Adrien Barton Jean-François Ethier Paul Fabry An ontology of laboratory test specifications - full version, imports merged. Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label editor preferred term example of usage has curation status definition definition editor note term editor alternative term definition source curator note imported from elucidation has associated axiom(nl) has associated axiom(fol) has axiom label An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC alternative term has_exact_synonym is part of 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 https://code.google.com/p/obo-relations/wiki/ROAndTime 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 http://www.obofoundry.org/ro/#OBO_REL:part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes has measurement unit label An information artifact IA mentions an entity E exactly when it has a component/part that denotes E 7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity) 7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation "mentions" in it's (logical) definition PERSON: Jonathan Rees Person: Alan Ruttenberg mentions The inverse relationship of directs. directed by The relationship between a directive information entity and the process it directs. directs has minimal value has maximal value x is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence 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. bearer_of is bearer of bearer of 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 participates_in participates in 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. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant 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, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. 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). 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 specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes 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. is role of role_of role of 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 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 disposition of An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member A relation between a value specification and a number that quantifies it. A range of 'real' might be better than 'float'. For now we follow 'has measurement value' until we can consider technical issues with SPARQL queries and reasoning. PERSON: James A. Overton OBI has specified numeric value A relation between a value specification and a literal. This is not an RDF/OWL object property. It is intended to link a value found in e.g. a database column of 'M' (the literal) to an instance of a value specification class, which can then be linked to indicate that this is about the biological gender of a human subject. OBI has specified value BFO:0000001 entity 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 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) BFO:0000003 occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant 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]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. 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]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] 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]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition 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. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity 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 To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality 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 a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant 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 role of being a doctor 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] 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 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role 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 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. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant 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]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function 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. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality 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. a marriage bond, an instance of requited love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) 1 HADO:0000004 An individual organism identifier that is used to identify a beneficiary of some health insurance. health insurance identifier 1 HADO:0000006 A CRID symbol that is sufficent to look up a patient file in a medical record registry. medical record identifier HADO:0000008 patient IAO:0000003 measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label IAO:0000005 objective specification 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? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000007 Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification IAO:0000009 datum label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 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. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ 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 PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000028 symbol 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). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. 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. PERSON: Chris Stoeckert OBI_0000142 information content entity IAO:0000033 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000104 plan specification 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 that, when concretized, 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. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum IAO:0000300 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. PERSON: Lawrence Hunter text textual entity IAO:0000302 author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification IAO:0000310 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 PERSON: Lawrence Hunter document IAO:0000314 document part An abstract, introduction, method or results section. an information content entity that is part of a document PERSON: Lawrence Hunter document part IAO:0000577 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. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID symbol Original proposal from Bjoern, discussions at IAO calls centrally registered identifier symbol IAO:0000578 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. 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. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID Original proposal from Bjoern, discussions at IAO calls centrally registered identifier IAO:0000579 PubMed is a CRID registry. It has a dataset of PubMed identifiers associated with journal articles. A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process. PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls centrally registered identifier registry IAO:0000590 written name "Bill Clinton" "The Eiffel Tower" "United States of America" A textual entity that denotes a particular in reality. PERSON: Bill Hogan https://github.com/information-artifact-ontology/IAO/issues/114 The qualifier "written" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so "All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT" would be a name. written name 1 LABO:0000004 'accession-id #150' in 'accession-id #150 whole blood 3 ml' A centrally registered identifier that denotes a particular specimen on which a laboratory test is intended to be executed or has already been executed. TODO identification d'échantillon d'examen de laboratoire laboratory test specimen ID LABO:0000005 'whole blood' in 'accession-id #150 whole blood 3 ml' An information content entity about the type of the specimen to be used for some laboratory tests. Une donnée qui est supposée être une proposition vraie à propos du type de l'échantillon pour lequel des tests ont été prescrits. laboratory test specimen type specification spécification de type d'échantillon LABO:0000006 A measurement datum specifying how much of a person's blood is made of red blood cells. Une mesure qui spécifie quelle portion du sang d'une personne est composée de cellules rouges. https://www.urmc.rochester.edu/encyclopedia/content.aspx?contenttypeid=167&contentid=hemoglobin This measurement datum is a volume/volume measure which compares the volume of hemoglobin in one's blood to the total volume of blood in one's body. hematocrit result résultat d'hématocrite LABO:0000007 A measurement datum which specifies the amount of hemoglobin in a person's blood. Une mesure qui spécifie la quantité d'hémoglobine dans le sang d'une personne. https://www.mayoclinic.org/tests-procedures/hemoglobin-test/about/pac-20385075 This measurement datum is a mass/volume measure which compares the mass of hemoglobin in one's blood to the total volume of blood in one's body. hemoglobin test result résultat de test d'hémoglobine LABO:0000008 A data item intended to be a truthful statement about the sampling method used to extract a sample from an entity. Une donnée supposée être une proposition vraie à propos de la méthode d'échantillonnage utilisée pour extraire un échantillon particulier d'une entité. sampling method specification spécification de méthode échantillonnage LABO:0000009 A measurement datum specifying the average size of a person's red blood cells. Une mesure qui spécifie la taille moyenne des cellules rouges d'une personne. https://www.urmc.rochester.edu/encyclopedia/content.aspx?contenttypeid=167&contentid=complete_blood_count mean corpuscular volume result résultat de volume corpusculaire moyen LABO:0000010 A measurement datum specifying the average size of the platetels in a person's blood. Une mesure qui spécifie la taille moyenne des plaquette du sang d'une personne. https://en.wikipedia.org/wiki/Mean_platelet_volume mean platelet volume result résultat de volume moyen des plaquettes LABO:0000011 A measurement datum which specifies the number of platelet cells in a person's blood. Une mesure qui spécifie le nombre de plaquettes dans le sang d'une personne. https://www.urmc.rochester.edu/encyclopedia/content.aspx?contenttypeid=167&contentid=platelet_count platelets count result résultat de dénombrement de plaquettes LABO:0000012 A measurement datum which specifies the number of red blood cell in a person's blood. Une mesure qui spécifie le nombre de cellules rouges dans le sang d'une personne. https://www.urmc.rochester.edu/encyclopedia/content.aspx?contenttypeid=167&contentid=red_blood_cell_Count red blood cell count result résultat de dénombrement de cellules rouges LABO:0000013 A measurement datum which specifies the range of variation of the size of red blood cell in a person's blood. Une mesure qui spécifie l'étendue de la variation de la taille des cellules rouges dans le sang d'une personne. https://en.wikipedia.org/wiki/Red_blood_cell_distribution_width red cell distribution width result résultat de variation de taille des cellules rouges LABO:0000017 An information content entity that encompasses all relevant information pertaining to a given laboratory test prescription. TODO information de compte-rendu de test de laboratoire prescribed laboratory test complete reporting information LABO:0000018 A health care prescription specifying the realization of one or several laboratory test(s). laboratory test prescription prescription de test de laboratoire LABO:0000019 An information content entity which reports on some aspect of a particular laboratory test. Une entité de contenu informationnel qui documente un ou plusieurs aspects d'un certain test de laboratoire. information de résultat pour un test de laboratoire (WIP) laboratory test reporting information LABO:0000020 'serum sodium 140 mmol/L, 2018/08/14' (à revoir) Une partie d'un document d'analyse de laboratoire qui spécifie le résultat d'un test spécifique qui a été soit prescrit par une prescription de test de laboratoire, soit réalisé comme conséquence d'une prescription de test de laboratoire. A laboratory test reporting item that includes the result of the laboratory test. laboratory test result item LABO:0000021 Example 1: 'CBC: - WBC 12.1 10^9/L - RBC 5.2 10^12/L [...]' in a report on tests directed by a complete blood count prescription. Example 2: 'serum sodium in progress' A laboratory test reporting information which reports on the test(s) directed by one laboratory test directive item. Une partie d'un document d'analyse de laboratoire qui spécifie des résultats des tests. A laboratory test reporting group does not necessarily provide the reporting information concerning a laboratory test directive item in a prescription - the directive item can also be specified e.g. in a research protocol. A laboratory test reporting group can, but doesn't have to, include a laboratory test reporting item, as in 'CBC in progress' (which is not a laboratory test reporting item, because it reports on several tests, not just one). groupement de résultats pour un test de laboratoire laboratory test reporting group LABO:0000023 A value specification that is the the lower bound or the upper bound of a range. bound valeur limite 1 1 1 LABO:0000100 'serum sodium in progress, 2018/07/25' 'serum sodium 140 mmol/L, 2018/08/14' 'blood group O, 2018/07/12 12:34 pm' A laboratory test reporting information that is part of a laboratory test reporting group, that is about a laboratory test, and that mentions which characteristic of a specimen this test was supposed to assess, and a time at which this information was valid. laboratory test reporting item LABO:0000101 'in progress' in 'FSC, in progress, 2018/07/25' 'resulted' in 'blood group O, resulted, 2018/07/12 12:34 pm' 'validated' in 'serum sodium 140 mmol/L, validated, 2018/07/28' A laboratory test reporting information that specifies the status of a laboratory test or a group of laboratory tests. laboratory test status specification LABO:0000102 'serum sodium concentration' in 'serum sodium concentration 140 mmol/L, validated, 2018/07/28' An information content entity that specifies a particular characteristic of a specimen or a class of characteristics of specimens. specimen characteristic specification LABO:0000103 A document reporting on a laboratory test. laboratory test report document 1 LABO:0000104 All tests (white blood cells, red blood cells, etc.) realized when executing a prescription of CBC for John Smith on 2018/07/28. A health care process assay that is the mereological sum of laboratory test(s) that are directed by a single prescription directive item. directed laboratory test group LABO:0000105 'complete blood count' 'serum sodium' An action specification that directs one or several laboratory tests and such that none of its proper parts directs some but not all of those laboratory tests. A laboratory test directive item can direct several tests - consider e.g. 'CBC' (complete blood count), which directs more than 20 tests (red blood cells, white blood cells, hemoglobin, etc.) Many laboratory test directive items are parts of a prescription, but not all - consider e.g. an instruction directing a laboratory test as part of a research study. laboratory test directive item LABO:0000106 '2018/08/22' in 'CBC on 2018/08/22' An information content entity that specifies at what time a laboratory test should start. Not all laboratory test prescription items specify a start time. It is sometimes implicit when it is to be done. laboratory test start time specification LABO:0000107 A measurement assay that has as input a specimen derived from an organism and that aims as having as output a data item that is about an entity related to the specimen. Not all laboratory tests are directed by a prescription, e.g. a laboratory test executed as part of a research project, or an additional test realized by a laboratory technician in case a first prescribed laboratory test led to an abnormal result. A laboratory test is directed by some instruction that is part of a plan specification with the objective to assess some entity related to a specimen (e.g. one of its quality) specified by a specimen characteristic specification. However, a laboratory test can be interrupted without leading to a completed laboratory test. laboratory test LABO:0000108 A completed laboratory test that has as specified output a laboratory finding. A completed laboratory test that involved a problem of calibration can lead to some result, but this result does not support an inference about a quality of the patient, and therefore is not a laboratory finding. validated laboratory test LABO:0000109 A representation of an entity related to a specimen that is the output of a laboratory test. A laboratory result is not necessarily a laboratory finding, as it cannot always support an inference to an assertion about some quality of the patient. For example, the serum sodium result of a miscalibrated machine is not a laboratory finding. Also, a laboratory result by automatic detection "70.10^3 /microliter" for platelets might be falsely low due to platelets clumping. However, a laboratory finding is always a laboratory result. laboratory result LABO:0000110 '2018/07/25, 12:34 pm' in a laboratory test reporting information 'serum sodium in progress, 2018/07/25, 12:34 pm' A laboratory test reporting information that specifies a time at which a laboratory test reporting item was valid. This time specification does not refer to the time when a given lab document was generated, but rather the moment at which information from the laboratory test process was created as it unfolded. laboratory test reporting item time specification LABO:0000111 'to follow rhumatoid arthritis' on a prescription for a test of sedimentation rate 'to exclude pulmonary embolism' on a guideline document about d-dimer A health care objective specification that specifies why a laboratory test should be performed. laboratory test objective specification LABO:0000112 A laboratory test objective specification that is a part of a laboratory test prescription. prescription of laboratory test objective specification 1 LABO:0000113 'accession-id #150 whole blood 3 ml' An information content entity that denotes a particular specimen on which a laboratory test is intended to be executed or has already been executed. Une entité de contenu informationnel qui est à propos d'une entité biologique particulière ou d'une classe d'entité biologique sur laquelle quelqu'un a l'intention de prendre une mesure ou sur laquelle une mesure a déjà été prise. laboratory test specimen specification LABO:0000114 A generically dependent continuant that specifies a lower bound and an upper bound. It can also specify whether each bound is included or not in the interval. range 1 1 LABO:0000117 A range of values asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. Definition adapted from OGMS' definition for "normal value". "Normal value" and "normal range" should be coordinated. laboratory test result normal range LABO:0000120 A bound that is the lower bound of a range. lower bound LABO:0000121 A bound that is the upper bound of a range. upper bound LABO:0000122 A lower bound value of a laboratory test result normal range. laboratory test result normal range lower bound LABO:0000123 An upper bound value of a laboratory test result normal range. laboratory test result normal range upper bound LABO:0000124 'CBC, INR q2h start 2h post-op for 24h' composed by the items 'CBC' and 'INR' and a starting condition statement '2h post-op', a continuing condition statement 'for 24h' and a testing condition statement 'q2h' 'CBC' that is composed by a single laboratory test directive item. An action specification that has as parts one or several laboratory test directive items, as well as possibly some statements specifying a starting condition, a stopping condiiton and a testing condition. laboratory test directive item group LABO:0000129 A laboratory test result normal range that is reported in a laboratory test reporting item. reported laboratory test result normal range LABO:0000130 '140 g/L' as a result of hemgolobin concentration A laboratory result that has a scalar value specification. scalar laboratory result LABO:0000131 '[20,80] APL units' as a result of anticardiolipin antibody A laboratory result that is given as a range. range laboratory result LABO:0000132 'negative' as a result of HIV test A laboratory result that is given as a textual entity. textual laboratory result LABO:0000133 [0, 100000] ppm of Hg [-10 V,+30 V[ A range of values asserted as possible valid values by the testing lab or the kit manufacturer. It is about all laboratory results from all laboratory tests of a given kind. laboratory test definition range LABO:0000134 result range 1 1 1 1 LABO:0000135 A range value specification that specifies a lower and an upper bound and wether each bound is included or excluded. fully specified range value specification LABO:0000136 - " [ " in "]1,3[" - "] " "]1,3[" - "strictly" in "lower or equal to 6 and strictly greater than 0" - "or equal" in "lower or equal to 6 and strictly greater than 0" An information content entity that specifies whether a cutoff value should be included or excluded in a range. range inclusion specification LABO:0000137 A range inclusion specification written with interval notation. There are only two individuals. interval-notation range inclusion specification LABO:0000138 A range inclusion specification for the lower bound of a range. lower bound inclusion specification LABO:0000139 A lower bound inclusion specification specifying the lower bound is included. included lower bound inclusion specification LABO:0000140 A lower bound inclusion specification specifying the lower bound is excluded. excluded lower bound inclusion specification LABO:0000141 A range inclusion specification for the upper bound of a range. upper bound inclusion specification LABO:0000142 An upper bound inclusion specification specifying the upper bound is included. included upper bound inclusion specification LABO:0000143 An upper bound inclusion specification specifying the upper bound is excluded. excluded upper bound inclusion specification LABO:0000144 '[0,10[ ml/m2' is the derived normalized result of laboratory result: '<10 ml/m2'. A range laboratory result that is represented in a normalized way and that is the result of the transformation of an original laboratory result. derived normalized range laboratory result 1 LABO:0000145 closed range laboratory result 1 1 1 1 LABO:0000146 scalar range 1 1 LABO:0000149 derived normalized closed range laboratory result LABO:0000150 derived normalized scalar laboratory result LABO:0000152 derived normalized textual laboratory result LABO:0000153 A data item that was generated on the basis of a calculation. The definition is based on OBI's definition of 'predicted data item'. However, a data item that is generated on the basis of a calculation doesn't have to be the result of a prediction; it can be the result of an estimation. for example: the estimated glomerular filtration rate (eGFR) calculated data item 1 1 1 1 1 LABO:0000154 ' < 120 mmol' '[15, 20[' '3.5 to 10.5 billion/L' A value specification that has as part at least a lower bound or an upper bound. range value specification 1 1 LABO:0000155 closed range value specification 1 LABO:0000160 6% 0.08 154 ppm A value specification that specifies a ratio value, without any unit or with a dimensionless unit. ratio value specification LABO:0000161 'eGFR: 65 ml/min/1.73 m2' A calculated data item that is produced by a calculation process that has as input a laboratory result. laboratory result-based calculated data item LABO:0000162 '6%' as a result for HbA1C measurement '0.055' as a result for HbA1C measurement '50%' as a result for hematocrit measurement on a complete blood count A laboratory result that is given as a ratio. ratio laboratory result LABO:0000170 range calculated data item LABO:0000171 ratio calculated data item LABO:0000172 scalar calculated data item LABO:0000173 laboratory result-based scalar calculated data item LABO:0000174 laboratory result-based ratio calculated data item LABO:0000175 laboratory result-based range calculated data item LABO:0000176 derived normalized laboratory result-based range calculated data item LABO:0000177 laboratory test specification LABO:0000178 '12345' to refer to a serum creatinin test laboratory test identifier LABO:0000179 'serum creatinin test' laboratory test name 1 LABO:0000181 laboratory test reporting item identifier NCBITaxon:9606 human human being person human man Homo sapiens OBI:0000011 planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000093 patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch patient OBI, CDISC CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably patient role OBI:0000112 specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role OBI:0000659 drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process OBI:0000684 The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective OBI:0001141 individual organism identifier a CRID symbol used to distinguish one individual organism from another. PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual individual organism identifier OBI:0001616 specimen identifier A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation. Person: Chris Stoeckert, Jie Zheng specimen ID NIAID GSCID-BRC metadata working group Specimen ID NIAID GSCID-BRC specimen identifier 1 1 OBI:0001931 A value specification that consists of two parts: a numeral and a unit label PERSON:Bjoern Peters scalar value specification OBI:0001933 The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification OBI:0002076 collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0100051 specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen OGMS:0000014 A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z clinical finding OGMS:0000018 Can "a quality" be a mereological sum of qualities? For example, if a finding is "A+", which represents (at least) two qualities of the specimen, does it represent one quality that would be the mereological sume of those qualities? Note that a laboratory finding does not necessarily represent only a quality of a specimen. It can also represent e.g. a temporal duration (e.g. duration of coagulation). Therefore, we suggest changing the definition to "A representation of an entity related to a specimen that is the output of a laboratory test and that can support an inference to an assertion about some specifically dependent continuant of the patient." A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z laboratory finding OGMS:0000056 The output is not always about a quality of the specimen (it can be e.g. about a temporal duration when assessing the coagulation speed of a blood specimen). A measurement assay that has as input a patient-derived specimen and as output a data itme that is about a quality of the specimen. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:49:49Z A completed laboratory result might have as output several laboratory results such as a first nonvalidated result directly from the machine 'serum sodium 140 mmol/L' followed by a second validated result 'serum sodium 140 mmol/L'. laboratory test OGMS:0000096 A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient Albert Goldfain Sagar Jain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z editor date: 2017-04-18 health care process OGMS:0000108 A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. creation: 16MAY2017 Sagar Jain health care process assay OGMS:0000123 a data item that is about a patient and is the specified output of a health care process assay or diagnostic process creation date: 2018-11-27 clinical data item OMIABIS:0000060 A data set that contains the outcome of a survey. Alice Nzinga Mathias Brochhausen survey data OMIABIS:0001025 A plan specification that is realized by process of gathering information (e.g. by asking questions). Alice Nzinga Mathias Brochhausen survey plan specification OMIABIS:0001026 A document that contains information representing health-relevant qualities of a patient written in a chronological manner and that is primarily used for patient care in a clinical setting. Martin Fransson It is a chronological written account of examination, treatment, medical history or complaints. It is used interchangeably with health record and medical chart. https://en.wikipedia.org/wiki/Medical_record medical record OMIABIS:0001035 A planned process that realizes the concretization of a survey to generate an output(survey data.) survey execution OPMI:0000094 A name of a person, which can have different types human name https://en.wikipedia.org/wiki/Personal_name person name OPMI:0000095 Christian name forename given name https://en.wikipedia.org/wiki/Personal_name person first name OPMI:0000096 family name surname https://en.wikipedia.org/wiki/Personal_name person last name OPMI:0000097 https://en.wikipedia.org/wiki/Personal_name person middle name OPMI:0000098 https://en.wikipedia.org/wiki/Personal_name person full name OPMI:0000100 A person name that is given at birth birth name OPMI:0000102 A woman's surname before marriage Edison Ong, Oliver He https://en.wikipedia.org/wiki/Maiden_and_married_names maiden name OPMI:0000324 A person name that includes both the first and last name Edison Ong, Oliver He first and last name human first and last name person first and last name PDRO:0000001 "For patient: Mr Smith, should exercise for at least 30 minutes, 3 times weekly. signed Dr. Ronnie Shuz. Date: 15/11/01" A document authored by a health care provider that specifies how to realize some health care process for a particular patient. Un document créé par un fournisseur de soin indiquant comment réaliser une partie d'un processus de santé pour un patient particulier. prescription health care prescription prescription de santé 1 PDRO:0000003 A written name denoting a particular patient. Un nom écrit faisant référence à un patient particulier. identification d'un patient patient identification PDRO:0000005 A textual entity that denotes the time of document creation. Une entité textuelle indiquant l'instant de création d'un document. the granular time at which the author considers the document whole, ie ready for interpretation document creation time identification identification de l'instant de création d'un document PDRO:0000129 An information content entity that describes some relationships between some entities and whose truthfullness is a prerequisite for something. Une entité de contenu informationnel qui décrit des relations entre certaines entités et dont la véracité est un prérequis pour quelque chose. condition condition PDRO:0010010 "The alleviation of a symptomatic cough" "The prevention of malaria" "The diagnosis of what ails John Smith" An objective specification that specifies the objective of a health care process. Une spécification d'objectif d'un processus de soin ou d'une de ses parties. health care objective specification spécification d'objectif de santé owl:Thing 1 1 1 1 1 1 has part 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. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime 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 This document is about information artifacts and their representations is_about is 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. person:Alan Ruttenberg 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. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 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 person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification Note that a laboratory finding does not necessarily represent only a quality of a specimen. It can also represent e.g. a temporal duration (e.g. duration of coagulation). Therefore, we suggest changing the definition to "A value for an entity reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population." We suggest renaming this entity "lab report normal value", as "normal values" can appear in a variety of contexts. It seems that "normal value" should be classified under "value specification". To be changed using value specifications. inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in Adrien Barton Jean-François Ethier Paul Fabry An ontology of laboratory test specifications - full version, imports merged.