiers.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Sampling_(statistics)#Minimax_sampling

complete randomization
type: Class
subclass of: group randomization
has curation status: ready for release
definition: complete randomization is a group randomization where experimental units are randomly assigned to the entire set of groups defined by the experimental treatments.
term editor: Philippe Rocca-Serra
definition source: STATO
R command: crPar(N, K = 2, ratio = rep(1, K), groups = LETTERS[1:K]) from: https://www.rdocumentation.org/packages/randomizeR/versions/1.4/topics/crPar

data imputation
type: Class
subclass of: data transformation
has curation status: ready for release
definition: Data imputation is a data transformation process whereby missing data is replaced with an estimated value for the missing element. The substituted values are intended to create a data record that does not fail edits. Various methods may be used to produce these substituted values.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia and from the OECD glossary of statistical terms https://stats.oecd.org/glossary/detail.asp?ID=3406

last observation carried forward data imputation
type: Class
subclass of: data imputation
has curation status: ready for release
definition: last observation carried forward data imputation is a type of data imputation which uses a very simple, self explanatory method for substituted a missing value for an observation. It should be noted that this method gives a biased estimate of the treatment effect and underestimates the variability of the estimated result and should be used cautiously.
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Analysis_of_clinical_trials#Last_observation_carried_forward

regression data imputation
type: Class
subclass of: data imputation
has curation status: ready for release
definition: regression data imputation is a type of data imputation where missing values are replaced with the value of a regression function coefficient.
term editor: Philippe Rocca-Serra

substitution by the mean data imputation
type: Class
subclass of: data imputation
has curation status: ready for release
definition: substitution by the mean data imputation is a type of data imputation where missing values are replaced with the value the variable mean.
term editor: Philippe Rocca-Serra

multivariate imputation with chained equations
type: Class
subclass of: data imputation
example of usage: https://www.r-bloggers.com/imputing-missing-data-with-r-mice-package/
has curation status: ready for release
definition: multivariate imputation with chained equations (MICE) is a type of data imputation which uses an algorithm devised by Stef van Buuren and Karin Groothuis-Oudshoorn
term editor: Philippe Rocca-Serra
definition source: MICE: Multivariate Imputation by Chained Equations in R by Stef van Buuren and Karin Groothuis-Oudshoorn. Journal of Statistical Software, http://www.stefvanbuuren.nl/publications/mice%20in%20r%20-%20draft.pdf
STATO alternative term: MICE
R command: library(mice) miceMod <- mice(BostonHousing[, !names(BostonHousing) %in% "medv"], method="rf") # perform mice imputation, based on random forests.

k-nearest neighbour data imputation
type: Class
subclass of: data imputation
has curation status: ready for release
definition: k-nearest neighbour imputation is a data imputation which uses the k-nearest neighbour algorithm to compute a substitution value for the missing values. For every observation to be imputed, it identifies ‘k’ closest observations based on the euclidean distance and computes the weighted average (weighted based on distance) of these ‘k’ obs.
term editor: Philippe Rocca-Serra
definition source: adapted from: http://r-statistics.co/Missing-Value-Treatment-With-R.html
STATO alternative term: kNN data imputation
R command: library(DMwR) knnOutput <- knnImputation(BostonHousing[, !names(BostonHousing) %in% "medv"]) # perform knn imputation. anyNA(knnOutput) from: http://r-statistics.co/Missing-Value-Treatment-With-R.html

Matthews correlation coefficient
type: Class
subclass of: correlation coefficient
subclass of: ratio-based measure of association
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    some values from: covariance
  intersection of: Restriction
    on property: has denominator
    some values from: standard deviation
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    some values from: covariance
  intersection of: Restriction
    on property: has denominator
    some values from: Restriction
      on property: is about
      qualified cardinality: 2
      on class: standard deviation
subclass of: Restriction
  on property: is_proxy_for
  some values from: measure of association
has curation status: ready for release
definition: Matthews Correlation Coefficient (or MCC) is a correlation coefficient which is a measure of the quality of binary (two-class) classifications, introduced by biochemist Brian W. Matthews in 1975.
term editor: Philippe Rocca-Serra
alternative term: phi coefficient
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Matthews_correlation_coefficient and from: https://doi.org/10.1016/0005-2795(75)90109-9
STATO alternative term: MCC
R command: mcc(preds = NULL, actuals = NULL, TP = NULL, FP = NULL, TN = NULL, FN = NULL) from: https://www.rdocumentation.org/packages/mltools/versions/0.3.4/topics/mcc

covariance matrix
type: Class
subclass of: matrix
has curation status: ready for release
definition: a covariance matrix is a square matrix that contains the variances and covariances associated with several variables. The diagonal elements of the matrix contain the variances of the variables and the off-diagonal elements contain the covariances between all possible pairs of variables.
term editor: Philippe Rocca-Serra
STATO alternative term: dispersion matrix
STATO alternative term: variance-covariance matrix

numerator relationship matrix
type: Class
subclass of: matrix
example of usage: https://www.r-bloggers.com/setup-up-the-inverse-of-additive-relationship-matrix-in-r/
has curation status: ready for release
definition: the numerator relationship matrix is the matrix of *expected* additive genetic relationships between individuals. This matrix was originally used by Henderson (Henderson, C.R. 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32:69-83.) to account for covariances between random effects, and therefore to use information from relatives in estimation of breeding value. Among the properties of the NRM matrix (also known as the A matrix), it is symmetric, the diagonal value correspond to 1+ the inbreeding coefficient for an individual.
term editor: Philippe Rocca-Serra
alternative term: A matrix
definition source: adapted from: https://jvanderw.une.edu.au/Genetic_properties_of_the_animal_model.pdf and from: Henderson, C.R. 1976. A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32:69-83. https://doi.org/10.2307/2529339
STATO alternative term: NRM
R command: https://rdrr.io/cran/sommer/man/A.mat.html

denominator degrees of freedom
type: Class
subclass of: number of degrees of freedom
subclass of: Restriction
  on property: is_specified_input_of
  some values from: ANOVA
has curation status: ready for release
definition: The degree of freedom denominator is the number of degrees of freedom that the estimate of variance used in the denominator is based on. It is one of the parameters for the F-distribution used to compute probabilities in analysis of variance.
editor note: term request: https://github.com/ISA-tools/stato/issues/71
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
STATO alternative term: den df
STATO alternative term: df2

G matrix
type: Class
subclass of: matrix
has curation status: ready for release
definition: A matrix of relationships among a group of individuals, which can be used to predict breeding values, to manage inbreeding and in genetic conservation. It can be calculated from the pedigree, but it is also possible to calculate the relationship matrix from genotypes at genetic markers such as single-nucleotide polymorphisms (SNPs). Elements of the genomic relationship matrix are estimates of the realized proportion of the genome that two individuals share, whereas the pedigree-derived relationship matrix is the expectation of this proportion.
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.3168/jds.2007-0980
definition source: https://www.ncbi.nlm.nih.gov/pubmed/22059574
STATO alternative term: realized genomic relationship matrix
STATO alternative term: relationship matrix
R command: https://cran.r-project.org/web/packages/snpReady/snpReady.pdf

scaled t distribution
type: Class
subclass of: Student's t distribution
has curation status: ready for release
definition: a scaled t distribution is a kind of Student's t distribution which is shifted by 'mean' and scaled by standard deviation 'sd'.
term editor: Philippe Rocca-Serra
definition source: R documentation
R command: t.scaled(x, df, mean = 0, sd = 1, ncp, log = FALSE) from: https://www.rdocumentation.org/packages/metRology/versions/0.9-23-2/topics/Scaled%20t%20distribution

Bayesian model
type: Class
subclass of: statistical model
subclass of: Restriction
  on property: declares
  some values from: prior probability distribution
has curation status: ready for release
definition: a Bayesian model is a statistical model where inference is based on using Bayes theorem to obtain a posterior distribution for a quantity (or quantities) of interest for some model (such as parameter values) based on some prior distribution for the relevant unknown parameters and the likelihood from the model.
term editor: Philippe Rocca-Serra
definition source: adapted from several sources: Oxford Dictionary of Statistics: 10.1093/acref/9780199541454.001.0001 http://www.scholarpedia.org/article/Bayesian_statistics https://stats.stackexchange.com/questions/129017/what-exactly-is-a-bayesian-model

prior probability distribution
type: Class
subclass of: probability distribution
subclass of: Restriction
  on property: is declared by
  some values from: Bayesian model
has curation status: ready for release
definition: a prior probability distribution is a probability distribution used as input to a Bayesian model to represent a priori knowledge about a model parameter. Along with the acquired/observed data, it is used to compute a posterior distribution according to the Bayes theorem.
term editor: Philippe Rocca-Serra
definition source: Oxford Dictionary of Statistics: 10.1093/acref/9780199541454.001.0001

posterior probability distribution
type: Class
subclass of: data item
subclass of: probability distribution
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: model fitting
    intersection of: Restriction
      on property: has_specified_input
      some values from: Bayesian model
has curation status: ready for release
definition: a posterior probability distribution is a probability distribution computed in a Bayesian model approach given a prior distribution and a set of events/observations.
term editor: Philippe Rocca-Serra
definition source: Oxford Dictionary of Statistics: 10.1093/acref/9780199541454.001.0001

Bayes C pi
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
has curation status: ready for release
definition: Bayes C pi is a data transformation used to compute estimated breeding values using a Bayesian model and which assesses the SNP effect using MonteCarlo Markov chain methods. Bayes C pi treats the prior probability π that a SNP has zero effect as unknown. The method was devised to address short comings of Bayes A and Bayes B approaches
term editor: Philippe Rocca-Serra
definition source: adapted from: BMC Bioinformatics. 2011 May 23;12:186. doi: 10.1186/1471-2105-12-186. Extension of the bayesian alphabet for genomic selection. Habier D, Fernando RL, Kizilkaya K, Garrick DJ. but also https://cran.r-project.org/web/packages/gdmp/gdmp.pdf and https://jvanderw.une.edu.au/RFSlides.pdf
STATO alternative term: Bayes C pi

genetic inheritance model
type: Class
subclass of: statistical model
has curation status: ready for release
definition: genetic inheritance model is a data item defining the assumption used by a breeding value estimation method to consider when running the calculations.
term editor: Philippe Rocca-Serra
definition source: STATO

sampling from a probability distribution
type: Class
subclass of: data transformation
has curation status: ready for release
definition: sampling from a probability distribution is a data transformation which aims at obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult.
term editor: Philippe Rocca-Serra
definition source: STATO

Gibbs sampling
type: Class
subclass of: sampling from a probability distribution
has curation status: ready for release
definition: Gibbs sampling or a Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm for obtaining a sequence of observations which are approximated from a specified multivariate probability distribution, when direct sampling is difficult.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Gibbs_sampling Geman, S.; Geman, D. (1984). "Stochastic Relaxation, Gibbs Distributions, and the Bayesian Restoration of Images". IEEE Transactions on Pattern Analysis and Machine Intelligence. 6 (6): 721–741. doi:10.1109/TPAMI.1984.4767596

Metropolis–Hastings sampling
type: Class
subclass of: sampling from a probability distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: continuous multivariate probability distribution
    union of: discrete multivariate probability distribution
has curation status: ready for release
definition: the Metropolis–Hastings algorithm is a Markov chain Monte Carlo (MCMC) method for obtaining a sequence of random samples from a probability distribution for which direct sampling is difficult.
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Metropolis%E2%80%93Hastings_algorithm Hastings, W.K. (1970). "Monte Carlo Sampling Methods Using Markov Chains and Their Applications". Biometrika. 57 (1): 97–109. doi:10.1093/biomet/57.1.97

continuous multivariate probability distribution
type: Class
subclass of: continuous probability distribution
has curation status: ready for release
definition: a continuous multivariate probability distribution is a continuous probability distribution which describes the possible values, and corresponding probabilities, of two or more (usually three or more) associated random variables.
term editor: Philippe Rocca-Serra
definition source: http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1095

discrete multivariate probability distribution
type: Class
subclass of: discrete probability distribution
has curation status: ready for release
definition: a discrete multivariate probability distribution is a discrete probability distribution which describes the possible values, and corresponding probabilities, of two or more (usually three or more) associated random variables.
term editor: Philippe Rocca-Serra
definition source: http://www.oxfordreference.com/view/10.1093/acref/9780199541454.001.0001/acref-9780199541454-e-1095

reproducing kernel Hilbert space procedure
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
has curation status: ready for release
definition: A data transformation that produces a reproducing kernel Hilbert space (or RKHS), which is a Hilbert space of functions in which point evaluation is a continuous linear functional.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Reproducing_kernel_Hilbert_space
STATO alternative term: RKHS
R command: https://www.rdocumentation.org/packages/KGode/versions/1.0.1/topics/rkhs
R command: rkhs

state space model
type: Class
subclass of: statistical model
has curation status: ready for release
definition: a state space model is a kind of statistical model which describes the probabilistic dependence between the latent state variable and the observed measurement. The state or the measurement can be either continuous or discrete. The term “state space” originated in 1960s in the area of control engineering (Kalman, 1960). SSM provides a general framework for analyzing deterministic and stochastic dynamical systems that are measured or observed through a stochastic process.
term editor: Philippe Rocca-Serra
definition source: http://www.scholarpedia.org/article/State_space_model
STATO alternative term: SSM

genomic estimated breeding value
type: Class
subclass of: estimated breeding value
has curation status: ready for release
definition: genomic estimated breeding value (GEBV) is an estimated breeding value derived from information in an organism DNA (genotype). GEBV is calculated differently to conventional Estimated Breeding Values using advanced modeling technique to deal with high dimensionality data.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: adapted from: https://businesswales.gov.wales/farmingconnect/posts/genomic-breeding-values
STATO alternative term: GEBV

heritability
type: Class
subclass of: ratio
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    some values from: Class
      intersection of: variance
      intersection of: Restriction
        on property: is about
        some values from: genotype information
  intersection of: Restriction
    on property: has denominator
    some values from: Class
      intersection of: variance
      intersection of: Restriction
        on property: is about
        some values from: information content entity
has curation status: ready for release
definition: In a planned experiment where to covariance (genotype x environment) can be controlled and held at 0, the heritability is defined as the ratio of the variance of the genotypic variables to the variance of the phenotypic variables. H2 = Var(G)/Var(P) H2 is the broad-sense heritability. This reflects all the genetic contributions to a population's phenotypic variance including additive, dominant, and epistatic (multi-genic interactions), as well as maternal and paternal effects, where individuals are directly affected by their parents' phenotype, for example, milk production in mammals.
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Heritability
STATO alternative term: H2
STATO alternative term: broad sense heritability

narrow sense heritability
type: Class
subclass of: ratio
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    some values from: Class
      intersection of: variance
      intersection of: Restriction
        on property: is about
        some values from: genotype information
  intersection of: Restriction
    on property: has denominator
    some values from: Class
      intersection of: variance
      intersection of: Restriction
        on property: is about
        some values from: information content entity
has curation status: ready for release
definition: A particularly important component of the genetic variance is the additive variance, Var(A), which is the variance due to the average effects (additive effects) of the alleles. Since each parent passes a single allele per locus to each offspring, parent-offspring resemblance depends upon the average effect of single alleles. Additive variance represents, therefore, the genetic component of variance responsible for parent-offspring resemblance. The additive genetic portion of the phenotypic variance is known as Narrow-sense heritability and is defined as: h2 = Var(A)/Var(P)
term editor: Philippe Rocca-Serra
definition source: https://en.wikipedia.org/wiki/Heritability
STATO alternative term: h2

Bayes R
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: normal distribution
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: Bayes R is a data transformation used in the context of estimating breeding value, which relies on a Bayesian model to compute 'genomic estimated breeding values'. In contrast to Bayes B methods, the new method assumes that the true SNP effects are derived from a series of normal distributions, the first with zero variance, up to one with a variance of approximately 1% of the genetic variance.
term editor: Philippe Rocca-Serra
definition source: Erbe M, Hayes BJ, Matukumalli LK, Goswami S, Bowman PJ, Reich CM, et al. Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels. J Dairy Sci. 2012;95:4114–29 doi: 10.3168/jds.2011-5019. https://www.ncbi.nlm.nih.gov/pubmed/22720968

Laplace probability distribution
type: Class
subclass of: continuous probability distribution
subclass of: symmetric distribution
subclass of: Restriction
  on property: is denoted by
  some values from: Class
    intersection of: skewness
    intersection of: Restriction
      on property: has value
      has value: 0
has curation status: ready for release
definition: The double exponential distribution (a.k.a. Laplace distribution) is the distribution of differences between two independent variates with identical exponential distributions (Abramowitz and Stegun 1972, p. 930).
term editor: Philippe Rocca-Serra
definition source: http://mathworld.wolfram.com/LaplaceDistribution.html
STATO alternative term: double exponential probability distribution
R command: dLaplace(x, mu = 0, b = 1, params = list(mu, b), ...) https://www.rdocumentation.org/packages/ExtDist/versions/0.6-3/topics/Laplace
Python command: https://docs.scipy.org/doc/scipy-0.19.0/reference/generated/scipy.stats.laplace.html

sampling distribution estimation by bootstrapping
type: Class
subclass of: sampling from a probability distribution
has curation status: ready for release
definition: Bootstrapping is the practice of estimating properties of an estimator (such as its variance) by measuring those properties when sampling from an approximating distribution.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Bootstrapping_(statistics)
STATO alternative term: bootstrap

random forest procedure
type: Class
subclass of: data transformation
subclass of: class discovery data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: class discovery objective
has curation status: ready for release
definition: random forest procedure is a type of data transformation used in classification and statistical learning using regression. The random forest procedure is a meta estimator that fits a number of classifying decision trees on various sub-samples of the dataset (it operates by constructing a multitude of decision trees at training time) and use averaging to improve the predictive accuracy and control over-fitting. The sub-sample size is always the same as the original input sample size but the samples are drawn with replacement if bootstrap=True (default). The random forest procedure outputs the class that is the mode of the classes (classification) or mean prediction (regression) of the individual trees.
term editor: Philippe Rocca-Serra
definition source: adapted from: https://en.wikipedia.org/wiki/Random_forest and http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestRegressor.html
STATO alternative term: random forest
R command: # S3 method for formula randomForest(formula, data=NULL, ..., subset, na.action=na.fail) # S3 method for default randomForest(x, y=NULL, xtest=NULL, ytest=NULL, ntree=500, mtry=if (!is.null(y) && !is.factor(y)) max(floor(ncol(x)/3), 1) else floor(sqrt(ncol(x))), replace=TRUE, classwt=NULL, cutoff, strata, sampsize = if (replace) nrow(x) else ceiling(.632*nrow(x)), nodesize = if (!is.null(y) && !is.factor(y)) 5 else 1, maxnodes = NULL, importance=FALSE, localImp=FALSE, nPerm=1, proximity, oob.prox=proximity, norm.votes=TRUE, do.trace=FALSE, keep.forest=!is.null(y) && is.null(xtest), corr.bias=FALSE, keep.inbag=FALSE, ...) # S3 method for randomForest print(x, ...) from https://www.rdocumentation.org/packages/randomForest/versions/4.6-14/topics/randomForest
Python command: sklearn.ensemble.RandomForestClassifier(n_estimators=10, criterion=’gini’, max_depth=None, min_samples_split=2, min_samples_leaf=1, min_weight_fraction_leaf=0.0, max_features=’auto’, max_leaf_nodes=None, min_impurity_decrease=0.0, min_impurity_split=None, bootstrap=True, oob_score=False, n_jobs=1, random_state=None, verbose=0, warm_start=False, class_weight=None) from: http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestClassifier.html
Python command: sklearn.ensemble.RandomForestRegressor(n_estimators=10, criterion=’mse’, max_depth=None, min_samples_split=2, min_samples_leaf=1, min_weight_fraction_leaf=0.0, max_features=’auto’, max_leaf_nodes=None, min_impurity_decrease=0.0, min_impurity_split=None, bootstrap=True, oob_score=False, n_jobs=1, random_state=None, verbose=0, warm_start=False) from: http://scikit-learn.org/stable/modules/generated/sklearn.ensemble.RandomForestRegressor.html

log likelihood
type: Class
subclass of: data item
has curation status: ready for release
definition: log likelihood is a data item which corresponds to the natural logarithm of the likelihood. log likelihood is a data item commonly used to provide a measure of accuracy of a model.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia
R command: ogLik(object, ...) ## S3 method for class 'lm' logLik(object, REML = FALSE, ...) from: https://stat.ethz.ch/R-manual/R-patched/library/stats/html/logLik.html

Holm false discovery rate correction
type: Class
subclass of: false discovery rate correction method
has curation status: ready for release
definition: A data transformation process in which the Holm p-value procedure is applied with the aim of correcting false discovery rate
term editor: Philippe Rocca-Serra
definition source: Holm, S. (1979). A simple sequentially rejective multiple test procedure. Scandinavian Journal of Statistics, 6, 65–70. http://www.jstor.org/stable/4615733.
STATO alternative term: Holm fdr
R command: p.adjust(p, method = holm, n = length(p)) from: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html

Hommel false discovery rate correction
type: Class
subclass of: false discovery rate correction method
has curation status: ready for release
definition: A data transformation process in which the Hommel p-value procedure is applied with the aim of correcting false discovery rate
term editor: Philippe Rocca-Serra
definition source: Hommel, G. (1988). A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika, 75, 383–386. doi: 10.2307/2336190
STATO alternative term: Hommel fdr
R command: p.adjust(p, method = hommel, n = length(p)) from: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html

number of cross-validation segments
type: Class
subclass of: count
has curation status: pending final vetting
definition: number of cross-validation segments is a count which is used as input parameter in a cross validation procedure to evaluate a statistical model.
term editor: Philippe Rocca-Serra

number of predictive components
type: Class
subclass of: count
has curation status: pending final vetting
definition: number of predictive components is a count used as input to the principle component analysis (PCA)
term editor: Philippe Rocca-Serra

number of orthogonal components
type: Class
subclass of: count
has curation status: pending final vetting
definition: number of orthogonal components is a count used as input to the orthogonal partial least square discriminant analysis (OPLS-DA)
term editor: Philippe Rocca-Serra

statistical model term testing
type: Class
subclass of: data transformation
has curation status: requires discussion
definition: A statistical model term testing is a data transformation that accounts for the evaluation of a component of a statistical model or model term.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: STATO

Wald test
type: Class
subclass of: chi square test
subclass of: Restriction
  on property: has_specified_input
  some values from: false positive rate
subclass of: Restriction
  on property: has_specified_input
  some values from: covariance matrix
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
has curation status: ready for release
definition: the Wald test is statistical test which computes a Wald chi-squared test for 1 or more coefficients, given their variance-covariance matrix. The Wald test (also called the Wald Chi-Squared Test) is a way to find out if explanatory variables in a model are significant. “Significant” means that they add something to the model; variables that add nothing can be deleted without affecting the model in any meaningful way
term editor: Philippe Rocca-Serra
R command: Wald test for a term in a regression model: regTermTest(model, test.terms, null=NULL,df=Inf, method=c("Wald","LRT")) from: http://r-survey.r-forge.r-project.org/survey/html/regTermTest.html
R command: wald.test(Sigma, b, Terms = NULL, L = NULL, H0 = NULL, df = NULL, verbose = FALSE) from: https://www.rdocumentation.org/packages/aod/versions/1.3/topics/wald.test

Rao's score
type: Class
subclass of: statistic
has curation status: ready for release
definition: the Rao-Scott score is a statistic which is used to test the hypothesis that all coefficients associated with a particular regression term are zero (or have some other specified values). the LRT uses a linear combination of chi-squared distributions
term editor: Philippe Rocca-Serra
alternative term: Lagrange multiplier test
alternative term: Rao-Scott test
definition source: Rao, JNK, Scott, AJ (1984) "On Chi-squared Tests For Multiway Contingency Tables with Proportions Estimated From Survey Data" Annals of Statistics 12:46-60.
STATO alternative term: Rao score test
R command: regTermTest(model, test.terms, null=NULL,df=Inf, method=c("Wald","LRT")) from: http://r-survey.r-forge.r-project.org/survey/html/regTermTest.html

confidence level
type: Class
subclass of: dimensionless ratio
has curation status: ready for release
definition: the frequency (i.e., the proportion) of possible confidence intervals that contain the true value of their corresponding parameter. In other words, if confidence intervals are constructed using a given confidence level in an infinite number of independent experiments, the proportion of those intervals that contain the true value of the parameter will match the confidence level. A probability measure of the reliability of an inferential statistical test that has been applied to sample data and which is provided along with the confidence interval for the output statistic.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Confidence_interval and from: http://www.oxfordreference.com/view/10.1093/acref/9780191792236.001.0001/acref-9780191792236-e-103?rskey=tQCMI6&result=1

standard error of estimate
type: Class
subclass of: measure of dispersion
subclass of: estimate
subclass of: Restriction
  on property: estimate of
  some values from: statistic
example of usage: http://davidmlane.com/hyperstat/A121160.html
has curation status: ready for release
definition: The standard error is a measure of dispersion applied to estimates across hypothetical repeated random samples. It is a measure of how precise an estimate of a statistical parameter is. The standard error is the estimated standard deviation of an estimate. It measures the uncertainty associated with the estimate. Compared with the standard deviations of the underlying distribution, which are usually unknown, standard errors can be calculated from observed data.
term editor: Harold Lehmann, Kenneth Wilkins, Brian S. Alper, Xing Song, Joanne Dehnbostel, Muhammad Afzal, Philippe Rocca-Serra
definition source: adapted from wikipedia and from SAGE research method article http://methods.sagepub.com/reference/encyc-of-research-design/n435.xml
STATO alternative term: standard error of the estimate

biplot
type: Class
subclass of: graph
has curation status: ready for release
definition: Biplots are a type of exploratory graph used in statistics, a generalization of the simple two-variable scatterplot. A biplot is constructed by using the singular value decomposition (SVD) to obtain a low-rank approximation to a transformed version of the data matrix X, whose n rows are the samples (also called the cases, or objects), and whose p columns are the variables. The biplot was introduced by K. Ruben Gabriel (1971).
term editor: Philippe Rocca-Serra
definition source: Gabriel, K. R. (1971). The biplot graphic display of matrices with application to principal component analysis. Biometrika, 58(3), 453–467. adapted from: https://en.wikipedia.org/wiki/Biplot Last accessed: 04/07/2018
R command: biplot(x, y, var.axes = TRUE, col, cex = rep(par("cex"), 2), xlabs = NULL, ylabs = NULL, expand = 1, xlim = NULL, ylim = NULL, arrow.len = 0.1, main = NULL, sub = NULL, xlab = NULL, ylab = NULL, ...) from: http://stat.ethz.ch/R-manual/R-devel/library/stats/html/biplot.html last accessed: 04/07/2018

coefficient of determination
type: Class
subclass of: statistic
has curation status: ready for release
definition: The coefficient of determination is a data item measuring the proportion of the variance in the dependent variable that is predictable from the independent variable(s). In the case of a linear regression mode, the coefficient of determination r2 is the quotient of the variances of the fitted values and observed values of the dependent variable.
alternative term: r2
R command: > eruption.lm = lm(eruptions ~ waiting, data=faithful) > summary(eruption.lm)$r.squared from: http://www.r-tutor.com/elementary-statistics/simple-linear-regression/coefficient-determination

regression coefficient
type: Class
subclass of: measure of association
has curation status: ready for release
definition: a regression coefficient is a measure of association that is used as the coefficient of an independent variable in a regression model, of the dependent variable, which is linear in its parameters. A value of zero means no association. The sign (positive or negative) reflects the direction of association. a regression coefficient is a measure of association generated by a type of data transformation called a regression, which aims to model a response variable by expression the predictor variables as part of a function where variable terms are modified by a number. A regression coefficient is one such number.
editor note: Expert Working Group Agreement: 2023-02-07 vote 5-0 by Cauê Monaco, Harold Lehmann, Mario Tristan, Jesus Lopez-Alcalde, Eric Harvey
editor note: Harold Lehmann, Brian S. Alper, Kenneth Wilkins, Muhammad Afzal
term editor: Philippe Rocca-Serra

eigen value
type: Class
subclass of: data item
subclass of: clustered data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: principal components analysis dimensionality reduction
has curation status: ready for release
definition: An eigenvalue is a data item resulting from a data transformation known as eigen value decomposition. It also corresponds to a process of matrix diagonalization or any equivalent operation, ie. transforming the underlying system of equations into a special set of coordinate axes in which the matrix takes this canonical form. Each eigenvalue is paired with a corresponding so-called eigenvector.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: adapted from: http://mathworld.wolfram.com/Eigenvalue.html last accessed: 04/07/2018
R command: eigen(x, symmetric, only.values = FALSE, EISPACK = FALSE) https://stat.ethz.ch/R-manual/R-devel/library/base/html/eigen.html
Python command: In Python numpy linear algebra package (numpy.linalg) https://docs.scipy.org/doc/numpy-1.13.0/reference/routines.linalg.html linalg.eig(a) Compute the eigenvalues and right eigenvectors of a square array. linalg.eigh(a[, UPLO]) Return the eigenvalues and eigenvectors of a Hermitian or symmetric matrix. linalg.eigvals(a) Compute the eigenvalues of a general matrix. linalg.eigvalsh(a[, UPLO]) Compute the eigenvalues of a Hermitian or real symmetric matrix.

factor analysis
type: Class
subclass of: dimensionality reduction
subclass of: Restriction
  on property: has_specified_output
  some values from: loadings
subclass of: Restriction
  on property: has_specified_output
  some values from: score
definition: Factor analysis is a dimension reduction data transformation that is used to describe variability among observed, correlated variables in terms of a potentially lower number of unobserved variables called factors. Factor analysis is related to principal component analysis (PCA), but the two are not identical. Both PCA and factor analysis aim to reduce the dimensionality of a set of data, but the approaches taken to do so are different for the two techniques. Factor analysis is clearly designed with the objective to identify certain unobservable factors from the observed variables, whereas PCA does not directly address this objective; at best, PCA provides an approximation to the required factors.
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: https://en.wikipedia.org/wiki/Factor_analysis last accessed: 04/07/2018 Cattell, R. B. (1952). Factor analysis. New York: Harper
R command: factanal(x, factors, data = NULL, covmat = NULL, n.obs = NA, subset, na.action, start = NULL, scores = c("none", "regression", "Bartlett"), rotation = "varimax", control = NULL, ...)
R command: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/factanal.html

loadings
type: Class
subclass of: clustered data set
subclass of: model parameter
subclass of: Restriction
  on property: is_specified_output_of
  some values from: principal components analysis dimensionality reduction
has curation status: ready for release
definition: In factor analysis, factor loadings express the relationship of each variable to the underlying factor.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Serra-Serra
definition source: https://en.wikipedia.org/wiki/Factor_analysis
definition source: https://www.theanalysisfactor.com/factor-analysis-1-introduction/
STATO alternative term: factor loadings
R command: https://stat.ethz.ch/R-manual/R-devel/library/stats/html/loadings.html

score
type: Class
subclass of: clustered data set
subclass of: statistic
subclass of: Restriction
  on property: is_specified_output_of
  some values from: principal components analysis dimensionality reduction
has curation status: ready for release
definition: The score indicates how sensitive a likelihood function L(\Theta,X) is to its parameter \Theta. Explicitly, the score for \Theta is the gradient of the log-likelihood with respect to \Theta.
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Serra-Serra
definition source: https://en.wikipedia.org/wiki/Score_(statistics)
definition source: https://www.rdocumentation.org/packages/bnlearn/versions/4.3/topics/score
STATO alternative term: efficient score
STATO alternative term: informant
STATO alternative term: score function
R command: score

selectivity ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: The selectivity ratio (SR) is defined as the ratio of explained vexpl,i to residual variance vres,i for the variable i on the target projection (TP) component in the context of Partial Least Squares Analysis.
term editor: Philippe Rocca-Serra
definition source: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cem.1289
STATO alternative term: selectivity ratio

Partial Least Square regression
type: Class
subclass of: data transformation
subclass of: class discovery data transformation
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: non-iterative Partial Least Squares
    union of: SIMPLS
subclass of: Restriction
  on property: has_specified_input
  some values from: continuous variable
subclass of: Restriction
  on property: has_specified_input
  some values from: number of orthogonal components
subclass of: Restriction
  on property: has_specified_output
  some values from: partial least square weight
subclass of: Restriction
  on property: has_specified_output
  some values from: regression coefficient
subclass of: Restriction
  on property: has_specified_output
  some values from: loadings
subclass of: Restriction
  on property: has_specified_output
  some values from: score
subclass of: Restriction
  on property: has_specified_output
  some values from: selectivity ratio
subclass of: Restriction
  on property: has_specified_output
  some values from: variable importance in projection
has curation status: ready for release
definition: Partial least squares regression (PLS regression) is a data transformation that bears some relation to principal components regression; instead of finding hyperplanes of maximum variance between the response and independent variables, it finds a linear regression model by projecting the predicted variables and the observable variables to a new space. Because both the X and Y data are projected to new spaces, the PLS family of methods are known as bilinear factor models. Partial least squares Discriminant Analysis (PLS-DA) is a variant used when the Y is categorical. PLS is used to find the fundamental relations between two matrices (X and Y), i.e. a latent variable approach to modeling the covariance structures in these two spaces. A PLS model will try to find the multidimensional direction in the X space that explains the maximum multidimensional variance direction in the Y space. PLS regression is particularly suited when the matrix of predictors has more variables than observations, and when there is multicollinearity among X values. By contrast, standard regression will fail in these cases (unless it is regularized). Partial least squares was introduced by the Swedish statistician Herman O. A. Wold, who then developed it with his son, Svante Wold. An alternative term for PLS (and more correct according to Svante Wold[1]) is projection to latent structures, but the term partial least squares is still dominant in many areas. Although the original applications were in the social sciences, PLS regression is today most widely used in chemometrics and related areas. It is also used in bioinformatics, sensometrics, neuroscience and anthropology.
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
alternative term: PLS
definition source: adapted from wikipedia: last accessed on 24/07/2018 from: https://en.wikipedia.org/wiki/Partial_least_squares_regression
STATO alternative term: Partial least squares analysis
R command: https://rpubs.com/omicsdata/pls
Python command: http://scikit-learn.org/stable/modules/generated/sklearn.cross_decomposition.PLSRegression.html

Partial Least Square Discriminant Analysis
type: Class
subclass of: data transformation
subclass of: class discovery data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: categorical variable
subclass of: Restriction
  on property: has_specified_input
  some values from: number of orthogonal components
subclass of: Restriction
  on property: has_specified_output
  some values from: regression coefficient
subclass of: Restriction
  on property: has_specified_output
  some values from: loadings
subclass of: Restriction
  on property: has_specified_output
  some values from: score
has curation status: ready for release
definition: a version of PLS used for classification, where the input y-block are group labels (categorical variable) rather than a continuous variable
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
alternative term: PLS-DA
definition source: adapted from wikipedia
STATO alternative term: partial least squares discriminant analysis
R command: # S3 method for default plsda(x, y, ncomp = 2, probMethod = "softmax", prior = NULL, ...) https://www.rdocumentation.org/packages/caret/versions/6.0-80/topics/plsda
Python command: http://scikit-learn.org/stable/modules/generated/sklearn.cross_decomposition.PLSRegression.html

average value
type: Class
subclass of: measure of central tendency
has curation status: ready for release
definition: The arithmetic mean is defined as the sum of the numerical values of each and every observation divided by the total number of observations. S The arithmetic mean A is defined by the formula A=sum[Ai] / n where i ranges from 1 to n and Ai represents the value of individual observations. The arithmetic mean is significantly affected by extreme values and outliers. A better measure of central tendency is the median (http://purl.obolibrary.org/obo/STATO_0000574).
editor note: replaced OBI import following addition of restrictions and use in STATO. however the xref to OBI is kept as class metadata
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: STATO
STATO alternative term: arithmetic mean
Python command: http://docs.scipy.org/doc/numpy/reference/generated/numpy.mean.html
see also: average value (http://purl.obolibrary.org/obo/OBI_0000679)

center value
type: Class
subclass of: measure of central tendency
subclass of: quartile
has curation status: ready for release
definition: The median is that value of the variate which divides the total frequency into two halves. The median is measure of central tendency of data. It is obtained by arranging the observations in order from smallest to largest value. If there is an odd number of observations, the median is the middle value. If there is an even number of observations, the median is the average of the two middle values.
editor note: PRS and AGB added restriction about 'measure of central tendency' and quartile, june 2013 on 'centre value' OBI class.
editor note: replaced OBI import following addition of restrictions and use in STATO. however the xref to OBI is kept as class metadata
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
alternative term: second quartile
definition source: A Dictionary of Statistical Terms, 5th edition, prepared for the International Statistical Institute by F.H.C. Marriott. Published for the International Statistical Institute by Longman Scientific and Technical. and Wolfram Alpha
STATO alternative term: median
see also: center value (http://purl.obolibrary.org/obo/OBI_0000674)

non-iterative Partial Least Squares
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: part of
  some values from: Class
    union of: principal component regression
    union of: Partial Least Square regression
has curation status: metadata incomplete
definition: a data transformation which finds principal component by applying non-linear iterative partial least squares algorithm
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
alternative term: NIPALS
definition source: https://cran.r-project.org/web/packages/nipals/vignettes/nipals_algorithm.pdf
R command: nipals(x, ncomp = min(nrow(x), ncol(x)), center = TRUE, scale = TRUE, maxiter = 500, tol = 1e-06, startcol = 0, fitted = FALSE, force.na = FALSE, gramschmidt = TRUE, verbose = FALSE) https://www.rdocumentation.org/packages/mixOmics/versions/6.3.2/topics/nipals

SIMPLS
type: Class
subclass of: data transformation
has curation status: metadata incomplete
definition: A novel algorithm for partial least squares (PLS) regression, SIMPLS, is proposed which calculates the PLS factors directly as linear combinations of the original variables. The PLS factors are determined such as to maximize a covariance criterion, while obeying certain orthogonality and normalization restrictions. This approach follows that of other traditional multivariate methods. The construction of deflated data matrices as in the nonlinear iterative partial least squares (NIPALS)-PLS algorithm is avoided. For univariate y SIMPLS is equivalent to PLS1 and closely related to existing bidiagonalization algorithms. This follows from an analysis of PLS1 regression in terms of Krylov sequences. For multivariate Y there is a slight difference between the SIMPLS approach and NIPALS-PLS2. In practice the SIMPLS algorithm appears to be fast and easy to interpret as it does not involve a breakdown of the data sets. The acronym SIMPLS comes from 'straightforward implementation of a statistically inspired modification of the PLS method'
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Alejandra Gonzalez-Beltran
term editor: Philippe Rocca-Serra
definition source: SIMPLS: An alternative approach to partial least squares regression Sijmen de Jong https://doi.org/10.1016/0169-7439(93)85002-X
STATO alternative term: straightforward implementation of a statistically inspired modification of the PLS method
R command: simpls(X, Y, ncomp, stripped = FALSE, ...) https://www.rdocumentation.org/packages/cocorresp/versions/0.3-0/topics/simpls

PLS1
type: Class
subclass of: Partial Least Square regression
has curation status: ready for release
definition: a partial least square regression applied when there is only one variable in Y (the matrix of response variables), or it is desirable to model and optimize separately the performance of each of the variables in Y. This case is usually referred to as PLS1 regression (J = 1).
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
definition source: A comparison of nine PLS1 algorithms, Martin Andersson. https://doi.org/10.1002/cem.1248
R command: plsreg1(x, y, nc = 2, cv = FALSE) https://www.rdocumentation.org/packages/plspm/versions/0.2-2/topics/plsreg1

PLS2
type: Class
subclass of: Partial Least Square regression
has curation status: ready for release
definition: a partial least square regression applied to a multivariate response variable.
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
definition source: a partial least square regression applied when there Y matrix of response variables is truely multivariate (J >1)
definition source: https://doi.org/10.1016/0003-2670(86)80028-9
R command: plsreg2(X, Y, nc = 2) https://www.rdocumentation.org/packages/plspm/versions/0.2-2/topics/plsreg2

improved Kernel PLS
type: Class
subclass of: data transformation
has curation status: ready for release
definition: improved kernel PLS is a data transformation which implement a very fast kernel algorithm for updating PLS models in a recursive manner and for exponentially discounting past data.
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
definition source: https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291099-128X%28199701%2911%3A1%3C73%3A%3AAID-CEM435%3E3.0.CO%3B2-%23
R command: kernelpls.fit(X, Y, ncomp, stripped = FALSE, ...) https://www.rdocumentation.org/packages/pls/versions/2.6-0/topics/kernelpls.fit

variable importance in projection
type: Class
subclass of: statistic
has curation status: ready for release
definition: variable importance in projection is a measure computed as part of a partial least square regression to accumulate the importance of each variable j being reflected by w from each component.
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
alternative term: VIP
definition source: https://doi.org/10.1016/j.chemolab.2012.07.010 and S. Wold, E. Johansson, M. Cocchi PLS: Partial Least Squares Projections to Latent Structures, 3D QSAR in drug design, 1 (1993), pp. 523-550
R command: vip(object) https://www.rdocumentation.org/packages/mixOmics/versions/6.3.2/topics/vip

singular value decomposition
type: Class
subclass of: data transformation
has curation status: ready for release
definition: a data transformation which compute the singular-value decomposition of a rectangular matrix. The singular-value decomposition is very general in the sense that it can be applied to any m × n matrix whereas eigenvalue decomposition can only be applied to certain classes of square matrices.
editor note: term request from Ralf Weber and Gavin Lloyd, University of Birmingham
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Singular-value_decomposition last accessed: 24/08/2018
R command: svd(x, nu = min(n, p), nv = min(n, p), LINPACK = FALSE) https://www.rdocumentation.org/packages/base/versions/3.5.1/topics/svd
Python command: numpy.linalg.svd(a, full_matrices=True, compute_uv=True) https://docs.scipy.org/doc/numpy-1.14.0/reference/generated/numpy.linalg.svd.html

best linear unbiased estimator
type: Class
subclass of: data transformation
subclass of: model parameter estimation
subclass of: breeding value estimation
subclass of: Restriction
  on property: has_specified_input
  some values from: genetic inheritance model
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: data set
    intersection of: Restriction
      on property: has part
      some values from: genotype information
subclass of: Restriction
  on property: has_specified_output
  some values from: model parameter estimate
subclass of: Restriction
  on property: has_specified_output
  some values from: estimated breeding value
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: best linear unbiased estimator
term editor: Philippe Rocca-Serra
definition source: Henderson C. R., 1984 Applications of Linear Models in Animal Breeding. University of Guelph, Guelph, Ontario, Canada. ftp://tech.obihiro.ac.jp/suzuki/Henderson.pdf
STATO alternative term: BLUE
STATO alternative term: best linear unbiaised estimator of the fixed effect

completely randomized design
type: Class
subclass of: realizable entity
subclass of: study design
subclass of: Restriction
  on property: realized in
  some values from: complete randomization
example of usage: https://www.ncbi.nlm.nih.gov/pubmed/24033541 "An experiment was conducted to investigate the effect of a prebiotic on performance of partridge. The experiment was carried out with a total of eighty-day-old male Chukar partridge (Alectoris chukar chukar) chicks in a completely randomized design. The dietary treatments consisted of a control and an experimental treatment, and each treatment was replicated four times with 10 chicks per replicate."
has curation status: ready for release
definition: a completely randomized design is a type of design of experiment where the observation unit receive treatments (independent variable level) entirely at random. In other words, the observations unit are randomly assigned to treatments. Completely randomized designs differ from randomized complete block design and should not be confused as in the latter, a blocking variable is first use to assign experimental units to blocks. Then only, the members of each block are then randomly assigned to different treatment groups
editor note: term request by Hanna Cwiek, https://github.com/ISA-tools/stato/issues/61
term editor: Philippe Rocca-Serra
definition source: adapted from http://www.stat.yale.edu/Courses/1997-98/101/expdes.htm and from A Dictionary of Statistics (3 ed.) , Graham Upton and Ian Cook Publisher: Oxford University Press Print Publication Date: 2014 Print ISBN-13: 9780199679188
R command: http://animsci.agrenv.mcgill.ca/StatisticalMethodsII/R/crd/index.html

Wald statistic
type: Class
subclass of: statistic
subclass of: Restriction
  on property: is_specified_input_of
  some values from: Wald test
has curation status: ready for release
definition: the Wald statistic is a statistic is used during a Wald test, a test of significance of the regression coefficient; it is based on the asymptotic normality property of maximum likelihood estimates, and is computed as: W = b * 1/Var(b) * b In this formula, b stands for the parameter estimates, and Var(b) stands for the asymptotic variance of the parameter estimates. The Wald statistic is tested against the Chi-square distribution in the Wald test.
editor note: term request from Hanna Cwiek: https://github.com/ISA-tools/stato/issues/67
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia and http://documentation.statsoft.com/STATISTICAHelp.aspx?path=glossary/GlossaryTwo/W/WaldStatistic

degree of freedom calculation
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: part of
  some values from: statistical test hypothesis
subclass of: Restriction
  on property: has_specified_output
  some values from: number of degrees of freedom
has curation status: ready for release
definition: degree of freedom calculation is a data transformation which is part of a stastical test and which aims to determine or estimate the number of degrees of freedom in a system.
editor note: term request from Hanna Cwiek: https://github.com/ISA-tools/stato/issues/68
term editor: Philippe Rocca-Serra
definition source: STATO

restricted randomized design
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: realized in
    some values from: restricted randomization
  intersection of: Restriction
    on property: declares
    some values from: blocking variable
subclass of: realizable entity
subclass of: study design
subclass of: block design
has curation status: ready for release
definition: a restricted randomized design is a kind of study design which uses randomization to allocate observation unit to treatment but where intuitively poor allocations of treatments to experimental units are avoided, while retaining the theoretical benefits of randomization. This is often the case when so-called 'hard to change' factors are used in an experimental design.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia

percentage of variance
type: Class
subclass of: clustered data set
subclass of: percentage
subclass of: Restriction
  on property: is_specified_output_of
  some values from: principal component regression
example of usage: https://www.nature.com/articles/srep35323/tables/1
has curation status: ready for release
definition: the percentage of variance is an output of principal component analysis (PCRA), which is obtained by forming the ratio of an eigen-value divided by the sum of all eigen-values. This produces a "percentage of variance" for each eigen-vector.
term editor: Philippe Rocca-Serra
definition source: adapted from: https://stats.stackexchange.com/questions/31908/what-is-percentage-of-variance-in-pca
STATO alternative term: PoV
Python command: http://scikit-learn.org/stable/modules/generated/sklearn.decomposition.PCA.html

scaled identity covariance structure
type: Class
subclass of: covariance structure
has curation status: ready for release
definition: the scaled identity covariance structure is a type of covariance structure which has constant variance. The assumption is that there is no correlation between any elements.
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
definition source: adapted from https://www.ibm.com/support/knowledgecenter/en/SSLVMB_24.0.0/spss/advanced/covariance_structures.html

TPM-transcript per million
type: Class
subclass of: count
has curation status: ready for release
definition: TPM, which stands for Transcript Per Million, is a data item produced during a normilization procedure of RNA-Seq data (i.e. transcription profiling reads produced by nucleic acid sequencing) and corresponds to the count per length of transcript (kb) per million reads mapped. -TPM considers the gene length and sequencing depth for normalization -TPM proposed as an alternative to RPKM due to inaccuracy in RPKM measurement (Wagner et al., 2012) -TPM is suitable for sequencing protocols where reads sequencing depends on gene length -TPM is RPKM scaled by a constant to make sure the sum of all values is 1 million. -TPM (transcript per million) = 1,000,000*θi/(ℓi*c), where c is a constant value, sum_[j](θj/ℓj), sum_[i]TPM=1,000,000 Recommended use: -TPM measure is suited for gene count comparisons within a sample or between samples of the same sample group. -TPM measure is NOT suited for Differential Expression analysis.
term editor: Philippe Rocca-Serra
alternative term: TPM
definition source: https://www.biostars.org/p/273537/ http://www.arrayserver.com/wiki/index.php?title=TPM https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html
term tracker item: https://github.com/ISA-tools/stato/issues/79 and https://github.com/mcourtot/FAIRPlus_squad2/issues/50
elucidation: TPM-transcript per million
STATO alternative term: TPM

median of the ratios corrected count
type: Class
subclass of: count
has curation status: ready for release
definition: median of the ratios corrected count is kind of count produced during an RNA-Seq data normalization procedure which corresponds to dividing counts by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene. It was first described by Anders and Huber in 2010 (https://doi.org/10.1186/gb-2010-11-10-r106) Recommended use: -"median of the ratios corrected count" is suited for Differential Expression analysis or between samples. -"median of the ratios corrected count" is NOT suited for gene count comparisons within a sample.
term editor: Philippe Rocca-Serra
definition source: https://doi.org/10.1186/gb-2010-11-10-r106
STATO alternative term: median of the ratios of observed counts

TMM-trimmed mean of M-values corrected count
type: Class
subclass of: count
has curation status: ready for release
definition: TMM or Trimmed Mean of M-Values is a measurement datum which is the output of the TMM normalization procedure for RNA-Seq data proposed by Robinson and Oshlack (2010). A scaling normalization method for differential expression analysis of RNA-seq data. The TMM procedure is doubly trimmed, by log-fold-changes (sample k relative to sample r for gene g) and by absolute intensity (A g ). It was first release as part of the R package edgeR, 10.1093/bioinformatics/btp616 Recommended use: -TMM measure is suited for gene count comparisons within a sample or between samples of the same sample group. -TMM measure is suited for Differential Expression analysis.
term editor: Philippe Rocca-Serra
alternative term: TMM
definition source: https://doi.org/10.1186/gb-2010-11-3-r25 and https://doi.org/10.1093/bioinformatics/btp616 and https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html
STATO alternative term: TMM
R command: "calcNormFactors"(object, method=c("TMM","RLE","upperquartile","none"), refColumn=NULL, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10, p=0.75, ...) from: https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/calcNormFactors

Rand index
type: Class
subclass of: ratio
has curation status: ready for release
definition: the Rand index is a ratio, related to the notion of accuracy (STATO_0000415), which is used to compare the similarity of two clustering outcomes.
term editor: Philippe Rocca-Serra
alternative term: RI
definition source: Rand, W.M. 1971. Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association 66: 846--850. Hubert, L. and Arabie, P. 1985. Comparing partitions. Journal of Classification. 2: 193--218.
STATO alternative term: Rand index
R command: rand.index(group1, group2) from: https://www.rdocumentation.org/packages/fossil/versions/0.3.7/topics/rand.index

adjusted Rand index
type: Class
subclass of: Rand index
has curation status: ready for release
definition: the adjusted Rand index is a measure which rescales the Rand index, taking into account that random chance will cause some objects to occupy the same clusters, so the Rand Index will never actually be zero.
term editor: Philippe Rocca-Serra
alternative term: ARI
STATO alternative term: ARI
R command: adj.rand.index(group1, group2) from: https://www.rdocumentation.org/packages/fossil/versions/0.3.7/topics/rand.index

confusion matrix
type: Class
subclass of: matrix
subclass of: Class
  intersection of: Restriction
    on property: is about
    qualified cardinality: 1
    on class: dichotomous variable
  intersection of: Restriction
    on property: is about
    qualified cardinality: 1
    on class: Class
      intersection of: categorical variable
      intersection of: Restriction
        on property: specifies value of
        qualified cardinality: 2
        on class: data item
has curation status: ready for release
definition: a confusion matrix is a 2 by 2 contingency table used to evaluate the performance of a classifier, often a machine-learning classifier and that allows visualization of the performance of an algorithm, typically a supervised learning one. It defines two dimensions ("actual" and "predicted"), and identical sets of "classes" in both dimensions (each combination of dimension and class is a variable in the contingency table).
term editor: Philippe Rocca-Serra
alternative term: ready for release
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Confusion_matrix last accessed: 22.10.2019
STATO alternative term: ready for release
R command: https://www.rdocumentation.org/packages/caret/versions/3.45/topics/confusionMatrix from: https://www.rdocumentation.org/packages/caret/versions/3.45/topics/confusionMatrix

number of true positive
type: Class
subclass of: count
has curation status: ready for release
definition: the number of true positive is a count which denotes how many elements are correctly classified as having a feature they are actually known to be having (e.g. carrier of a pathogen).
term editor: Philippe Rocca-Serra
definition source: STATO

number of false positive
type: Class
subclass of: count
has curation status: ready for release
definition: the number of false positive is a count which denotes how many elements known to be void of feature are wrongly classified as having it (e.g. being diagnosed with a disease when one is totally healthy)
term editor: Philippe Rocca-Serra
definition source: STATO

number of true negative
type: Class
subclass of: count
has curation status: ready for release
definition: the number of true negative is a count which denotes how many elements are correctly classified as void of a feature they are actually known to be missing (e.g. free of pathogen).
term editor: Philippe Rocca-Serra
definition source: STATO

number of false negative
type: Class
subclass of: count
has curation status: ready for release
definition: the number of false negative is a count which denotes how many elements known to be having a feature are wrongly classified as being devoided of it (e.g. being given an all clear while being actually infected and carrier of a pathogen)
term editor: Philippe Rocca-Serra
definition source: STATO

point estimate
type: Class
subclass of: estimate
has curation status: ready for release
definition: a point estimate is a data item which provides a particular value evaluating a population parameter
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
term editor: Tom Nichols
term tracker item: https://github.com/ISA-tools/stato/issues/74

interval estimate
type: Class
subclass of: estimate
has curation status: ready for release
definition: an interval estimate is a data item corresponding to a range of values likely to contain the population parameter of interest
term editor: Hanna Cwiek
term editor: Philippe Rocca-Serra
term tracker item: https://github.com/ISA-tools/stato/issues/74

simultaneous multiple testing correction
type: Class
subclass of: multiple testing correction method
definition: simultaneous multiple testing method is a multiple testing correction method which...

sequential multiple testing correction method
type: Class
subclass of: multiple testing correction method
definition: sequential multiple testing method is a multiple testing correction method which...

alpha debt
type: Class
subclass of: sequential multiple testing correction method
definition: a sequential multiple correction procedure which does not maintain a constant false positive rate but allows it to grow controllably.
definition source: Thompson et al 2019. doi: http://dx.doi.org/10.1101/801696 https://www.biorxiv.org/content/biorxiv/early/2019/10/22/801696.full.pdf

alpha investing procedure
type: Class
subclass of: sequential multiple testing correction method
definition: a type of sequential multiple testing correction method
definition source: Aharoni, Ehud, and Saharon Rosset. 2014. “Generalized α -investing: definitions, optimality results and application to public databases.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 76 (4): 771–94. https: //doi.org/10.1111/rssb.12048.
definition source: Foster, Dean P, and Robert A Stine. 2008. “α-Investing: A procedure for sequential control of expected false discoveries.” Journal of the Royal Statistical Society. Series B: Statistical Methodology 70 (2): 429–44. https://doi.org/10. 1111/j.1467-9868.2007.00643.x.

alpha spending procedure
type: Class
subclass of: sequential multiple testing correction method
definition: a type of sequential multiple testing correction
definition source: Aharoni, Ehud, and Saharon Rosset. 2014. “Generalized α -investing: definitions, optimality results and application to public databases.” Journal of the Royal Statistical Society: Series B (Statistical Methodology) 76 (4): 771–94. https: //doi.org/10.1111/rssb.12048.

q-statistic
type: Class
subclass of: statistic
has curation status: metadata complete
definition: q is the basic statistic for the studentized range distribution, which is used for multiple comparison procedures, such as the single step procedure Tukey's range test, the Newman–Keuls method, and the Duncan's step down procedure, and establishing confidence intervals that are still valid after data snooping has occurred
term editor: Philippe Rocca-Serra
definition source: Student (1927). "Errors of routine analysis". Biometrika. 19 (1/2): 151–164. doi:10.2307/2332181
definition source: https://en.wikipedia.org/wiki/Studentized_range
STATO alternative term: studentized range

proportion
type: Class
subclass of: ratio
definition: a proportion is a ratio which corresponds to the fraction of the total presenting a particular feature
definition source: COKA group

area under the receiver operator characteristic curve
type: Class
subclass of: area under curve
subclass of: Restriction
  on property: denotes
  some values from: receiver operational characteristics curve
has curation status: ready for release
definition: An area under the curve where the curve is the true positive rate and the range of interest is the false positive rate.
term editor: Harold Lehmann, Kenneth Wilkins, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin
term editor: Philippe Rocca-Serra
alternative term: AUC
alternative term: AUROC
alternative term: C-statistic
alternative term: Harrell's C
alternative term: c-statistic
alternative term: concordance index
alternative term: concordance statistic
definition source: SEVCO group
R command: https://www.rdocumentation.org/packages/yardstick/versions/1.3.1/topics/roc_auc roc_auc()

measure of hypothesis testing
type: Class
subclass of: statistic
definition source: COKA/SEVCO group

measure of association
type: Class
subclass of: statistic
has curation status: ready for release
definition: measure of association is a statistic which quantitatively represents a relationship between two or more variables
editor note: Expert Working Group Agreement: 2022-03-16 vote 7-0 by Mario Tristan, Paola Rosati, Louis Leff, nisha mathew, Philippe Rocca-Serra, Harold Lehmann, Janice Tufte
term editor: Brian S. Alper, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal, Neeraj Ojha
definition source: COKA group

measure of correlation
type: Class
subclass of: measure of association
definition: measure of correlation is a measure of association between ordinal or continuous variables. A value of 0 means no association. A positive value means a positive association (as one variable increases, the other variable increases). A negative value means a negative association (as one variable increases, the other variable decreases). For correlation coefficients, the possible values range from +1 (perfect positive association) to -1 (perfect negative association)
editor note: Expert Working Group Agreement: 2022-11-16 vote 5-0 by Brian S. Alper, Philippe Rocca-Serra, Harold Lehman, Jesus Lopez-Alcalde, Eric Harvey
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao, Kenneth Wilkins, Harold Lehmann
alternative term: correlation
definition source: COKA group

Goodman and Kruskal's gamma
type: Class
subclass of: correlation coefficient
definition: A measure of correlation, ranging from -1 to 1, that measures the strength and direction of the relationship between ranks by value of two ordinal or continuous variables, and is calculated based on the difference in the number of concordant and discordant pairs of rankings divided by the total number of pairs of rankings, where ties are not counted among the pairs of rankings.
editor note: Expert Working Group Agreement: 2023-01-25 vote 5-0 by Mario Tristan, Jesus Lopez-Alcalde, Joanne Dehnbostel, Harold Lehmann, Eric Harvey
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel
alternative term: Goodman-Kruskal gamma
alternative term: gamma coefficient
alternative term: gamma statistic
definition source: adapted from: https://stats.stackexchange.com/questions/18112/how-do-the-Goodman-Kruskal-gamma-and-the-Kendall-tau-or-Spearman-rho-correlation

difference
type: Class
subclass of: statistic
definition: A statistic that is a subtraction of one quantity from another.
editor note: Expert Working Group Agreement: 2021-12-01 vote 5-0 by Philippe Rocca-Serra, Paola Rosati, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte
term editor: Harold Lehmann, Brian S. Alper, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra, Kenneth Wilkins, Joanne Dehnbostel, Janice Tufte
definition source: COKA group

absolute difference
type: Class
subclass of: difference
definition: A statistic that is a subtraction of one quantity from another, with no modification of the resulting value. As a type of statistic, "Absolute Difference" is the actual difference between two quantities and can be positive or negative depending on the order of subtraction. The term "Absolute Difference" should not be confused with the mathematical term 'absolute value' which is a numerical value without a negative sign.
editor note: Expert Working Group Agreement: 2021-12-01 vote 5-0 by Philippe Rocca-Serra, Paola Rosati, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte
term editor: Brian S. Alper, Harold Lehmann, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal, Khalid Shahin, Janice Tufte
definition source: COKA/SEVCO group

relative difference
type: Class
subclass of: difference
definition: A statistic that is a difference between 1 and a ratio of the two quantities being compared. Relative Difference = 1 - ( a / b ). Because 1 - ( a / b ) is not equal to 1 - ( b / a ), Relative Difference may be expressed as "Relative Difference with respect to b" when referring to 1 - ( a / b ). The relative difference can also be defined as a statistic that is a ratio of the absolute difference (of the two quantities being compared) to the reference value (one of the quantities being compared). Relative Difference = ( b - a ) / ( b ) where b is the reference value and this may also be called "Relative Difference with respect to b".
editor note: Expert Working Group Agreement: 2022-06-29 vote 5-0 by Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Harold Lehmann, Eric Harvey
term editor: Brian S. Alper, Muhammad Afzal, Kenneth Wilkins, Joanne Dehnbostel
definition source: COKA group

count difference
type: Class
subclass of: absolute difference
definition: A statistic that is a subtraction of one count from another. The term Count Difference is used to specify the Absolute Difference is with respect to a count or number of items (such as number of events, platelet counts, sample size e.g. number of people in the group) to distinguish from differences in other types of statistics (mean difference, median difference, risk difference, etc.)
editor note: Expert Working Group Agreement: 2021-12-15 vote 6-0 by Robin Ann Yurk, Janice Tufte, Paola Rosati, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal
term editor: Harold Lehmann, Brian S. Alper, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra, Kenneth Wilkins, Joanne Dehnbostel, Janice Tufte
definition source: COKA group

median difference
type: Class
subclass of: absolute difference
definition: A difference that is a subtraction of one median from another.
editor note: Expert Working Group Agreement: 2021-12-01 vote 6-0 by Philippe Rocca-Serra, Paola Rosati, Robin Ann Yurk, Joanne Dehnbostel, Jesus Lopez-Alcalde, Janice Tufte
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Janice Tufte, Muhammad Afzal, Kenneth Wilkins
alternative term: difference in median
definition source: COKA group

Cohen's d
type: Class
subclass of: standardized mean difference
has curation status: ready for release
definition: A standardized mean difference which is calculated as a difference between two means, divided by a square root of an average of the variances of the two groups. In Cohen's d statistic, the statistical measure of dispersion is specified as the square root of an average of the variances of the two groups being compared. The variances of the two groups are based on within-group standard deviations. For sample sizes < 50, a correction factor is used.
editor note: Expert Working Group Agreement: 2022-07-20 vote 5-0 by Philippe Rocca-Serra, Mario Tristan, Jesus Lopez-Alcalde, Harold Lehmann, Eric Harvey
term editor: Harold Lehmann, Brian S. Alper, Kenneth Wilkins, Muhammad Afzal, Joanne Dehnbostel
definition source: COKA/SEVCO

negative predictive value
type: Class
subclass of: proportion
definition: A proportion in which the numerator represents the correctly non-detected items within the denominator that represents all items not detected.
editor note: Expert Working Group Agreement: 2022-01-26 vote 8-0 by Robin Ann Yurk, Janice Tufte, Harold Lehmann, Philippe Rocca-Serra, Paola Rosati, Mario Tristan, Brian S. Alper, Jesus Lopez-Alcalde
editor note: In a population of people with and without a disease, and a test which is positive (suggesting the disease) or negative (suggesting not having the disease), the negative predictive value is the proportion of true negatives (all people without the disease who test negative) within all the people with a negative test (true negatives plus false negatives). NPV = TN / (TN + FN).
term editor: Harold Lehmann, Ken Wilkins, Philippe Rocca-Serra, Joanne Dehnbostel
definition source: COKA/SEVCO

risk
type: Class
subclass of: proportion
definition: A proportion in which the numerator represents the cases in which an event or characteristic occurs and the denominator represents all possible cases.
editor note: Expert Working Group Agreement: 2022-06-29 vote 6-0 by Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Janice Tufte, Harold Lehmann, Eric Harvey
editor note: In the English language, 'risk' may be used synonymously with 'hazard', 'chance', 'likelihood', 'relative likelihood', 'probability' and many other terms. In SEVCO the term 'risk' is explicitly defined for how it is used in other terms such as 'Risk Ratio' and 'Relative Risk Difference' The statistical definition of 'risk' does not have a negative or undesirable connotation.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte
definition source: COKA/SEVCO

diagnostic yield
type: Class
subclass of: proportion
definition: diagnostic yield is a proportion in which the numerator represents the correctly detected items within the denominator that represents all items tested.
editor note: 2022-08-10 vote 5-0 by Philippe Rocca-Serra, Mario Tristan, Harold Lehmann, Eric Harvey, Paola Rosati
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins
definition source: "Diagnostic yield was defined as the number of participants with positive findings for advanced neoplasia relative to all participants" in https://pubs.rsna.org/doi/10.1148/radiol.12112486 Other 'definitions' found include synonymous use with sensitivity, and 'diagnostic yield' describing the statistic array of TP, FP, TN, and FN data.

ratio-based measure of association
type: Class
equivalent class: Class
  intersection of: Class
    intersection of: Restriction
      on property: has numerator
      some values from: data item
    intersection of: Restriction
      on property: has denominator
      some values from: data item
  intersection of: Restriction
    on property: is_proxy_for
    some values from: measure of association
subclass of: ratio
subclass of: measure of association
has curation status: ready for release
definition: ratio-based measure of association is a measure of association which relies on a quotient of 2 quantities to indicate the strength of the association.
definition source: COKA group

measure of agreement
type: Class
subclass of: measure of association
has curation status: ready for release
definition: A measure of association of two variables representing measurements of the same attribute of an entity.
editor note: Expert Working Group Agreement: 2022-12-21 vote 5-0 by Mario Tristan, Philippe Rocca-Serra, Eric Harvey, Janice Tuft, Harold Lehmann
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel
definition source: COKA/SEVCO/STATO

Gini index
type: Class
subclass of: measure of dispersion
definition: The Gini index, or Gini coefficient, is a statistical measure of dispersion which assesses the pattern of data in a frequency distribution, in particular it measures the inequality among values. Geometrically, the Gini index can be defined as the ratio of 2 areas delineated by 2 curves, the line of equality (curve 1) and the Lorenz curve (curve 2). The numerator of the ratio corresponds to the area defined between curve 1 and curve 2 , while the denominator corresponds to the entire area below curve 1. Mathematically, the Gini index is defined as half of the relative mean absolute difference. It was therefore originally used to assess income inequality and is named after the italian statistician Corrado Gini who published it in 1912.
definition source: COKA group
R command: https://search.r-project.org/CRAN/refmans/dineq/html/gini.wtd.html

relative mean difference
type: Class
subclass of: relative difference
definition: A statistic that is a difference between 1 and a ratio of the two mean values being compared. Relative Mean Difference = 1 - ( a / b ) where a and b are mean values. The relative mean difference can also be defined as a statistic that is a ratio of the difference in means to the reference mean value. Relative Mean Difference = ( b - a ) / ( b ) where b is the reference mean value and a is another mean value.
editor note: Expert Working Group Agreement: 2022-06-29 vote 6-0 by Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Janice Tufte, Harold Lehmann, Eric Harvey
term editor: Brian S. Alper, Muhammad Afzal, Kenneth Wilkins, Joanne Dehnbostel
definition source: COKA group

relative risk difference
type: Class
subclass of: relative difference
definition: A statistic that is a difference between 1 and a ratio of the two risk values being compared. Relative Risk Difference = 1 - ( a / b ) where a and b are risk values. The relative risk difference can also be defined as a statistic that is a ratio of the risk difference to the risk used as a reference. Relative Risk Difference = ( b - a ) / ( b ) where b is the reference risk value and a is another risk value.
term editor: Expert Working Group Agreement: 2022-06-22 vote 6-0 by Mario Tristan, Eric M Harvey, Jesus Lopez-Alcalde, Robin Ann Yurk, Paola Rosati, Janice Tufte
definition source: COKA group

odds
type: Class
subclass of: ratio
has curation status: ready for release
definition: odds correspond to a ratio in which the numerator represents the probability that an event will occur and the denominator represents the probability that an event will not occur. 'Odds' and 'Odds ratio' are different terms. 'Odds' is a ratio of probabilities. 'Odds ratio' is a ratio of two different odds. Odds are calculated as p / (1-p) where p is the probability of event occurrence. When p = 0, the odds = 0. When p = 1, the odds may be expressed as not calculable or as "odds against = 0". Odds may be expressed as p:(1-p). Odds may be expressed as p:q where q = 1-p. Odds may be expressed as a:b where a and b are multiples of p and (1-p). Examples of different expressions of the same odds include 3:2, 3/2, 0.6:0.4, 0.6/0.4, and 1.5. Odds may be expressed as "odds for" or "odds in favor" (e.g. 1:5 for a "3" on a 6-sided die) or "odds against" (e.g. 5:1 against a "3" on a 6-sided die). The term "betting odds" used in gambling that involves financial amounts in the formulation is not an "Odds" in the definition of the Scientific Evidence Code System.
editor note: Expert Working Group Agreement: 2022-03-22 vote 5-0 by Muhammad Afzal, Jesus Lopez-Alcalde, Philippe Rocca-Serra, Mario Tristan, Robin Ann Yurk
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Kenneth Wilkins, Muhammad Afzal

F1 score
type: Class
subclass of: F-beta score
example of usage: https://pubmed.ncbi.nlm.nih.gov/35508113/
has curation status: ready for release
definition: A ratio representing the harmonic mean of recall and precision. The F1-score is used as a measure of quality for classification algorithms and information retrieval strategies, where 1 represents the best precision and recall and 0 represents the worst precision and recall. A harmonic mean of a set of quantities is the reciprocal of the arithmetic mean of the reciprocals of each quantity. The F score is thus calculated as 1 / (the arithmetic mean of the reciprocals), or: F = 1 / ( ( (1/recall) + (1/precision) ) / 2 ) F = 2*( (precision*recall) / (precision+recall) ) Recall is sensitivity STATO:0000233 Precision (PPV) is STATO:0000416
editor note: Expert Working Group Agreement: 2022-10-19 vote 6-0 by Joanne Dehnbostel, Muhammad Afzal, Jesus Lopez-Alcalde, Mario Tristan, Eric Harvey, Harold Lehmann
editor note: term request: https://github.com/ISA-tools/stato/issues/93
term editor: Harold Lehmann, Kenneth Wilkins, Muhammad Afzal, Joanne Dehnbostel, Brian S. Alper, Philippe Rocca-Serra
alternative term: F score
alternative term: F-measure
alternative term: F-score
alternative term: F1 measure
alternative term: F1-score
Python command: sklearn.metrics.f1_score(y_true, y_pred, *, labels=None, pos_label=1, average='binary', sample_weight=None, zero_division='warn') source: https://scikit-learn.org/stable/modules/generated/sklearn.metrics.f1_score.html

Scott's pi
type: Class
subclass of: kappa
has curation status: ready for release
definition: A Kappa statistic where the expected agreement between two raters is expressed in terms of the square of arithmetic means of marginal proportions of each assessment category. Scott's pi is a kappa statistic for two raters that assumes the likelihood of each category for assignment is based on the same distribution of rater responses, leading to the use of squared arithmetic means of the marginal proportion of each assessment category as its estimate of "chance agreement." Pr(expected) is calculated using squared "joint proportions" which are squared arithmetic means of the marginal proportions of each assessment category, in contrast to Cohen's Kappa which uses squared geometric means. Scott's pi = ( p[a] - p[e] ) / ( 1 - p[e] ) where p[a] is the observed percent agreement and p[e] is the expected chance agreement expressed as the squared joint proportions of the marginal sums.
editor note: Expert Working Group Agreement: 2022-10-19 vote 6-0 by Joanne Dehnbostel, Muhammad Afzal, Jesus Lopez-Alcalde, Mario Tristan, Eric Harvey, Harold Lehmann
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins

Cohen's kappa
type: Class
subclass of: kappa
has curation status: ready for release
definition: A Kappa statistic in which the expected agreement by chance is based on an assumption that the likelihood of each category for assignment is based on the proportion observed, and the number of raters is 2.
editor note: Expert Working Group Agreement: 2022-09-14 vote 6-0 by Nisha Mathew, Philippe Rocca-Serra, Harold Lehmann, Eric Harvey, Jesus Lopez-Alcalde, Khalid Shahin
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins
alternative term: Cohen's kappa statistic
definition source: COKA/SEVCO/STATO

modified Cohen’s kappa for more than 2 raters
type: Class
subclass of: kappa
has curation status: ready for release
definition: A Kappa statistic in which the expected agreement by chance is based on an assumption that the likelihood of each category for assignment is based on the proportion observed, and the number of raters is more than 2. A Kappa statistic is a measure of agreement among categorical assessments, corrected for chance agreement. In the modified Cohen's kappa for more than 2 raters, the expected chance agreement is modeled as the summation of the differences, between the square of the expected probability of the category and the quotient of its variance divided by the number of raters, for each category. The modified Cohen's kappa for more than 2 raters is calculated as ( p[a] - p[e] ) / ( 1 - p[e] ) where p[a] is the observed percent agreement and p[e] is the expected chance agreement.
editor note: Expert Working Group Agreement: 2022-09-14 vote 5-0 by Nisha Mathew, Philippe Rocca-Serra, Harold Lehmann, Eric Harvey, Jesus Lopez-Alcalde
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins

misclassification rate
type: Class
subclass of: measure of agreement
has curation status: ready for release
definition: A ratio of the number of incorrect results to the total number tested.
editor note: Expert Working Group Agreement: 2022-10-19 vote 5-0 by Joanne Dehnbostel, Muhammad Afzal, Janice Tufte, Mario Tristan, Eric Harvey
term editor: Brian S. Alper, Muhammad Afzal, Joanne Dehnbostel
alternative term: classification error
definition source: COKA/SEVCO/STATO

cutoff
type: Class
subclass of: information content entity
has curation status: requires discussion
definition: a cutoff is an information content entity that represents or sets the boundary at which something changes.
editor note: Expert Working Group Agreement: 5/5 as of 10/11/2021: Janice Tufte, Joanne Dehnbostel, Louis Leff, Vignesh Subbian, Robin Ann Yurk
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Kenneth Wilkins, Khalid Shahin
alternative term: cutoff point
alternative term: cutoff value
alternative term: limit
alternative term: threshold value
definition source: COKA/SEVCO

reciprocal of difference
type: Class
subclass of: statistic
has curation status: ready for release
definition: A statistic that is a quotient of one and a difference.
editor note: Expert Working Group Agreement: 2022-07-20 vote 5-0 by Philippe Rocca-Serra, Mario Tristan, Jesus Lopez-Alcalde, Harold Lehmann, Eric Harvey
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel
definition source: COKA/SEVCO

number needed to treat
type: Class
subclass of: reciprocal of difference
has curation status: requires discussion
definition: A statistic that represents the number of units that needs to be treated to prevent one additional undesired outcome. The Number Needed to Treat is calculated as the reciprocal of a treatment effect estimate, where the effect estimate is expressed as a risk difference. The Number Needed to Treat (NNT) value is often rounded up to the next highest whole integer
editor note: Expert Working Group Agreement: 2022-07-20 vote 7-0 by Cauê Monaco, Janice Tufte, Philippe Rocca-Serra, Mario Tristan, Jesus Lopez-Alcalde, Harold Lehmann, Eric Harvey
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte
alternative term: NTT
alternative term: NTTB
alternative term: number needed to treat to benefit
definition source: COKA/SEVCO

number needed to screen to prevent
type: Class
subclass of: reciprocal of difference
example of usage: Number needed to screen was then calculated by dividing the number needed to treat for treating risk factors by the prevalence of disease that was unrecognised or untreated. https://www.bmj.com/content/317/7154/307.long
has curation status: ready for release
definition: A statistic that represents the number of units that needs to be tested to prevent one additional adverse outcome, assuming that positive testing will lead to preventive intervention. The Number Needed to Screen to Prevent is calculated as the Number Needed to Treat divided by the prevalence. Comment for application: The Number Needed to Screen (NNS) value is often rounded up to the next highest whole integer. The Number Needed to Screen to Detect is distinct from the Number Needed to Screen to Prevent as the formulas to calculate are different, even though both may be abbreviated as NNS. The formula may be adjusted for test performance characteristics (e.g. dividing by the sensitivity) or assumptions regarding acceptance or adherence of interventions.
editor note: Expert Working Group Agreement: 2022-08-03 vote 5-0 by Jesus Lopez-Alcalde, Janice Tufte, Eric Harvey, Philippe Rocca-Serra, Harold Lehmann
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte
alternative term: NNS
definition source: Number needed to screen was then calculated by dividing the number needed to treat for treating risk factors by the prevalence of disease that was unrecognised or untreated. https://www.bmj.com/content/317/7154/307.long

number needed to screen to detect
type: Class
subclass of: reciprocal of difference
has curation status: ready for release
definition: A statistic that represents the number of units that needs to be tested to identify one additional case. The Number Needed to Screen to Detect is calculated as the reciprocal of a difference in rate of detected cases with and without screening. The Number Needed to Screen (NNS) value is often rounded up to the next highest whole integer. The Number Needed to Screen to Detect is distinct from the Number Needed to Screen to Prevent as the formulas to calculate are different, even though both may be abbreviated as NNS.
editor note: Expert Working Group Agreement: 2022-08-03 vote 5-0 by Jesus Lopez-Alcalde, Janice Tufte, Eric Harvey, Philippe Rocca-Serra, Harold Lehmann
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte
alternative term: NNS

number needed to harm
type: Class
subclass of: reciprocal of difference
has curation status: requires discussion
definition: A statistic that represents the number of units that, if treated or exposed to the intervention, lead to one additional undesired outcome. The Number Needed to Harm is calculated as the reciprocal of a treatment effect estimate, where the effect estimate is expressed as a risk difference.
alternative term: NNH
alternative term: NNTH
alternative term: number needed to treat to harm
definition source: https://www.cebm.ox.ac.uk/resources/ebm-tools/glossary

percentage
type: Class
subclass of: ratio
has curation status: ready for release
definition: A ratio formed between a numerator and a denominator (both described by the same unit), and that is multiplied by 100.
editor note: Expert Working Group Agreement: 2022-01-07 vote 7-0 by Harold Lehmann, Robin Ann Yurk, Janice Tufte, C P Ooi, Louis Leff, Jesus Lopez-Alcalde, Mario Tristan
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Janice Tufte, Muhammad Afzal, Khalid Shahin, Philippe Rocca-Serra
alternative term: %
definition source: COKA/SEVCO/STATO

log-rank test
type: Class
subclass of: statistical test hypothesis
subclass of: data transformation
subclass of: survival analysis data transformation
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: survival analysis objective
has curation status: ready for release
definition: The logrank test is a statistical hypothesis test used to compare the survival distributions of two or more groups. It is commonly employed in survival analysis, where the primary interest lies in comparing the survival experiences of different groups over time.
term editor: Philippe Rocca-Serra
alternative term: Mantel-Cox test
alternative term: logrank test
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Logrank_test AND adapted from ChatGPT3.5 with the following prompt: "Please define 'logrank Test' in statistics"

Friedman test
type: Class
subclass of: data transformation
subclass of: between group comparison statistical test
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: between group comparison objective
has curation status: requires discussion
definition: The Friedman test is a non-parametric statistical test used to determine whether there are statistically significant differences among multiple related groups. It is an extension of the Wilcoxon signed-rank test for more than two related samples.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia https://en.wikipedia.org/wiki/Friedman_test and adapted from ChatGPT3.5 with the following prompt: "Please define 'Friedman Test' in statistics"

matrix
type: Class
subclass of: information content entity
has curation status: ready for release
definition: a matrix is a rectangular array of numbers, which are called entries of the matrix.
term editor: Philippe Rocca-Serra
definition source: adapted from: https://en.wikipedia.org/wiki/Matrix_(mathematics)

variance for sample
type: Class
subclass of: variance
subclass of: Restriction
  on property: denotes
  some values from: statistical sample
has curation status: ready for release
definition: the sample variance is a variance computed over the actual observations made, which correspond to a sample drawn from a population in an experiment. the sample variance can be used to estimate the true variance of the underlying population/distribution.
editor note: Expert Working Group Agreement: 2023-11-20 vote 5-0 by Brian S. Alper, Jesus Lopez-Alcalde, Harold Lehmann, Muhammad Afzal, Eric Harvey
term editor: Kenneth Wilkins, Brian S. Alper, Muhammad Afzal
alternative term: sample variance
definition source: STATO and COKA group: adapted from: https://guilhermejacob.github.io/2020/06/variance-sampling/

sign test
type: Class
subclass of: statistical test hypothesis
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: statistical hypothesis test objective
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: paired observation comparison objective
has curation status: ready for release
definition: The sign test is a non-parametric hypothesis test used to assess whether the median of a single population is equal to a specified value, typically referred to as the null hypothesis. The sign test is particularly useful when the data are not normally distributed or when the assumptions required for parametric tests are not met. Note that the 'sign test' is related but different from the "Wilcoxon signed rank test'. Sign test: It does not assume any specific distribution for the data. It only requires paired data and makes no assumptions about the shape of the underlying distribution. Wilcoxon signed-rank test: It assumes that the differences between paired observations come from a symmetric distribution. It's also more powerful than the sign test when the distribution is continuous and symmetric.
term editor: Philippe Rocca-Serra
definition source: adapted from wikipedia and adapted from ChatGPT3.5

rate
type: Class
subclass of: ratio
has curation status: ready for release
definition: A ratio in which the numerator represents any quantity and the denominator represents an interval of time.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal
definition source: COKA/SEVCO Group

population variance
type: Class
subclass of: variance
definition: the population variance is a variance of the true population from which a sample is derived. the population variance describes the variability of a characteristic in the population.
term editor: Philippe Rocca-Serra
alternative term: distribution variance
definition source: STATO and COKA group adapted from : https://guilhermejacob.github.io/2020/06/variance-sampling/

standard error of the proportion
type: Class
subclass of: standard error of estimate
has curation status: ready for release
definition: A measure of dispersion applied to proportions across hypothetical repeated random samples. A standard error is used to quantify the uncertainty around a statistical estimate due to random sampling error.
editor note: Expert Working Group Agreement: 2024-01-22 vote 5-0 by Homa Keshavarz, Eric Harvey, Brian S. Alper, Harold Lehmann, Yasser Sami Amer
term editor: Brian S. Alper, Kenneth Wilkins, Xing Song, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal
definition source: COKA/SEVCO group

standard error of the difference between independent means
type: Class
subclass of: standard error of estimate
has curation status: ready for release
definition: A measure of dispersion applied to differences between means of independent groups across hypothetical repeated random samples. A standard error is used to quantify the uncertainty around a statistical estimate due to random sampling error.
editor note: Expert Working Group Agreement: 2024-02-12 vote 5-0 by Lenny Vasanthan, Xing Song, Eric Harvey, Harold Lehmann, Homa Keshavarz
term editor: Harold Lehmann, Kenneth Wilkins, Brian S. Alper
definition source: COKA/SEVCO group

standard error of the difference between independent proportions
type: Class
subclass of: standard error of estimate
has curation status: ready for release
definition: A measure of dispersion applied to differences between proportions arising from independent groups across hypothetical repeated random samples. A standard error is used to quantify the uncertainty around a statistical estimate due to random sampling error.
editor note: Expert Working Group Agreement: 2024-02-12 vote 5-0 by Lenny Vasanthan, Xing Song, Eric Harvey, Harold Lehmann, Homa Keshavarz.
term editor: Harold Lehmann, Kenneth Wilkins, Brian S. Alper
definition source: COKA/SEVCO group

sampling variance
type: Class
subclass of: variance
subclass of: estimate
subclass of: Restriction
  on property: is about
  some values from: statistical sampling
subclass of: Restriction
  on property: estimate of
  some values from: population variance
definition: sampling variance refers to the variability in the estimates of a population parameter that arises from random sampling. sampling variance is a variance of the sampling distribution of a random variable and estimates the dispersion of sample estimates about their expected value in hypothetical repetitions of the sample.
definition source: STATO and COKA group. adapted from: https://dx.doi.org/10.4135/9781412963947.n515

statistical sample
type: Class
subclass of: independent continuant
subclass of: Restriction
  on property: is_specified_output_of
  some values from: statistical sampling
subclass of: Restriction
  on property: has member
  some values from: continuant
definition: the output of a statistical sampling, a draw from a distribution or a population of physical or immaterial entities.
term editor: Philippe Rocca-Serra
definition source: STATO

calibration
type: Class
subclass of: data transformation
has curation status: ready for release
definition: calibration in statistics refers to the process of ensuring that the predicted probabilities or scores from a statistical model accurately reflect the true probabilities or outcomes observed in the data. It is an essential aspect of predictive modeling to ensure the reliability and interpretability of model predictions, where the goal is to estimate the likelihood of certain events or outcomes.
term editor: Philippe Rocca-Serra
alternative term: predictive model calibration
definition source: STATO adapted from ChatGPT3.5 with the following prompt: "define 'calibration' in the context of statistics"

Hosmer-Lemeshow goodness-of-fit test
type: Class
subclass of: data transformation
subclass of: goodness of fit statistical test
subclass of: Restriction
  on property: has part
  some values from: binomial logistic regression for analysis of dichotomous dependent variable
subclass of: Restriction
  on property: has_specified_input
  some values from: number of degrees of freedom
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-square probability distribution
subclass of: Restriction
  on property: has_specified_input
  some values from: regression model
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: goodness of fit testing objective
has curation status: ready for release
definition: The Hosmer-Lemeshow test is a statistical test used to assess the goodness of fit of a logistic regression model. It evaluates how well the predicted probabilities from the model match the observed outcomes in the data. The test helps determine whether the logistic regression model adequately captures the relationship between the predictor variables and the binary outcome variable. The test statistic follows a chi-square distribution with degrees of freedom equal to the number of groups minus the number of parameters estimated in the logistic regression model.
term editor: Philippe Rocca-Serra
definition source: STATO adapted from ChatGPT3.5 with the following prompt: "define Hosmer-Lemeshow test in statistics"
R command: hltest(model, verbose = TRUE, ...) from: https://search.r-project.org/CRAN/refmans/glmtoolbox/html/hltest.html

paired observation comparison objective
type: Class
subclass of: statistical hypothesis test objective
subclass of: Restriction
  on property: has part
  some values from: absence of difference hypothesis
definition: the objective of a data transformation to test a null hypothesis of absence of difference within subject holds.
term editor: Philippe Rocca-Serra
definition source: STATO

calibration plot
type: Class
subclass of: line graph
has curation status: ready for release
definition: calibration plot is a line graph which plots values resulting from predictions againts values obtained through observation.
term editor: Philippe Rocca-Serra
definition source: STATO
R command: https://cran.r-project.org/web/packages/predtools/vignettes/calibPlot.html

slope
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: line graph
has curation status: ready for release
definition: the slope of a line graph is a data item denoting the rate of change between the two variables represented on the graph. the slope is used to visualize and interpret the relationship between two variables.
term editor: Philippe Rocca-Serra
definition source: STATO

intercept
type: Class
subclass of: data item
subclass of: Restriction
  on property: denotes
  some values from: line graph
has curation status: ready for release
definition: an intercept is a data item which corresponds to where a graph line cuts (intercepts) an coordinates axis.
term editor: Philippe Rocca-Serra
definition source: STATO

mean time-to-event
type: Class
subclass of: average value
has curation status: ready for release
definition: A mean of values in which each value is the duration of time between the start of observation and the occurrence of an event.
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao
definition source: COKA/SEVCO group

median time-to-event
type: Class
subclass of: center value
has curation status: ready for release
definition: A median of values in which each value is the duration of time between the start of observation and the occurrence of an event.
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Yuan Gao
definition source: COKA/SEVCO group

posterior predictive value
type: Class
subclass of: quantitative confidence value
definition: A hypothesis testing measure that is the predictive probability that a statistic is equal to or more extreme than that observed under the assumptions of the model.
editor note: Hypothesis testing measure is defined as a statistic that represents the result of evaluating the congruence between a hypothesis and the statistics derived from the observed data. A posterior predictive p-value includes assumptions of prior probability of the hypothesis or parameters in the model Within the frequentist framework, use 'one-sided p-value" or "two sided pvalue"
term editor: Brian S. Alper
term editor: Harold Lehmann
term editor: Kenneth Wilkins
term editor: Philippe Rocca-Serra
alternative term: Bayesian p-value
definition source: COKA/SEVCO group
R command: pppvalue(x, parameter = "mu", value = 0.0, alternative = c("two.sided", "less", "greater"), statistic = "median", rejection.region, n = 10, prior = FALSE, quietly = FALSE, parallel, seed, ...) from: https://search.r-project.org/CRAN/refmans/bayesmeta/html/pppvalue.html

p-value for one-sided test
type: Class
subclass of: quantitative confidence value
subclass of: Restriction
  on property: is_specified_output_of
  some values from: statistical test hypothesis
subclass of: Restriction
  on property: is about
  qualified cardinality: 1
  on class: null hypothesis
has curation status: ready for release
definition: A p-value which represents the probability of obtaining a result at least as far, in one direction, from the value actually obtained as the value expected, assuming the null hypothesis is true.
editor note: P-value is defined as a hypothesis testing measure that represents the probability of obtaining a result at least as far from the value actually obtained as the value expected, assuming the null hypothesis is true. A p-value for one-sided test interprets 'at least as far from' with either the direction of 'greater than' or the direction of 'less than' but not with both possible directions.
term editor: Brian S. Alper
term editor: Harold Lehmann
term editor: Kenneth Wilkins
term editor: Philippe Rocca-Serra
alternative term: one-sided test p-value
alternative term: one-tailed test p-value
definition source: COKA/SEVCO group

p-value for two-sided test
type: Class
subclass of: quantitative confidence value
subclass of: Restriction
  on property: is_specified_output_of
  some values from: statistical test hypothesis
subclass of: Restriction
  on property: is about
  qualified cardinality: 2
  on class: null hypothesis
has curation status: ready for release
definition: A p-value which represents the probability of obtaining a result at least as far, in either direction, from the value actually obtained as the value expected, assuming the null hypothesis is true. A p-value for two-sided test interprets 'at least as far from' with both the direction of 'greater than' and the direction of 'less than'. For hypothesis test interpretation, the two-tailed p-value is compared to the alpha setting divided by 2.
editor note: P-value is defined as a hypothesis testing measure that represents the probability of obtaining a result at least as far from the value actually obtained as the value expected, assuming the null hypothesis is true. A p-value for one-sided test interprets 'at least as far from' with either the direction of 'greater than' or the direction of 'less than' but not with both possible directions.
term editor: Brian S. Alper
term editor: Harold Lehmann
term editor: Kenneth Wilkins
term editor: Philippe Rocca-Serra
alternative term: two-sided test p-value
alternative term: two-tailed test p-value
definition source: COKA/SEVCO group

F-beta score
type: Class
subclass of: measure of agreement
has curation status: ready for release
definition: The F-beta score is a measure of a model's accuracy, specifically designed to evaluate the performance of binary classification models. It is a generalized form of the F1 score, which itself is the harmonic mean of precision and recall. The F-beta score introduces a way to weigh recall more heavily than precision (or vice versa) depending on the value of beta.
editor note: https://github.com/ISA-tools/stato/pull/86
term editor: Philippe Rocca-Serra
term editor: Shawn Tan
definition source: adapted from ChatGPT using the following prompt: [what is the F-beta score in statistics] last accessed: July 2024
Python command: sklearn.metrics.fbeta_score(y_true, y_pred, *, beta, labels=None, pos_label=1, average='binary', sample_weight=None, zero_division='warn')[source] https://scikit-learn.org/stable/modules/generated/sklearn.metrics.fbeta_score.htm

mean of differences
type: Class
subclass of: average value
definition: A mean of values in which each value is the subtraction of one quantity from another.
editor note: The primary use of this term is in analyzing within-individual differences.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Khalid Shahin, Janice Tufte, Muhammad Afzal, Kenneth Wilkins
alternative term: average difference
alternative term: average of differences
alternative term: mean of paired differences
definition source: COKA/SEVCO working group

difference in differences
type: Class
subclass of: absolute difference
definition: A statistic that is a subtraction of one difference from another.
editor note: The term 'Difference-in-differences' may be used to assess the incremental benefit or harm of an intervention or exposure, where the effect of the exposure is measured as a difference (for example, pre-post testing comparison of values before and after the exposure) in two groups being compared.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Janice Tufte
definition source: COKA group

maximum possible value
type: Class
subclass of: statistic
definition: A statistic that represents the largest value that could occur.
editor note: This term may be used to denote the upper limit of a scale or score.
term editor: Brian S. Alper, Joanne Dehnbostel,Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Khalid Shahin.
definition source: COKA group

minimum possible value
type: Class
subclass of: statistic
definition: A statistic that represents the smallest value that could occur.
editor note: This term may be used to denote the lower limit of a scale or score.
term editor: Brian S. Alper, Joanne Dehnbostel,Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Khalid Shahin.
definition source: COKA group

absolute value
type: Class
subclass of: statistic
definition: A statistic that represents the distance of a value from zero.
editor note: The | symbol is used around the value to denote the absolute value, e.g. |x|, such that if x = -3, then |x| = 3.
term editor: Brian S. Alper, Kenneth Wilkins, Harold Lehmann.
definition source: COKA group

incidence rate
type: Class
subclass of: rate
has curation status: ready for release
definition: A rate in which the number of new events per total at risk is divided by an interval of time.
editor note: Incidence is defined as a proportion in which the numerator represents new events and the denominator represents the total at risk for events. Rate is defined as a ratio in which the numerator represents any quantity and the denominator represents an interval of time. The interval of time used for the denominator may be data-dependent when the duration of observation varies across the observations. In the method for calculating incidence rate (described at https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section2.html), the numerator is the "Number of new cases of disease or injury during the specified period" and the denominator is the "Time each person was observed, totaled for all persons"
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal
alternative term: average hazard rate
alternative term: incidence density
definition source: adapted from: https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section2.html and NCIt: Incidence Rate = The frequency of new occurrences of an event during a specified time period.

hazard rate
type: Class
subclass of: rate
has curation status: ready for release
definition: A conditional instantaneous rate in which the numerator represents an incidence conditioned on survival to a specified time, and the denominator represents a time interval with a duration approaching zero.
editor note: In the definition of Hazard Rate, the term "survival" is not literally about life and death but is used to represent existence without experiencing the event. "Hazard" as a statistical term is not specific to "bad" or "dangerous" events. A hazard rate is expressed as a unitless numerator per unit of time, occurring at a specified time, and conditioned on survival to that time. A hazard rate is mathematically the negative derivative of the log of the survival function. The survival function is the probability of surviving past a specified point in time, expressed as Pr{ T >= t }. A hazard rate is also mathematically defined as lim(dt -> 0) [ Pr{ ( t <= T < t + dt ) | ( T >= t ) } / dt ]
term editor: Harold Lehmann, Kenneth Wilkins, Joanne Dehnbostel, Brian S. Alper
alternative term: hazard
alternative term: hazard function
alternative term: instantaneous hazard rate
definition source: SEVCO group

event rate
type: Class
subclass of: rate
has curation status: ready for release
definition: The number of occurrences per unit of time.
editor note: An event rate is a ratio in which the numerator represents a count and the denominator represents an interval of time. When the numerator represents a count: -If the denominator includes an interval of time, the type of ratio is an Event Rate. -If the denominator includes a count without an interval of time, the type of ratio is an Event Frequency. -If the denominator includes a count and an interval of time, the type of ratio is an Event Frequency Rate. -If the denominator includes an interval of space, the type of ratio is a Number Density
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann.
definition source: SEVCO group

event frequency rate
type: Class
subclass of: rate
has curation status: ready for release
definition: A ratio in which the numerator represents an event frequency and the denominator represents an interval of time.
editor note: When the numerator represents a count: -If the denominator includes an interval of time, the type of ratio is an Event Rate. -If the denominator includes a count without an interval of time, the type of ratio is an Event Frequency. -If the denominator includes a count and an interval of time, the type of ratio is an Event Frequency Rate. -If the denominator includes an interval of space, the type of ratio is a Number Density
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann
definition source: SEVCO group

frequency
type: Class
subclass of: ratio
has curation status: ready for release
definition: A ratio in which the numerator represents a count and the denominator represents a count (without involving an interval of time).
editor note: When the numerator represents a count: -If the denominator includes an interval of time, the type of ratio is an Event Rate. -If the denominator includes a count without an interval of time, the type of ratio is an Event Frequency. -If the denominator includes a count and an interval of time, the type of ratio is an Event Frequency Rate. -If the denominator includes an interval of space, the type of ratio is a Number Density
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann
definition source: SEVCO group

density
type: Class
subclass of: ratio
has curation status: ready for release
definition: A ratio in which the numerator represents any quantity and the denominator represents an interval of space (distance, area, or volume).
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann
definition source: SEVCO group

number density
type: Class
subclass of: density
has curation status: ready for release
definition: A ratio in which the numerator represents a count and the denominator represents an interval of space (distance, area, or volume).
editor note: adapted from: The number density (symbol: n or ?N) is an intensive quantity used to describe the degree of concentration of countable objects (particles, molecules, phonons, cells, galaxies, etc.) in physical space: three-dimensional volumetric number density, two-dimensional areal number density, or one-dimensional linear number density. Population density is an example of areal number density. IUPAC Gold Book https://goldbook.iupac.org/terms/view/N04262 number density, n Number of particles divided by the volume they occupy.
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann
definition source: SEVCO group

hazard ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: A measure of association that is the ratio of the hazard rate of an event in one group to the hazard rate of the same event in another group.
editor note: Hazard rate is defined as: A conditional instantaneous rate in which the numerator represents an incidence conditioned on survival to a specified time, and the denominator represents a time interval with a duration approaching zero. The groups being compared are often the exposed group versus the unexposed group, but hazard ratio can also be applied to comparisons of one exposure relative to another exposure. A hazard ratio of one means there is no difference between two groups in terms of their hazard rates, based on whether or not they were exposed to a certain substance or factor, or how they responded to two interventions being compared. A hazard ratio of greater than one implies an association of greater risk, and a hazard ratio of less than one implies an association of lower risk. The hazard ratio can be calculated from studies in which the proportion of exposed participants who had the event is known, the proportion of unexposed participants who had the event is known, and the timing of events for each participant is known or estimable, such as a cohort study or clinical trial.
term editor: Brian S. Alper, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal
definition source: NCIt: Hazard ratio = A measure of how often a particular event happens in one group compared to how often it happens in another group, over time. In cancer research, hazard ratios are often used in clinical trials to measure survival at any point in time in a group of patients who have been given a specific treatment compared to a control group given another treatment or a placebo. A hazard ratio of one means that there is no difference in survival between the two groups. A hazard ratio of greater than one or less than one means that survival was better in one of the groups. https://www.statisticshowto.com/hazard-ratio/ The hazard ratio is a comparison between the probability of events in a treatment group, compared to the probability of events in a control group. Hazard Ratio in Clinical Trials (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC478551/) The hazard ratio is an estimate of the ratio of the hazard rate in the treated versus the control group. The hazard rate is the probability that if the event in question has not already occurred, it will occur in the next time interval, divided by the length of that interval. The time interval is made very short, so that in effect the hazard rate represents an instantaneous rate. The Hazards of Hazard Ratios (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653612/) The hazard ratio (HR) is the main, and often the only, effect measure reported in many epidemiologic studies. For dichotomous, non–time-varying exposures, the HR is defined as the hazard in the exposed groups divided by the hazard in the unexposed groups. For all practical purposes, hazards can be thought of as incidence rates and thus the HR can be roughly interpreted as the incidence rate ratio. The HR is commonly and conveniently estimated via a Cox proportional hazards model, which can include potential confounders as covariates.

prevalence ratio
type: Class
subclass of: ratio-based measure of association
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    some values from: prevalence
  intersection of: Restriction
    on property: has denominator
    some values from: prevalence
has curation status: ready for release
definition: A measure of association that is the ratio of two prevalences.
editor note: Prevalence (SEVCO STATO:0000412) is defined as: A proportion in which the numerator represents all events of interest (for example, both new and preexisting cases of a disease) in the population, which is represented by the denominator. The Prevalence Ratio indicates the magnitude of the prevalence of an event/outcome in one group of subjects/individuals (with characteristics/attribute) relative to another group (with different characteristics/attributes), such as the prevalence of the disease among the exposed persons to the prevalence of the disease among the unexposed persons.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal, Janice Tufte
definition source: https://www.ctspedia.org/do/view/CTSpedia/PrevalenceRatio#:~:text=Reference-,Definition%20of%20Prevalence%20Ratio,the%20proportion%20with%20the%20exposure. The ratio of the proportion of the persons with disease over the proportion with the exposure. Calculation is described here: https://sphweb.bumc.bu.edu/otlt/MPH-Modules/PH717-QuantCore/PH717-Module3-Frequency-Association/PH717-Module3-Frequency-Association12.html

diagnostic odd ratio
type: Class
subclass of: ratio
has curation status: ready for release
definition: A measure of association that is the ratio of the odds of a positive test in those with disease relative to the odds of a positive test in those without disease.
term editor: Harold Lehmann, Brian S. Alper, Joanne Dehnbostel, Kenneth Wilkins
alternative term: DOR
definition source: AHRQ https://effectivehealthcare.ahrq.gov/products/test-performance-metrics/appendixes: The diagnostic odds ratio (DOR) describes the odds of a positive test in those with disease relative to the odds of a positive test in those without disease.4 It can be computed in terms of sensitivity and specificity as well as in terms of positive and negative likelihood ratios (DOR = LR+/LR-). Thus this single measure includes information about both sensitivity and specificity and tends to be reasonably constant despite diagnostic threshold. However, it is impossible to use diagnostic odds ratios to weigh sensitivity and specificity separately, and to distinguish between tests with high sensitivity and low specificity and tests with low sensitivity and high specificity. Another disadvantage is that it is difficult for clinicians to understand and apply, limiting its clinical value. This is partly because they are not often exposed to diagnostic odds ratios. A diagnostic odds ratio is similar to an odds ratio that measures strength of association in an observational study or effect size in a trial. However, contrary to the typical effect size magnitudes of such odds ratios (often between 0.5 and 2), diagnostic odds ratios can attain much larger values (often greater than 100).

incidence rate ratio
type: Class
subclass of: ratio-based measure of association
subclass of: Class
  intersection of: Restriction
    on property: has numerator
    some values from: incidence rate
  intersection of: Restriction
    on property: has denominator
    some values from: incidence rate
has curation status: ready for release
definition: A measure of association that is the ratio of two incidence rates.
editor note: Incidence Rate (SEVCO STATO_0000680) is defined as: A rate in which the number of new events per total at risk is divided by an interval of time. The incidence rates may refer to the same event comparing two different groups, or the same group comparing two different events
term editor: Brian S. Alper, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal
term editor: Philippe Rocca-Serra
alternative term: IRR

standardized incidence ratio
type: Class
subclass of: incidence rate ratio
has curation status: ready for release
definition: An incidence rate ratio in which the numerator is the incidence rate in a group and the denominator is the incidence rate for a reference population.
editor note: The incidence rate used for the denominator may be an expected incidence rate for a reference population. The reference population may refer to a general population of the geographic area from which the cohort was selected.
term editor: Brian S. Alper, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal
alternative term: SIR

kappa
type: Class
subclass of: measure of agreement
has curation status: ready for release
definition: A measure of agreement among categorical assessments, corrected for chance agreement.
editor note: In the literature, the same eponymic term (e.g., 'Cohen's kappa') is used with different formulas. In SEVCO, we define each term with a single formula, and recommend annotators to choose the SEVCO term based on the formula. This is a widely used term to measure inter-rater reliability. Refer to measures of association to see other terms: for example, intra-class correlation coefficient (ICC).
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Kenneth Wilkins, Muhammad Afzal
alternative term: kappa statistic
definition source: SEVCO group

simple chance-corrected agreement coefficient
type: Class
subclass of: kappa
has curation status: ready for release
definition: A Kappa statistic in which the expected agreement by chance is based on an assumption that all possible categories for assignment are equally likely.
editor note: A Kappa statistic is a measure of agreement among categorical assessments, corrected for chance agreement. In the simple chance-corrected agreement coefficient, the expected chance agreement is modeled as the inverse of the number of categories (1/q) where q is the number of possible categories for assignment. The simple chance-corrected agreement coefficient is calculated as ( p[a] - 1/q ) / ( 1 - 1/q ) where p[a] is the observed percent agreement and q is the number of possible categories for assignment.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins
definition source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965565 Gwet KL. Testing the Difference of Correlated Agreement Coefficients for Statistical Significance. Educ Psychol Meas. 2016 Aug;76(4):609-637. doi: 10.1177/0013164415596420. Epub 2015 Jul 28. PMID: 29795880; PMCID: PMC5965565. Brennan and Prediger (1981) proposed a simple chance-corrected agreement coefficient, which generalizes to multiple raters and multiple categories, the G-index previously proposed by Holley and Guilford (1964) for two raters and two categories. What is known as the Holley–Guilford G-index was previously proposed independently by various authors under different names. Among them are Guttman (1945), Bennett, Alpert, and Goldstein (1954), and Maxwell (1977). For an interrater reliability experiment involving r raters who classify n subjects into one of q possible categories, the Brennan-Prediger coefficient is given by k[BP] = ( p[a] - 1/q ) / ( 1 - 1/q ), where the percent agreement p[a] is defined by Equation (3 -- see https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5965565/#disp-formula3-0013164415596420), and the percent chance agreement is a constant representing the inverse of the number of categories.

standard deviation for sample
type: Class
subclass of: standard deviation
has curation status: ready for release
definition: A standard deviation that is the square root of the quotient of the summation across data points of the square of the distance from each data point to the sample mean, and the degrees of freedom (where the degrees of freedom is sample size minus one).
editor note: Standard deviation is defined as a measure of dispersion that represents the average of the distances from the mean of the dataset to each data point in the dataset. Standard deviation for sample is a standard deviation in which the dataset is a sample. The formula for the standard deviation for sample ( s s) is: s = ∑ n i = 1 ( x i − x ‾ ) 2 n − 1 s= n−1 ∑ n i=1 ​ (x i ​ − x ) 2 ​ ​ where n n is the sample size (the number of independent observations, indexed by i i), x x is observed value, and x ‾ x is the sample mean. The formula to calculate degrees of freedom depends on the model. For the degrees of freedom for a sample standard deviation, given the sample mean, it is n-1, because the nth observation is no longer independent, given the n-1 other observations and the sample mean.
term editor: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Khalid Shahin, Kenneth Wilkins

mesure of calibration
type: Class
subclass of: statistic
has curation status: ready for release
definition: A measure of association between a variable representing known or true values and a variable representing measured or predicted values.
editor note: Calibration is often used for measurement devices. The known or true values may be called the reference standard. Calibration is also used for predictive models and other contexts comparing computed or expected probabilities with empirical frequencies. A measure of calibration indicates the degree to which the computed values are underestimated or overestimated.
term editor: Brian S. Alper, Joanne Dehnbostel, Harold Lehmann, Kenneth Wilkins
term editor: Philippe Rocca-Serra
definition source: SEVCO group

mean calibration
type: Class
subclass of: mesure of calibration
has curation status: ready for release
definition: A measure of calibration that is the average of a function of the difference between the expected values and the observed values.
editor note: For predictive modeling of non-continuous variables, the mean calibration is a measure of calibration that is the average of a function of the difference between the expected probabilities and the observed frequencies. The expected values may be computed (as in predictive models) or may be derived from reference data (as typical for a measurement device). When the function is the square of the difference and the variables are binary (0 or 1), the measure is called the Brier score.
term editor: Harold Lehmann, Kenneth Wilkins, Muhammad Afzal, Brian S. Alper
term editor: Philippe Rocca-Serra
definition source: SEVCO group

calibration slope
type: Class
subclass of: mesure of calibration
has curation status: ready for release
definition: A measure of calibration that is the rate of change in the appropriately transformed value per unit change of the correspondingly transformed predicted value.
editor note: For calibration of binary outcome variables (0 or 1), the calibration slope is computed from a statistical model where the log odds of the predicted probabilities is a linear function of the empirical frequencies (logistical regression). The transformation is log odds (logit, the link function for a generalized linear model for the expected value of the outcome). For calibration of count outcome variables (0, 1, 2, 3, ...), the calibration slope may be computed from a statistical model where the log of the predicted mean counts is a linear function of the empirical frequencies determined by unique combinations of the covariates. The transformation is log, the link function, of the counts. There are other types of outcome variables for which the calibration slope may be obtained. Slopes further away from 1.0 indicate, at upper and lower values, over- or under-confidence in the prediction.
term editor: Harold Lehmann, Ken Wilkins, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin
term editor: Philippe Rocca-Serra
alternative term: calibration in the small
definition source: SEVCO group

calibration intercept
type: Class
subclass of: mesure of calibration
has curation status: ready for release
definition: A measure of calibration that is the difference between the mean expected value and the mean observed value.
editor note: For calibration of binary outcome variables (0 or 1), the calibration intercept is computed from a statistical model where the log odds of the predicted probabilities is a linear function of the empirical frequencies. For calibration of count outcome variables (0, 1, 2, 3, ...), the calibration intercept may be computed from a statistical model where the log of the predicted mean counts is a linear function of the empirical frequencies determined by unique combinations of the covariates. There are other types of outcome variables for which the calibration-in-the-large measure may be obtained. The notion of calibration in the large is that the intercept is a gross assessment of whether the average prediction matches the average outcome, however, this interpretation is exquisitely sensitive to the choice of referent factors within the prediction model.
term editor: Harold Lehmann, Ken Wilkins, Muhammad Afzal, Joanne Dehnbostel, Khalid Shahin.
term editor: Philippe Rocca-Serra
definition source: SEVCO group

partial area under the receiver operator characteristic curve
type: Class
subclass of: area under curve
has curation status: ready for release
definition: An area under the curve where the curve is the true positive rate and the range of interest is a specified portion of the range of possible values for the false positive rate and/or range of possible values for the true positive rate.
editor note: Area under the ROC curve is defined as an area under the curve where the curve is the true positive rate and the range of interest is the false positive rate. ROC stands for Receiver Operating Characteristic. The area under the ROC curve is used to assess the performance of a classifier used to distinguish between two or more groups. Another term for true positive rate is sensitivity and another term for false positive rate is 1-specificity.
term editor: Kenneth Wilkins, Brian S. Alper, Muhammad Afzal, Harold Lehmann and SEVCO group
term editor: Philippe Rocca-Serra
definition source: SEVCO group

area under the value-time curve
type: Class
subclass of: area under curve
subclass of: Restriction
  on property: denotes
  some values from: value-time curve
has curation status: ready for release
definition: An area under the curve where the curve is the repeated measures of a variable over time and the domain of interest is time.
term editor: Kenneth Wilkins, Harold Lehmann
term editor: Philippe Rocca-Serra
alternative term: area under the value versus time curve
alternative term: area under the value vs. time curve
alternative term: area under the value-by-time curve
definition source: SEVCO group

area under the precision-recall curve
type: Class
subclass of: area under curve
subclass of: Restriction
  on property: denotes
  some values from: precision-recall curve
has curation status: ready for release
definition: An area under the curve where the curve is the precision and the domain of interest is the recall.
term editor: Kenneth Wilkins, Harold Lehmann, Brian S. Alper
term editor: Philippe Rocca-Serra
alternative term: AUC-PR
alternative term: AUCPR
alternative term: AUPRC
definition source: SEVCO group
R command: https://www.rdocumentation.org/packages/PRROC/versions/1.3.1/topics/pr.curve pr.curve()

probability distribution mean
type: Class
subclass of: average value
has curation status: ready for release
definition: A probability distribution attribute that represents the expected value of a variable that has that distribution.
editor note: For a normal distribution, the distribution parameter mean (also called µ or mu) coincides with the mean of the distribution.
term editor: Brian S. Alper, Harold Lehmann, Kenneth Wilkins, Joanne Dehnbostel, Muhammad Afzal
term editor: Philippe Rocca-Serra
alternative term: mu
definition source: SEVCO group

probability distribution variance
type: Class
subclass of: variance
has curation status: metadata incomplete
definition: A distribution variance is defined as a probability distribution attribute that is the expected value of the square of the difference of the value of a variable that has that distribution from its expected value.
term editor: Brian S. Alper, Harold Lehmann, Kenneth Wilkins
term editor: Philippe Rocca-Serra
definition source: SEVCO group

probability distribution standard deviation
type: Class
subclass of: standard deviation
has curation status: ready for release
definition: A probability distribution attribute that is the square root of the distribution variance.
editor note: A distribution variance is defined as a probability distribution attribute that is the expected value of the square of the difference of the value of a variable that has that distribution from its expected value. For a normal distribution, the distribution parameter standard deviation (also called s or sigma) coincides with the standard deviation of the distribution. Standard deviation is defined as a measure of dispersion that represents the average of the distances from the mean of the dataset to each data point in the dataset.
term editor: Brian S. Alper, Harold Lehmann, Kenneth Wilkins
term editor: Philippe Rocca-Serra
definition source: SEVCO group

precision-recall curve
type: Class
subclass of: graph
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: x-axis
    intersection of: Restriction
      on property: denotes
      some values from: true positive rate
subclass of: Restriction
  on property: has part
  some values from: Class
    intersection of: y-axis
    intersection of: Restriction
      on property: denotes
      some values from: precision
has curation status: ready for release
definition: The precision-recall curve is a graph which plots the sensitivity or recall on the X-axis and the precision on the Y-axis. The precision-recall curves focuses on the trade-off between Precision and Recall at various thresholds. It also highlights the performance of the model for the positive class (often the minority or more important class). It is particularly suited for for imbalanced datasets where the positive class is rare. The PR-curve is more sensitive to class imbalance. As precision drops significantly if the model predicts too many false positives, it makesthe PR-curve better for evaluating performance on imbalanced datasets.
term editor: Philippe Rocca-Serra
alternative term: PR-curve
definition source: adapted from ChatGPT using the prompt: "What is the difference between ROC curve and PR curve"

value-time curve
type: Class
subclass of: graph
has curation status: ready for release
definition: a value-time curve is a graph which plot time on the x-axis versus the value of a variable of interest as delivered by a process. It is used to represent the relationship there is the value and the time it takes to achieve that value. It is commonly used in project management or business analysis to evaluate and optimize how efficiently value is delivered over time.
term editor: Philippe Rocca-Serra
definition source: adapted from ChatGPT using the prompt: "what is a value-time curve?"

homogeneity test
type: Class
equivalent class: Restriction
  on property: achieves_planned_objective
  some values from: homogeneity test objective
subclass of: statistical test hypothesis
has curation status: ready for release
definition: an homogeneity test is a statistical test aiming at evaluate if the statisical measure from several random samples are similar
term editor: Philippe Rocca-Serra
definition source: STATO

t-score
type: Class
subclass of: statistic
has curation status: ready for release
definition: A t-score generally refers to the value resulting from standardizing a sample statistic (e.g., sample mean) in terms of the t-distribution. It quantifies how far the sample statistic is from the hypothesized population parameter in units of the estimated standard error. A t-score is a statistic that represents a measure of the divergence of an individual experimental result from a specified mean, taking sample size into account and expressed in terms of the number of standard errors from the mean value.
term editor: Brian S. Alper, Harold Lehmann, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins
term editor: Philippe Rocca-Serra
alternative term: T score
alternative term: T-Score
alternative term: t score
alternative term: t-value

p-value
type: Class
subclass of: quantitative confidence value
subclass of: Restriction
  on property: is about
  some values from: null hypothesis
subclass of: Restriction
  on property: is_specified_output_of
  some values from: statistical test hypothesis
definition: A hypothesis testing measure that represents the probability of obtaining a result at least as far from the value actually obtained as the value expected, assuming the null hypothesis is true.
editor note: Within the frequentist framework, a p-value is typically a p-value for two-sided test and the criterion for rejecting the null hypothesis is typically expressed as a p-value that is less than an alpha setting divided by 2. In some cases, the p-value is a p-value for one-sided test, and the criterion for rejecting the null hypothesis is typically expressed as a p-value that is less than an alpha setting. A p-value is preferably coded more precisely as a p-value for two-sided test or a p-value for one-sided test rather than using the code for p-value without specification. The code for p-value (without specification) may be used in contexts where the p-value reported is ambiguous. Within the Bayesian framework, use the posterior predictive p-value.
alternative term: P value
alternative term: P-value
alternative term: PValue
alternative term: p value
definition source: SEVCO group

Chi-square test for homogeneity
type: Class
subclass of: odds ratio homogeneity test
subclass of: homogeneity test
subclass of: Restriction
  on property: has_specified_input
  some values from: Chi-Squared statistic
subclass of: Restriction
  on property: has_specified_output
  some values from: p-value
has curation status: ready for release
definition: a statistical test which test for homogeneity of proportions, which is used when comparing proportions observed across multiple groups. It relies on frequencies calculated in contingency tables. It determines is proportions are consistent.
term editor: Philippe Rocca-Serra
definition source: STATO

prior probability
type: Class
subclass of: statistic
has curation status: ready for release
definition: A statistic that represents the likelihood of a parameter of interest, before accounting for the observed data from the study.
editor note: This term is core to Bayesian statistics, where the focus is on estimation of the parameter of interest (unlike frequentist statistics, where the focus is on the likelihood of producing an estimate given a specific value of the parameter). The prior probability may be constructed in several ways: from prior research, from raw data in a database, from expert opinion, or specified as "non-informative" (meaning pure ignorance). The likelihood of the parameter is usually represented as a distribution over all possible values of the parameter.
term editor: Harold Lehmann, Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal
term editor: Philippe Rocca-Serra
definition source: SEVCO

posterior probability
type: Class
subclass of: statistic
has curation status: ready for release
definition: A statistic that represents the likelihood of a parameter of interest, after updating its prior probability with the observed data from the study.
editor note: This term is core to Bayesian statistics, where the focus is on estimation of the parameter of interest (unlike frequentist statistics, where the focus is on the likelihood of producing an estimate given a specific value of the parameter). The prior probability is the likelihood of a parameter of interest from before the study. For calculating the posterior probability of a parameter, the prior probability is updated using Bayes' Theorem' and the likelihood function.
term editor: Harold Lehmann, Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal
term editor: Philippe Rocca-Serra
definition source: SEVCO

concentration
type: Class
subclass of: scalar measurement datum
has curation status: ready for release
definition: A concentration is the measure of the amount of solute dissolved in a unit quantity of solvent or solution. It describes the strength or intensity of a solution in terms of its solute content. It is therefore a ratio in which the numerator is a measure of the solute and the denominator is a measure of the solvent.
term editor: Philippe Rocca-Serra
definition source: Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal, Kenneth Wilkins, Harold Lehmann

measurement accuracy as a percentage
type: Class
subclass of: percentage
has curation status: requires discussion
definition: Measurement accuracy refers to how close a measured value is to the true or accepted value of the quantity being measured. It is a percentage in which the numerator represents the absolute value of one minus the difference between the true value and the observed value, and the denominator represents the true value. Accuracy is often expressed as a percentage of the true value, based on the relative error: Accuracy (%)= (1 −∣Measured Value−True Value∣/True Value)×100 True Value: The reference or accepted value. Measured Value: The value obtained during the measurement.
term editor: Brian S. Alper, Harold Lehmann, Muhammad Afzal, Joanne Dehnbostel

Bayesian inference
type: Class
subclass of: statistical inference
has curation status: ready for release
definition: A statistical inference paradigm in which the assumptions are that parameters are random variables with probability distributions, that prior knowledge can be represented with such distributions, and that one learns from data by updating those prior distributions using Bayes' Rule.
editor note: Regarding random variables with probability distribution: These random variables are often used to represent population parameters, but there are other types of random variables, e.g., representing typical methodological concerns, where the typical notion of “population” does not apply. Regarding prior knowledge: The notion of representing prior knowledge as a probability distribution is the core of disagreement among statisticians around Bayesian inference. For those interpreting “probability” as “measure of belief”, prior probability distributions encodes belief about the parameters (“subjectivist Bayes”), and ignorance is represented as a “non-informative” prior. For those with a more frequentist interpretation of probability, such priors summarizes frequency knowledge seen in the past (“empirical Bayes”). Regarding Bayes’ Rule: Probability theory, with no assumptions beyond regular probability, says that P(A|B) = P(B|A) P(A). Bayes Rule says that one can (should) use this formula to update knowledge from data: P(parameter value | data) = P(data | parameter value) P(Data), with P(data | parameter value) being called the “likelihood function,” communicating how likely data are, given parameter values (and what type of distribution the parameter(s) connote), and could be use to reflect sampling, if relevant.
term editor: Harold Lehmann, Kenneth Wilkins
term editor: Philippe Rocca-Serra
alternative term: Bayesian approach
definition source: SEVCO

frequentist inference
type: Class
subclass of: statistical inference
has curation status: ready for release
definition: A statistical inference paradigm in which the assumptions are that probabilities reflect relative frequencies of events and that the probability of observing data are governed by fixed yet unknown population parameters.
editor note: The frequentist inference is based on hypothetical repeated sampling and the resulting relative frequencies in the long run. Inferences are based on point and interval estimates. For hypothesis testing, the inference is based on the probability of obtaining values equal to or more extreme than the observed data.
alternative term: classical statistical approach
alternative term: frequentist approach
alternative term: frequentist statistical inference paradigm
definition source: SEVCO Group

Cochran-Armitage Chi-Square Statistic for Trend
type: Class
subclass of: Chi-Squared statistic
has curation status: ready for release
definition: A chi-square statistic used to test whether a dichotomous variable and an ordinal variable are related. The statistic is calculated using a weighted sum of the differences between observed and expected frequencies, where the weights are based on the scores assigned to the ordered categories. Mathematically, it's often expressed as: Z = ∑(wi(Oi-Ei)/sqr( wi^2.Ei(1-Ei)) where wi are the scores, Oi observed frequencies, and Ei expected frequencies.
term editor: Kenneth Wilkins, Brian S. Alper, Joanne Dehnbostel
term editor: Philippe Rocca-Serra
definition source: Cochran, W. G., & Armitage, P. (1954). The χ² Test for Trend. Biometrika, 41(1-2), 171–178.
definition source: SEVCO & STATO

material anatomical entity
type: Class
subclass of: material entity
editor preferred label: material anatomical entity
definition: Anatomical entity that has mass.
imported from: obi.owl
imported from: uberon.owl

anatomical cluster
type: Class
subclass of: material entity
editor preferred label: anatomical cluster
definition: Anatomical group that has its parts adjacent to one another.
imported from: obi.owl
imported from: uberon.owl

length unit
type: Class
subclass of: measurement unit label
editor preferred label: length unit
definition: A unit which is a standard measure of the distance between two points.
imported from: obi.owl
imported from: uo.owl

mass unit
type: Class
subclass of: measurement unit label
editor preferred label: mass unit
definition: A unit which is a standard measure of the amount of matter/energy of a physical object.
imported from: obi.owl
imported from: uo.owl

time unit
type: Class
subclass of: measurement unit label
editor preferred label: time unit
definition: A unit which is a standard measure of the dimension in which events occur in sequence.
imported from: obi.owl
imported from: uo.owl

sum
type: Class
subclass of: statistic
definition: A statistic that represents the result of adding all the values in a collection of values.
editor note: Brian S. Alper, Joanne Dehnbostel,Muhammad Afzal, Janice Tufte, Bhagvan Kommadi, Khalid Shahin.
alternative term: total
definition source: COKA group

Chi-squared statistic for homogeneity
type: Class
subclass of: Chi-Squared statistic
has curation status: ready for release
definition: A Chi-squared statistic used to test whether observed data from two or more groups follow the same distribution.
editor note: In meta-analysis, a chi-square statistic for homogeneity is often used to determine the appropriateness of combining the statistics to represent a common population.
term editor: Kenneth Wilkins, Brian S. Alper, Joanne Dehnbostel, Harold Lehmann
term editor: Philippe Rocca-Serra
definition source: SEVCO group

example to be eventually removed
type: NamedIndividual
type: curation status specification

metadata complete
type: Thing
type: NamedIndividual
type: curation status specification
definition: Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.

organizational term
type: Thing
type: NamedIndividual
type: curation status specification
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release
term editor: PERSON:Alan Ruttenberg

ready for release
type: Thing
type: NamedIndividual
type: curation status specification
definition: Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."

metadata incomplete
type: Thing
type: NamedIndividual
type: curation status specification
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: Thing
type: NamedIndividual
type: curation status specification
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: Thing
type: NamedIndividual
type: curation status specification
definition: All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.

to be replaced with external ontology term
type: NamedIndividual
type: curation status specification
definition: Terms with this status should eventually replaced with a term from another ontology.
term editor: Alan Ruttenberg
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
definition: A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
term editor: Alan Ruttenberg
definition source: group:OBI

axiom holds for all times
definition: ## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation

5 % false positive rate
definition: a false positive rate whose value is 5 per cent
definition source: STATO
term editor: Alejandra Gonzalez-Beltran
editor note: Following discussion with OBCS, deprecated of class STATO_0000043 and creation of instance
term editor: Orlaith Burke
term editor: Philippe Rocca-Serra

1 % false positive rate
term editor: Philippe Rocca-Serra
editor note: Following discussion with OBCS, deprecated of class STATO_0000281 and creation of instance
definition: a false positive rate whose value is 1 per cent
term editor: Alejandra Gonzalez-Beltran
definition source: STATO
term editor: Orlaith Burke

obi.owl
creator: Liju Fan
creator: James A. Overton
creator: Tanya Gray
creator: Frank Gibson
creator: Richard Scheuermann
creator: Matthew Brush
creator: Melanie Courtot
creator: Chris Stoeckert
creator: Alan Ruttenberg
creator: Gilberto Fragoso
creator: Jessica Turner
creator: Lawrence Hunter
creator: John Westbrook
creator: Jie Zheng
creator: Yongqun He
creator: Monnie McGee
default language: en
creator: Bill Bug
creator: Trish Whetzel
Format: OWL-DL
creator: Larisa Soldatova
creator: Dirk Derom
creator: Chris Taylor
creator: Susanna-Assunta Sansone
creator: James Malone
creator: Helen C. Causton
creator: Cristian Cocos
creator: Stefan Wiemann
creator: Philippe Rocca-Serra
creator: Norman Morrison
creator: Ryan R. Brinkman
creator: Jay Greenbaum
creator: Dawn Field
creator: Helen Parkinson
creator: Melissa Haendel
subject: An ontology for the annotation of biomedical and functional genomics experiments.
creator: Robert Stevens
creator: Philip Lord
creator: Bjoern Peters
creator: Matthew Pocock
creator: Eric Deutsch
Contributor: Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
creator: Kevin Clancy
comment: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them.
creator: Daniel Schober
creator: Chris Mungall
creator: Carlo Torniai
creator: Daniel Rubin
creator: Barry Smith
creator: Joe White
creator: Christian Bolling
creator: Pierre Grenon
creator: Mervi Heiskanen
creator: Richard Bruskiewich
description: The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
version info: 2018-05-23
license: http://creativecommons.org/licenses/by/4.0/
OBO foundry unique label: Ontology for Biomedical Investigations
creator: Luisa Montecchi
creator: Jennifer Fostel
creator: Jeffrey Grethe
creator: Elisabetta Manduchi
date: 2009-07-31
creator: Allyson Lister
creator: Tina Hernandez-Boussard
creator: Holger Stenzhorn

Class
intersection of: scalar measurement datum
intersection of: Restriction
  on property: is about
  qualified cardinality: 1
  on class: study design dependent variable

Restriction
on property: has value
has value: true

Restriction
on property: has quality
some values from: Class
  intersection of: study group population size
  intersection of: Restriction
    on property: has value
    some values from: Datatype
      on datatype: int
      with restrictions:
        max inclusive: 5

Restriction
on property: has value
has value: true

Restriction
on property: is denoted by
some values from: Class
  intersection of: normal distribution hypothesis
  intersection of: Restriction
    on property: has value
    has value: true

Restriction
on property: has value
has value: true

Restriction
on property: has value
has value: 0

Restriction
on property: has value
has value: 0

Restriction
on property: has value
has value: true

Restriction
on property: has value
has value: true