Jörg Waitelonis, Oleksandra Bruns, Tabea Tietz, Etienne Posthumus, Hossein Beygi Nasrabadi, Harald Sack. NFDIcore Ontology. Revision: v3.0.4. Retrieved from: https://nfdi.fiz-karlsruhe.de/ontology/3.0.4
The National Research Data Infrastructure (NFDI) initiative has led to the formation of various consortia, each focused on developing a research data infrastructure tailored to its specific domain. To ensure interoperability across these consortia, the NFDIcore ontology has been developed as a mid-level ontology for representing metadata related to NFDI resources, including individuals, organizations, projects, data portals, and more. Further infomration can be found at GitHub: https://github.com/ISE-FIZKarlsruhe/nfdicore/
NFDIcore Ontology
Ontology Specification
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.
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not.
example of usage
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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.
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.
editor note
A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
alternative label
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
term replaced by
'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . }
Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.
An alternative lexical label for a resource.
Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
A statement or formal explanation of the meaning of a concept.
editorial note
A note for an editor, translator or maintainer of the vocabulary.
example
An example of the use of a concept.
preferred label
The preferred lexical label for a resource, in a given language.
scope note
A note that helps to clarify the meaning and/or the use of a concept.
readable IRI label
A term tracker annotation is an editor note used to track the history of an entity. For each change, it records the related GitHub issue and pull request.
term tracker annotation
adapted from http://openenergy-platform.org/ontology/oeo/OEO_00020426
A relation between an entity and its abbreviated form, representing a shortened version of the original term or phrase.
has acronym
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
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.
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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
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'.
part_of
part of
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
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.
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'.
has_part
has part
has realization
realized in
b has realization c =Def c realizes b
As for realizes
realizes
(Elucidation) realizes is a relation between a process b and realizable entity c such that c inheres in some d & for all t, if b has participant d then c exists & the type instantiated by b is correlated with the type instantiated by c
A balding process realizes a disposition to go bald; a studying process realizes a student role; a process of pumping blood realizes the pumping function of a heart
Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link>
preceded by
b preceded by c =Def b precedes c
The temporal region occupied by the second half of the match is preceded by the temporal region occupied by the first half of the match
precedes
(Elucidation) precedes is a relation between occurrents o, o' such that if t is the temporal extent of o & t' is the temporal extent of o' then either the last instant of o is before the first instant of o' or the last instant of o is the first instant of o' & neither o nor o' are temporal instants
The temporal region occupied by Mary's birth precedes the temporal region occupied by Mary's death.
Each temporal region is its own temporal extent. The temporal extent of a spatiotemporal region is the temporal region it temporally projects onto. The temporal extent of a process or process boundary that occupies temporal region t is t.
Precedes defines a strict partial order on occurrents.
occurs in
b occurs in c =Def b is a process or a process boundary & c is a material entity or site & there exists a spatiotemporal region r & b occupies spatiotemporal region r & for all time t, if b exists at t then c exists at t & there exist spatial regions s and s' where b spatially projects onto s at t & c occupies spatial region s' at t & s is a continuant part of s' at t
A process of digestion occurs in the interior of an organism; a process of loading artillery rounds into a tank cannon occurs in the interior of the tank
exists at
(Elucidation) exists at is a relation between a particular and some temporal region at which the particular exists
First World War exists at 1914-1916; Mexico exists at January 1, 2000
has occurrent part
b has occurrent part c =Def c occurrent part of b
Mary's life has occurrent part Mary's 5th birthday
has proper occurrent part
b has proper occurrent part c =Def b has occurrent part c & b and c are not identical
As for has occurrent part.
has temporal part
b has temporal part c =Def c temporal part of b
Your life has temporal part the first year of your life
occurrent part of
(Elucidation) occurrent part of is a relation between occurrents b and c when b is part of c
Mary's 5th birthday is an occurrent part of Mary's life; the first set of the tennis match is an occurrent part of the tennis match
proper temporal part of
b proper temporal part of c =Def b temporal part of c & not (b = c)
As for temporal part of.
proper occurrent part of
b proper occurrent part of c =Def b occurrent part of c & b and c are not identical
As for occurrent part of.
temporal part of
b temporal part of c =Def b occurrent part of c & (b and c are temporal regions) or (b and c are spatiotemporal regions & b temporally projects onto an occurrent part of the temporal region that c temporally projects onto) or (b and c are processes or process boundaries & b occupies a temporal region that is an occurrent part of the temporal region that c occupies)
Your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating; the 4th year of your life is a temporal part of your life, as is the process boundary which separates the 3rd and 4th years of your life; the first quarter of a game of football is a temporal part of the whole game
temporally projects onto
(Elucidation) temporally projects onto is a relation between a spatiotemporal region s and some temporal region which is the temporal extent of s
The world line of a particle temporally projects onto the temporal region extending from the beginning to the end of the existence of the particle
has proper temporal part
b has proper temporal part c =Def c proper temporal part of b
As for has temporal part.
environs
contains process
b environs c =Def c occurs in b
Mouth environs process of mastication; city environs traffic
history of
(Elucidation) history of is a relation between history b and material entity c such that b is the unique history of c
This life is the history of this organism
has history
b has history c =Def c history of b
This organism has history this life
specifically depended on by
s-depended on by
b specifically depended on by c =Def c specifically depends on b
Coloured object specifically depended on by colour
specifically depends on
s-depends on
(Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c
A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other
The analogue of specifically depends on for occurrents is has participant.
bearer of
b bearer of c =Def c inheres in b
A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality
inheres in
b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c
A shape inheres in a shaped object; a mass inheres in a material entity
occupies temporal region
p occupies temporal region t =Def p is a process or process boundary & the spatiotemporal region occupied by p temporally projects onto t
The Second World War occupies the temporal region September 1, 1939 - September 2, 1945
occupies spatiotemporal region
(Elucidation) occupies spatiotemporal region is a relation between a process or process boundary p and the spatiotemporal region s which is its spatiotemporal extent
A particle emitted by a nuclear reactor occupies the spatiotemporal region which is its trajectory
first instant of
t first instant of t' =Def t is a temporal instant & t' is a temporal region t' & t precedes all temporal parts of t' other than t
An hour starting at midnight yesterday has first instant midnight yesterday
has first instant
t has first instant t' =Def t' first instant of t
The first hour of a year has first instant midnight on December 31
last instant of
t last instant of t' =Def t is a temporal instant & t' is a temporal region & all temporal parts of t' other than t precede t
Last midnight is the last instant of yesterday
has last instant
t has last instant t' =Def t' last instant of t
The last hour of a year has last instant midnight December 31
This document is about information artifacts and their representations
A (currently) primitive relation that relates an information artifact to an entity.
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.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
is about
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.
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
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
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes
inverse of the relation 'denotes'
denoted by
this fragility is a characteristic of this vase
this red color is a characteristic of this apple
a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence.
characteristic of
this apple is bearer of this red color
this vase is bearer of this fragility
Inverse of characteristic_of
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.
has characteristic
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates in
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
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.
has participant
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).
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).
A relationship between a generically dependent continuant and a specifically dependent continuant or process, in which the generically dependent continuant depends on some independent continuant or process in virtue of the fact that the specifically dependent continuant or process also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants or processes.
is concretized as
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).
A relationship between a specifically dependent continuant or process 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 or process also depends on that same independent continuant. Multiple specifically dependent continuants or processes can concretize the same generically dependent continuant.
concretizes
this catalysis function is a function of this enzyme
a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence
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.
function of
this red color is a quality of this apple
a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence
A quality inheres in its bearer at all times for which the quality exists.
quality of
this investigator role is a role of this person
a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence
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.
role of
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
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.
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
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.
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
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.
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
my brain is located in my head
this rat is located in this cage
a relation between two independent continuants, the target and the location, in which the target is entirely within the location
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
Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
located in
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p.
has output
An organism that is a member of a population of organisms
is member of is a mereological relation between a item and a collection.
member of
has member is a mereological relation between a collection and an item.
has member
input of
output of
has broader
Relates a concept to a concept that is more general in meaning.
By convention, skos:broader is only used to assert an immediate (i.e. direct) hierarchical link between two conceptual resources.
has broader transitive
skos:broaderTransitive is a transitive superproperty of skos:broader.
By convention, skos:broaderTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application.
has exact match
skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
has narrower
Relates a concept to a concept that is more specific in meaning.
has narrower transitive
skos:narrowerTransitive is a transitive superproperty of skos:narrower.
By convention, skos:narrowerTransitive is not used to make assertions. Rather, the properties can be used to draw inferences about the transitive closure of the hierarchical relation, which is useful e.g. when implementing a simple query expansion algorithm in a search application.
URL de descarga
URL de téléchargement
URL di scarico
URL souboru ke stažení
URL μεταφόρτωσης
download URL
downloadURL
رابط تحميل
ダウンロードURL
Ceci est un lien direct à un fichier téléchargeable en un format donnée. Exple fichier CSV ou RDF. Le format est décrit par les propriétés de distribution dcterms:format et/ou dcat:mediaType.
La URL de un archivo descargable en el formato dato. Por ejemplo, archivo CSV o archivo RDF. El formato se describe con las propiedades de la distribución dcterms:format y/o dcat:mediaType.
Questo è un link diretto al file scaricabile in un dato formato. E.g. un file CSV o un file RDF. Il formato è descritto dal dcterms:format e/o dal dcat:mediaType della distribuzione.
The URL of the downloadable file in a given format. E.g. CSV file or RDF file. The format is indicated by the distribution's dcterms:format and/or dcat:mediaType.
URL souboru ke stažení v daném formátu, například CSV nebo RDF soubor. Formát je popsán vlastností distribuce dcterms:format a/nebo dcat:mediaType.
URL til fil der kan downloades i et bestemt format. Fx en CSV-fil eller en RDF-fil. Formatet for distributionen angives ved hjælp af egenskaberne dcterms:format og/eller dcat:mediaType.
Είναι ένας σύνδεσμος άμεσης μεταφόρτωσης ενός αρχείου σε μια δεδομένη μορφή. Π.χ. ένα αρχείο CSV ή RDF. Η μορφη αρχείου περιγράφεται από τις ιδιότητες dcterms:format ή/και dcat:mediaType της διανομής.
رابط مباشر لملف يمكن تحميله. نوع الملف يتم توصيفه باستخدام الخاصية dcterms:format dcat:mediaType
is subject of
A relation between an information content entity and its specific value.
has value
A relation between an information content entity and its specific url.
has url
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
entity
(Elucidation) An entity is anything that exists or has existed or will exist
Julius Caesar; the Second World War; your body mass index; Verdi's Requiem
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.
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
continuant
(Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity
A human being; a tennis ball; a cave; a region of space; someone's temperature
An entity that has temporal parts and that happens, unfolds or develops through time.
occurrent
(Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region
As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant.
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
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])
independent continuant
b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c
An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra
spatial region
(Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time
As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region
temporal region
(Elucidation) A temporal region is an occurrent over which processes can unfold
As for zero-dimensional temporal region and one-dimensional temporal region
two-dimensional spatial region
(Elucidation) A two-dimensional spatial region is a spatial region that is a whole consisting of a surface together with zero or more surfaces which may have spatial regions of lower dimension as parts
The surface of a sphere-shaped part of space; an infinitely thin plane in space
spatiotemporal region
(Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime
The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite
'Spacetime' here refers to the maximal instance of the universal spatiotemporal region.
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])
process
event
(Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant
An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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.
disposition
internally-grounded realizable entity
(Elucidation) A disposition b is a realizable entity such that if b 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
An atom of element X has the disposition to decay to an atom of element Y; the cell wall is disposed to transport cellular material through endocytosis and exocytosis; certain people have a predisposition to colon cancer; children are innately disposed to categorize objects in certain ways
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
realizable entity
(Elucidation) A realizable entity is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region & which is of a type some instances of which are realized in processes of a correlated type
The role of being a doctor; the role of this boundary to delineate where Utah and Colorado meet; the function of your reproductive organs; the disposition of your blood to coagulate; the disposition of this piece of metal to conduct electricity
zero-dimensional spatial region
(Elucidation) A zero-dimensional spatial region is one or a collection of more than one spatially disjoint points in space
The spatial region occupied at some time instant by the North Pole
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
quality
(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
The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold
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
of one-sided specifically dependent continuants: the mass of this tomato
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.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
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])
specifically dependent continuant
b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c
(with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates
(with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole
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.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
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.
role
externally-grounded realizable entity
(Elucidation) A role b is a realizable entity such that 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
The priest role; the student role; the role of subject in a clinical trial; the role of a stone in marking a property boundary; the role of a boundary to demarcate two neighbouring administrative territories; the role of a building in serving as a military target
fiat object part
(Elucidation) A fiat object part b is a material entity & such that if b exists then it is continuant part of some object c & demarcated from the remainder of c by one or more fiat surfaces
The upper and lower lobes of the left lung; the dorsal and ventral surfaces of the body; the Western hemisphere of the Earth; the FMA:regional parts of an intact human body
one-dimensional spatial region
(Elucidation) A one-dimensional spatial region is a whole consisting of a line together with zero or more lines which may have points as parts
An edge of a cube-shaped portion of space; a line connecting two points; two parallel lines extended in space
object aggregate
(Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit
The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank
'Exactly' means that there are no parts of the object aggregate other than its member parts.
The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts.
three-dimensional spatial region
(Elucidation) A three-dimensional spatial region is a whole consisting of a spatial volume together with zero or more spatial volumes which may have spatial regions of lower dimension as parts
A cube-shaped region of space; a sphere-shaped region of space; the region of space occupied by all and only the planets in the solar system at some point in time
site
(Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity
A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist
object
(Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested
An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube
A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide
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.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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])
generically dependent continuant
g-dependent continuant
(Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share
The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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.
function
(Elucidation) A function is a disposition that exists in virtue of its bearer's physical make-up & 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 artefacts) in order to realize processes of a certain sort
The function of a hammer to drive in nails; the function of a heart pacemaker to regulate the beating of a heart through electricity
process boundary
p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts
The boundary between the 2nd and 3rd year of your life
one-dimensional temporal region
(Elucidation) A one-dimensional temporal region is a temporal region that is a whole that has a temporal interval and zero or more temporal intervals and temporal instants as parts
The temporal region during which a process occurs
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
(Elucidation) A material entity is an independent continuant has some portion of matter as continuant part
A human being; the undetached arm of a human being; an aggregate of human beings
continuant fiat boundary
(Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity
As for fiat point, fiat line, fiat surface
immaterial entity
b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part
As for fiat point, fiat line, fiat surface, site
fiat line
(Elucidation) A fiat line is a one-dimensional continuant fiat boundary that is continuous
The Equator; all geopolitical boundaries; all lines of latitude and longitude; the median sulcus of your tongue; the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin
relational quality
b is a relational quality =Def b is a quality & there exists c and d such that c and d are not identical & b specifically depends on c & b specifically depends on d
A marriage bond; an instance of love; an obligation between one person and another
fiat surface
(Elucidation) A fiat surface is a two-dimensional continuant fiat boundary that is self-connected
The surface of the Earth; the plane separating the smoking from the non-smoking zone in a restaurant
fiat point
(Elucidation) A fiat point is a zero-dimensional continuant fiat boundary that consists of a single point
The geographic North Pole; the quadripoint where the boundaries of Colorado, Utah, New Mexico and Arizona meet; the point of origin of some spatial coordinate system
zero-dimensional temporal region
(Elucidation) A zero-dimensional temporal region is a temporal region that is a whole consisting of one or more separated temporal instants as parts
A temporal region that is occupied by a process boundary; the moment at which a finger is detached in an industrial accident
history
(Elucidation) A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by the material part of a material entity
The life of an organism from the beginning to the end of its existence
temporal interval
(Elucidation) A temporal interval is a one-dimensional temporal region that is continuous, thus without gaps or breaks
The year 2018.
A one-dimensional temporal region can include as parts not only temporal intervals but also temporal instants separated from other parts by gaps.
temporal instant
(Elucidation) A temporal instant is a zero-dimensional temporal region that has no proper temporal part
The millennium
In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction.
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.
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."
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.
Answers the question, why did you do this experiment?
goal specification
OBI Plan and Planned Process/Roles Branch
objective specification
Pour the contents of flask 1 into flask 2
A directive information entity that describes an action the bearer will take.
OBI Plan and Planned Process branch
action specification
R, Perl, Java
A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
programming language
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
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
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
data
data item
a serial number such as "12324X"
a stop sign
a written proper name such as "OBI"
An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity.
20091104, MC: this needs work and will most probably change
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).
based on Oxford English Dictionary
symbol
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity.
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).
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.
information content entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
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.
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.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
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
directive information entity
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.
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
curation status specification
A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"
OBI branch derived
data format specification
Data about an ontology part is a data item about a part of an ontology, for example a term
data about an ontology part
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified.
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.
2014-03-31: A plan specification can have other parts, such as conditional specifications.
2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231.
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
plan specification
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.
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
version number
The reason for which a term has been deprecated. 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.
The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology.
obsolescence reason specification
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
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.
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.
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.
text
textual entity
University of Colorado Denver School of Medicine
A textual entity intended to identify a particular institution
institutional identification
Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool.
A textual entity that describes a figure
caption
Textual characteristics of traditional and Open Access scientific journals are similar
A textual entity that names a document
document title
Any picture, diagram or table
An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something.
figure
The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities.
A denotator type indicates how a term should be interpreted from an ontological perspective.
Barry Smith, Werner Ceusters
denotator type
A textual entity that is used as directive to deliver something to a person, or organization
2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59
postal address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583
email address
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.
A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry.
Original proposal from Bjoern, discussions at IAO calls
centrally registered identifier symbol
An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs.
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').
Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation.
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.
centrally registered identifier
PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles.
A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process.
centrally registered identifier registry
"Bill Clinton"
"The Eiffel Tower"
"United States of America"
A textual entity that denotes a particular in reality.
written name
From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect.
A textual entity listing abbreviations and their expansions that are used in a document.
abbreviation textual entity
From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD.
A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document.
author information textual entity
Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).
A textual entity that discusses work from other publications and expresses their relevancy to the content of a document.
related work textual entity
A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.
"You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/]
This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)
Open Researcher and Contributor Identifier
ORCID identifier
An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
proper name
identifier
An identifier referring to an individual entity that is ascribed personhood by the user of the identifier.
personal name
A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name
first name
given name
An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children.
last name
surname
family name
An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things.
code map
code system
codeset
coding system
controlled vocabulary
code set
I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it.
ontology file
ontology module
An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies.
base ontology module
An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users.
source ontology module
editors ontology module
An ontology module that is intended to be the primary release product and the one consumed by the majority of tools.
TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module
main release ontology module
An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available.
reasoned ontology module
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.
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.
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.
organization
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a completely executed planned process.
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
branch derived
plan
A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence.
Modified from http://en.wikipedia.org/wiki/Software_license
licence
An information content entity that refers to digital creative works and services, and is utilized to organize the resources of NFDI. The most generic kind of a resource and may be associated with any kind of digital creative work, e.g. datasets, collections, metadata; offered products and services, e.g. data portals, data curation, data digitization.
obsolete NFDI resource
2024-03-25 - Sasha Bruns: This class is useful in nfdicore to provide a unified and structured representation of the diverse range of resources that contribute to the NFDI infrastructure. IMO, it helps to emphasize the scope of resources that can be contributed to the NFDI compared to all information content entites in IAO.
A process of a scientific or business endeavor that aims to conclude an investigation or to answer a research question.
project
Why "project" as an occurrent: - A project typically has a start and end time. - It involves a sequence of activities, such as planning, conducting experiments, analyzing data, and publishing results. - It has temporal parts (e.g., Phase 1, Phase 2, review stages). So, it aligns well with the occurrent category - more precisely, it can be considered a complex process made up of various subprocesses. But what about the organization or plan behind it? - The institution running or participating the project would be a continuant (consortium). - The project plan might be a generically dependent continuant (a kind of information content entity). - But the project as executed over time is an occurrent.
An object that represents a single human individual.
person
2024-03-24. Sasha Bruns - the class is not mapped to NCBITaxon_9606 (homo sapiens) due to different scope of the ontologies. "Person" in nfdicore represents entities with specific roles, responsibilities, and attributes within an organization, and is not limited to its biological characteristics.
Harald Sack, Tabea Tietz, Sasha Bruns, Etienne Posthumus
A site that refers to geographical locations, such as cities, countries, landmarks, and natural environments.
place
A spatial region, e.g. country, city or district.
Issue: https://github.com/ISE-FIZKarlsruhe/nfdicore/issues/75
An organisation that consists of multiple independent groups and individuals, who join together to collaborate on a specific goal.
consortium
A consortium of autonomous organizations collaborating towards a shared goal, operating within the framework of an agreement.
An independent continuant or information content entity that refers to a manifestation of someone's creative effort. A creative work refers to a digital intellectual or artistic resource, e.g. a dataset, metadata, a guideline, a software and other materials offering relevant information or instructions within their specific domains.
obsolete creative work
2024-03-22. Sasha Bruns - Unlike schema:CreativeWork, nfdicore:CreativeWork is specialized to cover digital creative works only. Through the mapping to "schema:CreativeWork and 'information content entity'", we exclude material creative works such as real paintings, architectural objects, and other physical artifacts, which fall outside the scope of nfdicore:CreativeWork.
TRANSRAZ Data Model, NFDI4Culture Knowledge Graph, Guide for digital collection management at art museums, NFDI4Culture SPARQL Endpoint, Registry for Tools & Services, RADAR4Culture service, etc.
An information content entity that refers to a structured collection of data, organized typically for a specific goal such as analysis, research, or reference. Dataset is structured information about a resource provided by an organization or a person.
dataset
2024-04-10. Sasha Bruns: nfdicore:dataset and ioa:data set are not equivalent, due to their differing conceptualizations of what constitutes a iao:data item, which is a superclass of iao:data set. In the nfdicore ontology, a dataset may not necessarily align perfectly with the definition of a data item, since this definition implies a level of accuracy that may not always apply to datasets in their entirety. While a nfdicore:dataset may contain data items, it doesn't necessarily qualify as a data item itself under the strict definition provided by ioa:dataset. This differentiation helps us avoid ambiguity and ensures that our modeling aligns with the intended semantics.
Fotothek Bibliotheca Hertziana Max-Planck-Institut für Kunstgeschichte 320px static derivates research dataset (https://doi.org/10.17617/3.SVH2BT)
A realizable entity that represents a structured set of intended actions or steps designed to achieve specific objectives or outcomes.
obsolete plan
A process of making information, such as literature, music, and software etc., available to the public for sale or for free.
publishing process
obsolete identifier
A process that has specified output a software product and that involves the creation of source code.
software development
A role inherent in an agent that is realized when representing, advocating, or communicating on behalf of an organization or group to convey messages or information.
spokesperson role
An event that focuses on scholarly activities and the exchange of knowledge, typically involving presentations, discussions, or collaborations among researchers, academics, and students, often in the context of conferences, workshops, seminars, symposia, or colloquia, to advance a specific field of study or interdisciplinary research.
academic event
A role inherent in an organization that is realized when coordinating, managing, or supporting academic activities, programs, or research to promote education and knowledge advancement.
academic organization role
A role inherent in an organization that is realized when promoting, regulating, or supporting industry-specific standards, practices, and collaboration to advance sector development and innovation.
industry organization role
A plan that specifies a sequence of tasks, processes, or operations, often involving multiple agents, tools, or systems, to achieve a specific goal or produce a desired outcome.
obsolete workflow
A workflow defines the logical order and dependencies of steps, the roles or entities responsible for each step, and the inputs and outputs required for and produced by each task. It is a realizable entity that can be enacted or executed within a defined context, such as a business process, computational framework, or organizational procedure.
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
document
An (nfdi) ontology is a data item that coherently represents all components of an ontology, including its versions, variants, modules and other associated artifacts. It is typically denoted by a name and/or an acronym, which is the term we use to communicate about it.
ontology
An ontology variant represents a self-contained, reusable subset of an ontology that provides a specific functionality while maintaining interoperability with the larger ontology. Typically, an ontology is released in different variants, which makes a variant a release artifact.
ontology variant
A document that has been accepted by a patent authority
patent
An (nfdi) ontology release version represents a particular release of an ontology.
ontology release version
A file data item is a data item that represents a file stored on a hard drive. It might also include essential attributes like its name, location, download URL, size, type, and timestamps for creation, modification, and access. It might also capture permissions and ownership details to control how the file can be accessed or modified.
file data item
A document that conveys information, data, or findings, typically structured in a formal or semi-formal manner, to communicate the results of an analysis, investigation, observation, or activity.
report
A report is created with the intent of informing specific audiences and may include textual descriptions, visualizations, metrics, or conclusions. It is a realizable entity that is produced and maintained as part of a process or workflow.
A document that organizes and stores source code files, associated metadata, and version history to facilitate the management, sharing, and collaborative development of software projects. It serves as a structured collection of information that tracks changes, maintains integrity, and supports workflows such as version control, branching, and merging.
source code repository
The source code repository stands for the CONTENT of the repository, which, e.g., you can copy to your hard drive. This distinguishes it from the website class which e.g. is used to publish the content.
An information content entity that specifies the subject area, domain or academic discipline of an entity. An academic discipline, a research field or domain of an entity, e.g. a domain of a data portal or a field of study of a person.
academic discipline
2024-03-26: SB & JW: Following the OMIT Ontology, the academy discilpine is defined as a subclass of bfo:quality (see e.g. http://purl.obolibrary.org/obo/OMIT_0001008)
2024-12-16: TT & JW: An academic discipline is not a quality, as assumed before, but an ICE. A discipline like philosophy or chemistry consists of structured knowledge, theories, and practices. These are abstract entities that represent and encode information.
Architecture, Art History, Musicology, Media Studies, Performing Arts
A process that organizes activities and resources to deliver a specific service, ensuring its efficiency, reliability, and alignment with intended goals.
service process
An independent continuant that acts autonomously and is entrusted with the authority to represent, negotiate, or act on behalf of another agent.
agent
A class that represents entities that are capable of autonomous actions, decision-making, or interaction within a given environment, e.g. persons or organizations.
Torsten Schrade, Linnaea Söhn, Academy of Sciences and Literature Mainz
A place that refers to a densely populated urban area.
city
A city or a town where the thing is located.
Berlin, Hannover, Kyiv
A material entity that represents a collection of material entities intended to be understood together as a whole.
collection
A tangible collection of valuables published or curated by an organization or a person.
A collection of arts displayed at the museum
A role inherent in an organization that is realized when the organization is a member of a consortium.
consortium member role
A process in which the contact information of an entity is provided.
contacting process
A role inherent in an agent that is realized when the agent is a contact point of a resource or a project.
contact point role
A process of contibuting or providing information to an endeavor.
contributing process
A role inherent in an agent that provides input, resources, or effort to support or enhance a project, work, or process.
contributor role
A place that refers to a defined geographical area distinguished by its territorial boundaries, governance structure, and sovereignty.
country
A country where the thing is located.
Software that provides large amounts of structured data from repositories and archives to the user. Usually the data can be uploaded, accessed, searched and/or downloaded via a web browser.
database software
The activity of managing and promoting the use of data from their point of creation to ensure that they are fit for contemporary purpose and available for discovery and reuse. For dynamic datasets this may mean continuous enrichment or updating to keep them fit for purpose. Higher levels of curation will also involve links with annotation and with other published materials
data curation service
A website that serves as a centralized platform for accessing, managing, and sharing datasets, information, or resources related to a specific topic, theme, or domain.
data portal
An online platform that provides access to datasets.
Bach digital, KultSam, MusiXplora
An process that represents an organized happening that unfolds in time.
A class that represents entities that occur or unfold in time, typically characterized by a specific organized happening or occurrence with temporal properties.
conferences, celebrations, workshops, meetings, or any other specific incident or happening that has been planned somehow.
A place that refers to a geographical territory forming part of a country.
federal state
A federal state where the thing is located.
Sachsen, Berlin
A role inherent in an organization that is realized when the organization serves as a funder to endevaours, e.g. projects.
funding organization role
Collection of pre-implemented functions for a specific task that can be accessed via a well-defined interface.
software library
An information content entity that refers to a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence.
obsolete license
A document that provides legal guidelines for the use of a resource, e.g. a software.
cc-by-3, Digital Peer Publishing Lizenz
A directive information entity that describes a media type a bearer has.
media type
A digital resource format or physical medium.
doc, avi, mpeg, epub, txt, MIME-type, record, cassette, VHS, LaserDiscs, CD, DVD, Blu-ray color lithograph, text book
A media type that serves as a standardized identifier for specifying the nature and format of data.
MIME-type
The MIME-type template of the resource
https://www.iana.org/assignments/media-types/application/dicom, https://www.iana.org/assignments/media-types/video/mp4, https://www.iana.org/assignments/media-types/text/n3
A plan specification that is used for implementing software.
obsolete programming language
A formal language used for implementing a software.
A publication that is the output of a publishing process and a creative process.
publication
A published scholarly work that reports on ongoing activity about or within a resource, e.g. a dataset.
MusiXplora: Visual analysis of a musicological encyclopedia, Textkategorien in kompositorischen Werkstattdokumenten
A role inherent in an agent that is realized when the bearer participates in the publishing of the document.
publisher role
A plan specification that comprises a set of instructions, programs, or algorithms designed to perform specific tasks or functions on a computer or other electronic devices.
software
A computer software provided by an organization or a person.
A directive information entity that defines the requirements, characteristics, or standards for the design, implementation, or operation of a system, product, or process.Specification is a set of requirements, guidelines, standards contributed by an organization or a person.
specification
2024-03-24. Sasha Bruns: specifications have dual nature - they are both directive information entities guiding actions (plan specification) and digital intellectual resources providing relevant information and guidelines (creative work).
Guidelines, technical specifications, design specifications
A specification that establishes a set of guidelines, criteria, or norms recognized and adopted by internationational community.
standard
An international standard and norm that can be used to evaluate or create a resource.
Provision of storage space for research data as a service to external users. Access is possible via web protocols.
storage service
Service with direct user contact for topics going beyond the support for specific single services.
support service
A plan specification that refers to a technology method employed for the creation, management, utilization, or control of a digital resource.
technological method specification
A technology, e.g. a web application or a programming framework used in a resource.
Groovy on Grails, Angular
Software that can be downloaded and executed locally on the users' hardware.
software application
Standalone training for self-study can be considered a technical service (usually a web application). Generally speaking, training materials often come in the form of specific measures or tutorials that are attached to a service and that are designed to improve the user’s service experience. Our joint understanding of training as a stand-alone service, however, is not limited to the above and includes materials designed for education in all fields of research data management.
training service
Software that is installed on a server and can be used by users via a web page and the internet, for example Software-as-a-service (SaaS).
web application software
An information content entity that represents a collection of interconnected web pages, multimedia content, and digital resources accessible via the World Wide Web.
website
A collection of webpages contributed by an organization or a person.
A process that involves generating, developing, and refining original ideas or concepts through exploration, experimentation, and problem-solving, aiming to produce innovative or expressive outcomes in artistic, scientific, or other creative fields.
creative process
A process that processes tasks, activities, or steps to achieve specific objectives efficiently within an organized workflow system.
workflow process
Role of an immaterial entity that facilitates the delivery or support of a service product, ensuring its proper execution and value realization.
service product role
Role of an independent continuant that is realized through an agent's actions, enabling the agent to perform specific functions or achieve particular outcomes within a system or context.
agent role
A role inherent in an agent that is realized when delivering services, managing processes, and ensuring the effective fulfillment of service product requirements.
service provider role
An immaterial entity that provides value through a service offering, delivering intangible benefits or functionality designed to fulfill specific needs or requirements, often in a structured process.
service product
A plan specification that defines the requirements, features, and parameters of a service, outlining its scope, performance, and delivery criteria.
service specification
A textual entity that uniquely identifies a specific software application, program, or system, often used for branding, categorization, and reference in documentation, licensing, and distribution.
software title
A textual entity intended to identify a particular publication.
citation
A plan specification that defines the sequence, dependencies, roles, and conditions governing the execution of tasks and processes within a workflow, ensuring structured and efficient task coordination, automation, and completion.
workflow specification
A project proposal is a detailed document that outlines the objectives, scope, requirements, and deliverables of a project. It serves as a blueprint for all stakeholders, ensuring everyone understands what needs to be accomplished.
project proposal
Gemeinsame Normdatei
Integrated Authority File
A centrally registered identifier that is issued by the German National Library. The Integrated Authority File (GND) is facilitates the collaborative use and administration of authority data. These authority data represent and describe entities, i.e. persons, corporate bodies, conferences and events, geographic entities, topics and works relating to cultural and academic collections.
GND identifier
GND
Virtual International Authority File
The centrally registered identifier VIAF (Virtual International Authority File) is an international authority file that links and integrates authority records from multiple national libraries and other organizations. It provides a unique identifier for authors, creators, and entities, facilitating better data sharing and cataloging across institutions.
VIAF identifier
VIAF
GeoNames
GeoNames is a geographical database that provides information on places, including names, coordinates, and administrative divisions. It integrates data from multiple sources and is widely used for geolocation, mapping, and geographic information systems (GIS).
GeoNames identifier
Wikidata
Wikidata is maintained by the Wikimedia Foundation and serves as a central repository for structured data used by Wikipedia, Wikimedia projects, and external applications.
Wikidata identifier
ROR (Research Organization Registry) is a global, open, and community-driven registry of research organizations. It provides unique identifiers for institutions involved in research, enabling better data integration, disambiguation, and interoperability across scholarly communication systems.
ROR identifier
ROR
International Standard Identifier for Libraries and Related Organizations
ISIL (International Standard Identifier for Libraries and Related Organizations) is a globally recognized identifier system used to uniquely identify libraries, archives, museums, and other cultural institutions. It facilitates resource sharing, cataloging, and data exchange across institutions and countries.
ISIL identifier
ISIL
FactGrid
FactGrid is a collaborative, structured knowledge database designed for historical research. It operates on Wikibase and focuses on documenting historical entities, events, and relationships.
FactGrid identifier
Répertoire International des Sources Musicales
RISM (Répertoire International des Sources Musicales) is an international catalog of historical music sources, including manuscripts, printed music, and treatises. It provides unique identifiers and bibliographic data to support music research and documentation.
RISM identifier
RISM
A directive information entity that defines the structural, syntactic, and encoding rules for representing data when it is exported from a system.
export format specification
A textual entity that describe some resource.
textual description
A textual entity that denotes some resource.
title
The act of foundation refers to the formal establishment or creation of an institution, organization, or entity, typically through a legal, administrative, or ceremonial process.
act of foundation
The act of dissolution refers to a formal legal or administrative event that officially terminates or dissolves an entity, relationship, or agreement.
act of dissolution
A namespace refers to a distinct, unique identifier that is used to distinguish concepts and entities within an ontology from those in other ontologies or systems. It's typically represented as a URL or URI (Uniform Resource Identifier) and ensures that each element within the ontology has a globally unique reference.
ontology namespace
A process by which something is brought into existence; having been brought into existence.
creation process
issue: https://github.com/ISE-FIZKarlsruhe/nfdicore/issues/95
A role inherent in an agent that originates, develops, or produces a work, product, or idea.
creator role
An information content entity that is part of a document.
document part
An abstract, introduction, method or results section.
A part of a document that enumerates the authors of the document
author list
A part of a document that enumerates the contributors of the document
contributor list
A part of a document that enumerates the creators of the document
creator list
A part of a document that has parts that are institution identifications associated with the authors of the document
institution list
A Uniform Resource Locator (URL), colloquially termed a web address, is a reference to a web resource that specifies its location on a computer network and a mechanism for retrieving it. [Wikipedia]
uniform resource locator
A work package textual entity is a textual entity that describes a structured unit of work within a project, outlining specific tasks, objectives, deliverables, and assigned responsibilities to achieve defined project outcomes.
work package textual entity
A comment textual entity is a textual entity that provides supplimentary information, feedback, opinions, clarifications, or annotations related to a specific subject.
comment textual entity
peer review comments on journal articles, user feedback on digital repositories, inline annotations in collaborative documents, explanatory remarks in software code documentation
A Digital Object Identifier (DOI) is a centrally registered identifier that provides a unique, persistent reference to digital objects such as publications, datasets, and software, ensuring reliable access and citation.
digital object identifier
National Research Data Infrastructure
Nationale Forschungsdateninfrastruktur
An NFDI Consortium is a collaborative organizational entity within the German National Research Data Infrastructure (NFDI) initiative, responsible for the development, management, and coordination of research data infrastructures in specific scientific domains.
The National Research Data Infrastructure (NFDI) is intended to sytematically manage scientifich and research data, provide long-term data storage, backup and accessibility, and network the data (inter-)nationally. The German Research Foundation (DFG) and the Joint Science Conference (GWK) are working together to establish and fund the NFDI, on the basis of the administrative agreement concluded by the Federal Government and the federal states on November 26, 2018. The NFDI is designed as a nationwide network, which is built gradually and cooperatively by the respective communities. The goal is to provide a reliable and sustainable service portfolio that covers generic and disciplinary requirements of research data management in Germany. The NFDI is developed step by step and science-oriented with services available to researchers from vaious disciplines, institutions, and federal states.
NFDI consortium
An academic title is an identifier that denotes an individual’s academic rank, qualification, or honorary designation within educational and research institutions.
academic title
Professor, Associate Professor, Dr., PhD, Dr. Ing.
An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail.
postal code
A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes.
zone improvement plan code
Av event that brings together individuals or groups for structured discussions, decision-making, planning, or coordination of research, educational, or institutional activities.
meeting
Data Analysis Software is a subclass of Software designed to process, visualize, and interpret structured and unstructured data using statistical, machine learning, and computational techniques.
data analysis software
An Electronic Lab Notebook (ELN) is a subclass of Software that provides a digital platform for recording, managing, and sharing experimental procedures, observations, and research data in scientific workflows.
electronic lab notebook
Image Processing Software is a subclass of Software that enables the manipulation, enhancement, analysis, and visualization of images obtained from experimental, computational, or simulation-based sources.
image processing software
An Operating System (OS) is a software system that manages computer hardware and software resources and provides common services for computer programs. It acts as an intermediary between users and the computer hardware, enabling the execution of application programs.
operating system
Concerning the content of ‘Software’ datasheet and its related knowledge graph, the ‘Operating System’ class wase created to respond to competency questions like what operating systems are compatible with a specific software.
Simulation Software is a subclass of Software that facilitates the modeling and numerical simulation of physical, chemical, or computational systems to study behaviors, interactions, and performance under different conditions
simulation software
Examples include COMSOL Multiphysics, LAMMPS, Quantum ESPRESSO, and ANSYS.
Workflow Management Software is a subclass of Software that provides tools for designing, automating, executing, and monitoring scientific or computational workflows in research and engineering domains.
workflow management software
An event implementation specification is a type of Directive Information Entity that provides formal guidelines, constraints, and details on how an event should be executed. It specifies the mode of implementation, including logistical, technical, and procedural aspects required to carry out an event successfully.
event implementation specification
HBN: Concerning the content of ‘Event’ datasheets and its related knowledge graph, the ‘Event Implementation Specification’ class and its instances were created to respond to competency questions like what are the implementation formats of a given event.
Specifications for organizing conferences, training workshops, and academic seminars in different formats such as virtual, in-person, or hybrid settings.
A funding specification is a directive information entity that provides structured guidelines, policies, and requirements for securing, managing, and allocating financial resources for various activities, projects, or organizations.
funding specification
HBN: Concerning the content of ‘Service’ datasheets and its related knowledge graph, the ‘Funding Specification’ class and its instances were created to respond to competency questions like what funding models exist for a given service.
An information access specification is a directive information entity that defines the policies, conditions, and mechanisms governing the accessibility of digital or physical information resources for users or organizations.
information access specification
HBN: Concerning the content of ‘Publication’ datasheet and its related knowledge graph, the ‘Information Access Specification’ class and its instances were created to respond to competency questions like: what access policies apply to a specific publication document, which resources are available under open access, etc.
An ontology version IRI is a unique identifier that points to a specific version of an ontology. It helps distinguish between different updates or revisions of the same ontology. This ensures consistent referencing and compatibility across systems using the ontology.
ontology version IRI
issue: issue: https://github.com/ISE-FIZKarlsruhe/nfdicore/issues/95
A Metadata Specification is a detailed document that describes metadata structures, guidelines, and usage policies for standardization and adoption.
metadata specification
The TGN Identifier refers to a unique ID within the Getty Thesaurus of Geographic Names (TGN), which is a controlled vocabulary developed to standardize geographic names for use in cultural heritage and library contexts. The TGN is part of the Getty Vocabulary Program by the Getty Research Institute.
TGN identifier
A status specification is a directive information entity that defines the current state, progress, or condition of an entity, process, or project based on predefined criteria and operational guidelines.
status specification
HBN: Concerning the content of ‘Service’ and 'International collabrations' datasheets and their related knowledge graphs, the ‘Status Specification’ class and its instances were created to respond to competency questions like: what is the current status of a service or collaboration project, which collabrations are in an active state, etc.
A role inherent in an agent that is realized when collaborating in planning, managing, and executing an event, project, or initiative alongside one or more primary organizers.
co organizer role
A role inherent in an agent that is realized when shareing the responsibilities of representing an organization, group, or initiative, typically communicating its views, policies, or findings to the public.
co spokesperson role
A role inherent in an agent that is realized when engageing in cooperative work with another individual or organization toward a shared goal, such as research, development, or business initiatives.
collaboration partner role
A role inherent in an agent that is realized when being responsible for producing goods, components, or materials through industrial or commercial processes.
manufacturer role
Siemens as a manufacturer of industrial automation equipment or Intel as a manufacturer of semiconductor chips
A role inherent in an agent that is realized when being responsible for planning, managing, and executing an event, project, or structured activity.
organizer role
event management firms organizing scientific symposiums or non-profit organizations coordinating community outreach programs
A role inherent in an agent that is realized when delivers presentations, lectures, or speeches at events, conferences, or public gatherings.
speaker role
invited speakers at scientific symposiums, keynote presenters at technology expos, and guest lecturers at universities
The LCNAF Identifier refers to a unique identifier assigned to entries in the Library of Congress Name Authority File (LCNAF). This file is a standardized authority database maintained by the Library of Congress, used to establish and control the names of people, organizations, geographic places, and titles in bibliographic records.
LCNAF identifier
The BnF Identifier refers to a unique identifier assigned to an authority record in the Bibliothèque nationale de France (BnF) catalog. It is part of the BnF’s authority files, used to standardize names of people, organizations, titles, places, and subjects across bibliographic records.
BnF identifier
A SPARQL Endpoint is a web application software that provides a queryable interface for accessing and retrieving structured data from RDF-based knowledge graphs using the SPARQL query language.
sparql endpoint
Wikidata Query Service, DBpedia SPARQL Endpoint, Linked Data Fragments
An agent role that exresses that an organization inhering that role actively collaborates within a consortium, contributing expertise, resources, or infrastructure to support shared research, development, or innovation goals.
consortium partner role
Identifier for institutions registered with the German Digital Library (Deutsche Digitale Bibliothek)
Identifikator für Institutionen, die bei der Deutschen Digitalen Bibliothek registriert sind
DDB organization identifier
identifier for a data repository in the re3data registry
re3data repository identifier
An added value textual entity is a textual entity that describes the achievements, benefits, or additional value generated by a project, service, or initiative, highlighting its impact, improvements, or contributions.
added value textual entity
In responce to competency questions like what are the added values of project X1 or service X2.
An affiliation is a textual entity that specifies the organizational or institutional association of an individual, group, or entity, typically used in academic, professional, or research contexts.
affiliation
FIZ Karlsruhe – Leibniz-Institute for Information Infrastructure Karlsruhe Institute of Technology, Institute of Applied Informatics and Formal Description Methods
A goal textual entity is a textual entity that describes the intended objectives, aims, or targets of a project, initiative, organization, or research effort, providing a clear statement of purpose and expected outcomes.
goal textual entity
A Conference Abstract is a brief summary of research findings or scholarly work submitted for presentation at an academic or professional conference, often serving as a precursor to a full paper or presentation.
conference abstract
A Conference Paper is a scholarly publication that presents research findings at an academic or professional conference, typically published in conference proceedings.
conference paper
A Conference Poster is a visual presentation of research findings, displayed at an academic or professional conference to facilitate discussion and knowledge exchange.
conference poster
An Interim Report is a report that provides a temporary or progress-based assessment of an ongoing project, research, or operational activity, documenting current findings, challenges, and future directions before the final report is completed.
interim report
A Research Data Repository is a data portal designed for the preservation, management, and sharing of research datasets, ensuring long-term accessibility and compliance with open science principles.
research data repository
Open Science Framework (OSF), Harvard Dataverse
A Repository Hosting Data Portal is a data portal that provides infrastructure and tools for hosting datasets, code, and publications in a structured and accessible format.
repository hosting data portal
An Experimental Dataset is a dataset that contains measured or observed data collected from laboratory experiments, physical tests, or scientific investigations.
experimental dataset
A Reference Dataset is a dataset that serves as a benchmark or standardized collection of data used for validation, comparison, and reproducibility in scientific research and engineering applications.
Reference data of materials - are documented according to certain standards as well as - are curated (i.e., generated, maintained, preserved, validated) according to certain standards - are quantitative data sets (i.e., data + their corresponding metadata) - have been measured or simulated to a particularly high standard, and - are generated for a material that has either experienced a well-documented process or is reference material or its composition and structure has been completely characterized. Reference data of materials can also be derived data from reference data. These data are distributed with a license (e.g., GPL). The here addressed standards for documentation, curation and measurement need to be defined for specific materials characteristics (e.g., creep tests) in terms of domain standards. These domain standards are the result of a steered community process. Standards should integrate as much as possible existing standards (e.g., the individual MatWerk domain standards should be as much as possible consistent).
reference dataset
BAM reference data: results of ASTM E139 -11 creep tests on a reference material of Nimonic 75 nickel-base alloy (https://doi.org/10.5281/zenodo.7764161)
A Simulation Dataset is a dataset that contains data generated from computational models, numerical simulations, or digital twin environments to predict material behaviors, properties, and interactions.
simulation dataset
Examples include DFT simulation datasets, molecular dynamics (MD) trajectory files, and phase-field modeling results.
A Large-Scale Facility is a service product that provides specialized, high-capacity infrastructure for scientific research, engineering, or computational purposes, supporting large-scale experiments, simulations, and data analysis in various domains.
large scale facility
HBN: Concerning the content of ‘Large-Scale Facility’ datasheet and its related knowledge graph, the ‘Large-Scale Facility’ class and its subclasses were created to define the types of used facilituies and respond to competency questions like: what large-scale facilities support research in field X, which organization provide facility Y, what is the contact point with facility Z, etc.
European Synchrotron Radiation Facility (ESRF), the Leibniz Supercomputing Centre (LRZ), CERN's Large Hadron Collider (LHC)
A Presentation Document is a document that consists of structured visual and textual content designed for conveying information to an audience, typically used in meetings, conferences, and educational settings.
presentation document
A place that provides a controlled environment equipped with specialized instruments and facilities for conducting scientific research, experiments, measurements, and testing across various disciplines.
laboratory
materials characterization laboratories, chemical analysis labs, high-energy physics laboratories
https://github.com/ISE-FIZKarlsruhe/nfdicore/issues/119 https://github.com/ISE-FIZKarlsruhe/nfdicore/issues/120
A Journal Article is a peer-reviewed scholarly publication that presents original research, review studies, or theoretical discussions, typically published in academic journals.
journal article
A Software Repository is a data portal designed to store, manage, and distribute software packages, source code, and related documentation for research, development, and deployment purposes.
software repository
GitHub, GitLab, Apache Software Foundation repositories
A Linked Data Portal is a data portal that supports the publication, access, and exploration of linked datasets using semantic web technologies and standardized data formats.
linked data portal
Wikidata Query Service, DBpedia, Europeana Linked Open Data portal
A data analysis portal is a data portal that provides tools, services, and computational resources for performing data analysis, visualization, and interpretation.
data analysis portal
JupyterHub platforms, KNIME analytics portals, R Shiny-based analysis environments
An event focused on interactive learning, where participants engage in hands-on activities or group work to develop specific skills or knowledge.
workshop
An event where experts and scholars gather to present research, exchange ideas, and discuss advancements in a particular field.
conference
An event where participants collaborate intensively over a short period to develop technological solutions, such as software or hardware projects.
hackathon
An event where a subject matter expert delivers a formal presentation to inform or educate an audience about a specific topic.
lecture
An event structured as a program of study, offering instruction on a particular subject, often leading to certification or academic credit.
course
An event held during the summer, providing specialized courses or workshops to supplement regular academic studies or offer additional learning opportunities.
summer school
An event where a small group of participants discuss a specific topic in depth, often involving presentations and interactive discussions.
seminar
An event where researchers and experts present and discuss their work, often centered around a specific theme or area of study.
symposium
An event featuring a group of experts who share their insights and engage in a moderated discussion on a particular subject, followed by audience questions.
panel discussion
A process that involves the collection, organization, cleaning, analysis, storage, and sharing of data to ensure its accuracy, accessibility, and usefulness for decision-making, research, or other applications. Data handling encompasses all stages from raw data generation to its final visualization or publication.
data handling process
A data handling process where raw data is generated through experiments, observations, or data collection tools, often as the initial step in the data lifecycle.
data producing process
A data handling process where raw data is cleaned, transformed, and analyzed to extract meaningful insights, patterns, or trends.
data processing process
A data handling process involving the organization and structuring of data into datasets for easier access, analysis, and sharing.
dataset creation process
A data handling process where metadata, descriptions, and details about datasets are recorded to ensure clarity, context, and proper usage by others.
dataset documenting process
A data handling process where incorrect, incomplete, or irrelevant data is identified and corrected or removed to improve the quality of the dataset.
data cleaning process
A data handling process involving the conversion of data into a different format, structure, or scale to make it compatible with analysis tools or systems.
data transformation process
A data handling process where data from multiple sources are combined or merged to create a cohesive and comprehensive dataset for analysis.
data integration process
A data handling process where data is securely stored in databases or other systems, ensuring it can be retrieved and accessed as needed.
data storage process
A data handling process where data is represented visually through charts, graphs, or other formats to aid in understanding and decision-making.
data visualization process
A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
software method
A software module is software composed of a collection of software methods.
software module
A software script is software whose instructions can be executed using a software interpreter.
software script
example to be eventually removed
The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job
failed exploratory term
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.
metadata complete
Term created to ease viewing/sort terms for development purpose, and will not be included in a release
organizational term
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."
ready for release
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
metadata incomplete
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
uncurated
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.
pending final vetting
placeholder removed
An editor note should explain what were the merged terms and the reason for the merge.
terms merged
This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use.
term imported
This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created.
term split
Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents.
A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf
universal
A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal
"definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal.
defined class
A named class expression is a logical expression that is given a name. The name can be used in place of the expression.
named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions
named class expression
Terms with this status should eventually replaced with a term from another ontology.
to be replaced with external ontology term
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.
requires discussion
The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not.
This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease.
An academic discipline that focuses on the study, design, and application of electrical systems and technologies. Electrical engineering involves the development of devices, circuits, and systems for power generation, communication, electronics, and automation.
electrical engineering
An academic discipline that focuses on the design, optimization, and operation of industrial processes to transform raw materials into valuable products. Process engineering applies principles of chemistry, physics, and engineering to improve efficiency, sustainability, and safety in industries such as manufacturing, energy, and pharmaceuticals.
process engineering
Russell, S., & Norvig, P. (2020). Artificial Intelligence: A Modern Approach. Pearson.
Artificial Intelligence (AI) is a sub-discipline of Computer Science that focuses on creating systems capable of performing tasks that require human-like intelligence, such as learning, reasoning, and problem-solving.
artificial intelligence
Deep learning for image recognition, reinforcement learning in robotics, and natural language processing fall under Artificial Intelligence.
Theoretical Computer Science is a sub-discipline of Computer Science that focuses on mathematical models of computation, computational complexity, and algorithmic problem-solving
theoretical computer science
Studies on Turing machines, complexity classes (P vs NP), and formal languages belong to Theoretical Computer Science.
Software Engineering is a sub-discipline of Computer Science that applies engineering principles to the design, development, testing, and maintenance of software systems.
software engineering
Agile software development, DevOps practices, and software architecture design fall under Software Engineering.
Provost, F., & Fawcett, T. (2013). Data Science for Business. O'Reilly Media.
Data Science is a sub-discipline of Computer Science that integrates statistical methods, machine learning, and data processing techniques to extract insights and knowledge from structured and unstructured data.
data science
Predictive analytics, big data visualization, and recommendation systems are part of Data Science.
Stallings, W. (2020). Network Security Essentials. Pearson.
Cybersecurity is a sub-discipline of Computer Science that focuses on protecting computer systems, networks, and data from cyber threats, vulnerabilities, and unauthorized access.
cybersecurity
Encryption techniques, intrusion detection systems, and ethical hacking studies belong to Cybersecurity.
Active Status is a status specification that indicates an entity, process, or project is currently operational, ongoing, or in execution.
active status
Cancelled Status is a status specification that indicates an entity, process, or project has been terminated before reaching completion due to internal or external factors.
cancelled status
Doctor (PhD or equivalent academic doctorate)
Dr.
Doctor of Engineering (German doctorate in engineering).
Dr.-Ing.
Finished Status is a status specification that indicates an entity, process, or project has successfully reached its intended goal and is considered complete.
finished status
Hybrid Implementation is an event implementation specification that defines the organization of an event that integrates both physical (on-site) and virtual (online) participation modes
hybrid implementation
Internal Access is an information access specification that defines policies and mechanisms restricting access to information exclusively within an organization, institution, or research group.
internal access
Master of Science (graduate degree in science/engineering).
M.Sc.
On-Site Implementation is an event implementation specification that defines the organization of an event that occurs exclusively at a physical location with in-person attendance.
on site implementation
Online Implementation is an event implementation specification that defines the organization of an event conducted entirely through virtual platforms, enabling remote participation via digital communication technologies.
online implementation
Open Access is an information access specification that defines policies allowing unrestricted public access to information resources, ensuring free availability without subscription or payment barriers.
open access
Organizational Funding is a funding specification that defines the financial structures, budgets, and resource allocation strategies for sustaining the operations of an organization or institution.
organizational funding
Paused Status is a status specification that indicates an entity, process, or project is temporarily halted but may resume at a later stage.
paused status
Paywall Access is an information access specification that defines policies requiring users to purchase, subscribe, or obtain institutional licenses to access digital or physical information resources.
paywall access
Privatdozent (Dr. with habilitation, qualified to teach at a university)
PD. Dr.
Privatdozent with Habilitation (higher academic qualification in Germany)
PD. Dr. habil.
Planning Status is a status specification that indicates an entity, process, or project is in a preparatory or strategic development phase before execution.
planning status
Professor (academic title for a senior faculty member).
Prof.
Prof. Dr.
Professor with a doctorate in engineering.
Prof. Dr.-Ing.
Project Funding is a funding specification that defines the financial mechanisms, grants, and investment strategies used to support specific research, development, or innovation projects.
project funding
Restricted Access is an information access specification that defines policies limiting access to specific users, organizations, or groups based on predefined criteria such as confidentiality, security, or legal regulations.
restricted access
Self-Funding is a funding specification that defines the use of personal, internal, or independently generated financial resources to support activities, projects, or organizations without relying on external funding sources.
self funding
Test Phase Status is a status specification that indicates an entity, process, or project is undergoing testing, evaluation, or validation before finalization.
test phase status
Two Doctor degrees (PhD or equivalent academic doctorate)
Dr. Dr.
An academic discipline focused on human culture, thought, and creativity, encompassing disciplines like literature, philosophy, and the arts.
humanity
An academic discipline that studies society and human behavior through disciplines like sociology, psychology, and economics.
social science
An academic discipline that studies living organisms, their structures, functions, growth, and interactions with their environment. Biology explores the diversity of life, from microscopic organisms to complex ecosystems, and seeks to understand the underlying processes of life, evolution, and heredity.
biology
An academic discipline that focuses on the science and practice of diagnosing, treating, and preventing illnesses and injuries. Medicine involves the study of human health, medical technologies, pharmaceuticals, and patient care to improve well-being and extend life.
medicine
An academic discipline that focuses on the science, practice, and business of cultivating plants, raising animals, and producing food, fiber, and other products. Agriculture involves the study of soil management, crop production, livestock care, and sustainable farming practices to ensure food security and environmental sustainability.
agriculture
An academic discipline that studies the natural world through observation, experimentation, and analysis. Natural science includes fields such as physics, chemistry, biology, and earth sciences, aiming to understand the laws and processes governing the universe and life on Earth.
natural science
An academic discipline that studies the composition, structure, properties, and reactions of matter. Chemistry focuses on understanding how substances interact, transform, and combine to form new materials, playing a crucial role in fields such as medicine, energy, and environmental science.
chemistry
An academic discipline that explores the fundamental principles governing the behavior of matter, energy, and the forces of nature. Physics seeks to understand the laws of the universe, from subatomic particles to cosmic phenomena, through experimentation, observation, and mathematical modeling.
physics
An academic discipline that involves the study of numbers, quantities, shapes, and patterns, using abstract concepts and logical reasoning. Mathematics is fundamental to various fields, including science, engineering, economics, and technology, providing tools for problem-solving, analysis, and modeling.
mathematics
An academic discipline that focuses on the study of the Earth’s structure, processes, and materials, including the atmosphere, oceans, and landforms. Geoscience encompasses fields such as geology, meteorology, and environmental science to understand Earth’s history, natural resources, and natural hazards.
geoscience
An academic discipline that focuses on the design, analysis, manufacturing, and maintenance of mechanical systems. Mechanical engineering applies principles of physics, materials science, and mathematics to develop machines, tools, and devices used in industries such as transportation, energy, and robotics.
mechanical engineering
An academic discipline that explores the properties, performance, and applications of materials, focusing on the relationship between a material's structure and its characteristics. Materials science and engineering involves the design, development, and testing of materials for use in a wide range of industries, including aerospace, electronics, and manufacturing.
materials science
An academic discipline that focuses on the study of algorithms, data structures, programming, and computational systems. Computer science explores how to design, develop, and analyze software and hardware solutions to solve complex problems and advance technology.
computer science
An academic discipline that focuses on the planning, design, and management of construction projects, including buildings, infrastructure, and other structures. Construction engineering integrates principles of civil engineering, project management, and materials science to ensure safety, efficiency, and sustainability in construction processes.
construction engineering