denotes
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
function of
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.
quality 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.
dataportal — NFDI-MatWerk ontology design pattern
Hossein Beygi Nasrabadi, Jörg Waitelonis, Ebrahim Norouzi, Kostiantyn Hubaiev, Harald Sack. NFDI MatWerk Ontology (mwo). Revision: v3.0.1. Retrieved from: http://purls.helmholtz-metadaten.de/mwo/3.0.1
CC BY 4.0 (repository); CC0 1.0 declared in the ontology header
Which data formats and PID systems does a given repository support?
Which data portals and repositories does NFDI-MatWerk reference?
Which organisation hosts a given portal, and what access conditions apply?
the dataportal tab of the NFDI-MatWerk curation workbook
Values become reusable and independently addressable, and one value may be shared by many entities. The cost: every `I` reference resolves by label, so labels must be unique and a typo yields a silently missing relation rather than an error.
To represent a data portal in the MatWerk Knowledge Graph: its identity, the value nodes that describe it, and its links to the other entities the NFDI-MatWerk consortium records.
SELECT ?x ?label WHERE { ?x a <https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0000123> ; <http://purl.obolibrary.org/obo/IAO_0000235> ?d . ?d <http://www.w3.org/2000/01/rdf-schema#label> ?label } LIMIT 10
ROBOT template directives, row 2 of the dataportal tab
“Crystallography Open Database Software (COD)” is a data portal, with name “Crystallography Open Database Software (COD)”; short description “Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.”; file formats “CIF, csv”.
has url
A relation between an information content entity and its specific url.
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
material entity
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.
(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
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
denoted by
inverse of the relation 'denotes'
participates in
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
role 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.
has disposition
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
disposition of
output of
licence
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
Crystallography Open Database Software (COD)
Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.
GraÅ¾ulis, S., DaÅ¡keviÄ, A., Merkys, A., Chateigner, D., Lutterotti, L., Quirós, M., Serebryanaya, N. R., Moeck, P., Downs, R. T. & LeBail, A. (2012). Crystallography Open Database Software (COD): an open-access collection of crystal structures and platform for world-wide collaboration. Nucleic Acids Research, 40, D420-D427. doi: 10.1093/nar/gkr900 (BibTeX, EndNote/Refer, plain text) Grazulis, S., Chateigner, D., Downs, R. T., Yokochi, A. T., Quiros, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le Bail, A. (2009). Crystallography Open Database Software â an open-access collection of crystal structures. Journal of Applied Crystallography, 42, 726-729. doi: 10.1107/S0021889809016690 (BibTeX, EndNote/Refer, plain text)
person
An object that represents a single human individual.
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
document
A journal article, patent application, laboratory notebook, or a book
A collection of information content entities intended to be understood together as a whole
contacting process
A process in which the contact information of an entity is provided.
data portal
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.
An online platform that provides access to datasets.
Bach digital, KultSam, MusiXplora
publication
A publication that is the output of a publishing process and a creative process.
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
specification
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.
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
website
An information content entity that represents a collection of interconnected web pages, multimedia content, and digital resources accessible via the World Wide Web.
A collection of webpages contributed by an organization or a person.
textual description
A textual entity that describe some resource.
title
A textual entity that denotes some resource.
process
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])
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
directive information 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
textual entity
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
has function
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 quality
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.
agent
An independent continuant that acts autonomously and is entrusted with the authority to represent, negotiate, or act on behalf of another 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
standard
A specification that establishes a set of guidelines, criteria, or norms recognized and adopted by internationational community.
An international standard and norm that can be used to evaluate or create a resource.
is subject of
disposition
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.
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
realizable entity
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.
(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
function
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.
(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
is about
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
has participant
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.
agent 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.
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time.
(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.
role
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.
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
generically dependent continuant
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])
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
characteristic of
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.
has output
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.
creative process
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.
entity
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
(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
continuant
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
(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
quality
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
(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
specifically dependent continuant
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])
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
has role
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.
independent continuant
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])
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
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity.
A generically dependent continuant that is about some thing.
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.
has characteristic
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.