en IAO_0020000-IAO_0020999 IAO_0021000-IAO_0021999 Adam Goldstein Alan Ruttenberg Albert Goldfain Amanda Hicks Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Clint Dowland Cooper Stansbury Darren Natale David Osumi-Sutherland Diya Mehta Emma Chappell Gwen Frishkoff Holger Stenzhorn J. Neil Otte J. Neil Otte James A. Overton James Malone Jane Ball Jennifer Fostel Jie Zheng John Judkins Jonathan Bona Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Matthew Diller Melanie Courtot Michel Dumontier Mihail Eduard Tudoreanu Nels D. Sanddal Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Robert J. Winchell Robert T. Maxson Rohit Pradhan Ron Rudnicki Rosemary Nabaweesi S. Clint Dowland S. Clint Dowland Sarah Bost Sarah Bost Satya Sahoo Sivaram Arabandi Stephen M. Bowman Werner Ceusters William Duncan William Hogan William R. Hogan William R. Hogan Yongqun (Oliver) He Amanda Hicks Laura Slaughter Mathias Brochhausen Mathias Brochhausen Mauricio B. Almeida The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). The ontology is based on a theory of document acts proposed by Barry Smith and Reinach's theory of social acts and legal entities: Reinach, A. (1989), Sämtliche Werke. Texkritische Ausgabe, Edited by Karl Schuhmann and Barry Smith, München: Philosophia Verlag. Smith, B. (2008) “Searle and de Soto: The new ontology of the social world”, The Mystery of Capital and the Construction of Social Reality, B. Smith, D.M. Mark and I. Ehrlich, United States, Open Court., 35-52. Smith, B. (2012) "How to Do Things With Documents", Rivista di estetica, 50 (2/2012), LII: 179-198. However, there are some amendments from our side which are to be found in the documentation. PNO http://creativecommons.org/licenses/by/4.0/ Information Artifact Ontology (IAO) Ontology of Organizational Structures of Trauma centers and Trauma Systems document act ontology proper name ontology http://creativecommons.org/licenses/by/3.0/ An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO Development of this ontology is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health. IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 2022-11-07 development version 2022-07-05 release version - 2025-01-24 release version 2021-06-11 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 The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label example of usage A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage in branch An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet. GROUP:OBI OBI_0000277 in branch has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obofoundry.org/obo/obi> editor note editor note term editor Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative label A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note curator note curator notes term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester is denotator type Relates an class defined in an ontology, to the type of it's denotator In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type') Alan Ruttenberg is denotator type imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from expand expression to ObjectProperty: RO_0002104 Label: has plasma membrane part Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones Chris Mungall expand expression to expand assertion to ObjectProperty: RO??? Label: spatially disjoint from Annotations: expand_assertion_to "DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom. Chris Mungall expand assertion to first order logic expression PERSON:Alan Ruttenberg first order logic expression antisymmetric property part_of antisymmetric property xsd:true Use boolean value xsd:true to indicate that the property is an antisymmetric property Alan Ruttenberg antisymmetric property OBO foundry unique label An alternative name for a class or property which is unique across the OBO Foundry. The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label has ID digit count Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix" annotation property value concatenated with an integer in the id range (left padded with "0"s to make this many digits) Person:Alan Ruttenberg has ID digit count has ID range allocated Datatype: idrange:1 Annotations: 'has ID range allocated to': "Chris Mungall" EquivalentTo: xsd:integer[> 2151 , <= 2300] Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms Person:Alan Ruttenberg has ID range allocated to has ID policy for Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relating an ontology used to record id policy to the ontology namespace whose policy it manages Person:Alan Ruttenberg has ID policy for has ID prefix Ontology: <http://purl.obolibrary.org/obo/ro/idrange/> Annotations: 'has ID prefix': "http://purl.obolibrary.org/obo/RO_" 'has ID digit count' : 7, rdfs:label "RO id policy" 'has ID policy for': "RO" Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with "0"s to make this many digits) to construct an ID for a term being created. Person:Alan Ruttenberg has ID prefix elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) is allocated id range Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. "IAO_0020000-IAO_0020999" PERSON:Alan Ruttenberg Add as annotation triples in the granting ontology is allocated id range retired from use as of relates a class of CRID to the date after which further instances should not be made, according to the central authority In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp Alan Ruttenberg retired from use as of has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. Nicolas Matentzoglu has ontology root term may be identical to A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged. David Osumi-Sutherland #40 VFB Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. may be identical to scheduled for obsoletion on or after Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date. Chris Mungall, Jie Zheng https://github.com/geneontology/go-ontology/issues/15532 https://github.com/information-artifact-ontology/ontology-metadata/issues/32 GO ontology scheduled for obsoletion on or after has axiom id Person:Alan Ruttenberg Person:Alan Ruttenberg A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI has axiom label instance unique identifier An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system. IUI term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by ISA alternative term IEDB alternative term This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL. OBO Operations call logical characteristic of object property 'part disjoint with' 'defined by construct' """ PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX : <http://example.org/ CONSTRUCT { [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?a ; owl:disjointWith [ a owl:Restriction ; owl:onProperty :part_of ; owl:someValuesFrom ?b ] ] } WHERE { ?a :part_disjoint_with ?b . } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. defined by construct A description of an OOSTT class that is aimed at the OOSTT user community and not meant to be definition for use in ontology development, curation or maintenance. Mathias Brochhausen OOSTT user-centered description A label that is used specifically by CAFE applications (www.cafe-trauma.org). Mathias Brochhausen CAFE application label An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation never in taxon never_in_taxon present in taxon present_in_taxon external_definition axiom_lost_from_external_ontology homology_notes has_relational_adjective taxon_notes Unique Apollo Label excluded subClassOf created by creation date has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 database_cross_reference An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has_obo_namespace An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has_synonym_type id in_subset label label 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of 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 http://purl.obolibrary.org/obo/ro.owl [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 site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process aggregate of aggregate_of is aggregate of The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. c = pattern in the ink b = paper + ink r = friend c specifically denotes r =def r is a portion of reality & c is a particular quality & c depends specifically on some independent continuant b & b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. Case 1 Memory trace as mark created when reading some description of some friend. The trace can denote. Case 2 Pattern of ink arrayed on paper as mark when writing down a friend's name Case 3 Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file. 8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_specifically denotes true 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 see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote obsolete_materially denotes true obsolete_describes true obsolete_represents true inverse of the relation 'denotes' Person: Jie Zheng, Chris Stoeckert, Mike Conlon denoted by relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point has coordinate unit label relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of inverse of the relation of is quality measurement of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg is quality measured as A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality. Person:Alan Ruttenberg Person:Bjoern Peters is quality specification of inverse of the relation of is quality specification of 2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship Person:Alan Ruttenberg Person:Bjoern Peters quality is specified as relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken Alan Ruttenberg has time stamp relates a time stamped measurement datum to the measurement datum that was measured Alan Ruttenberg has measurement datum x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.. Mathias Brochhausen obsolete_designates true x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place. Mathias Brochhausen is_borrowed_reference_to x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the. Mathias Brochhausen is_fixing_reference_to p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context. Mathias Brochhausen is designated by d socio-legally revokes s if s participates in d and at the end of d s no longer exists. It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question. Mathias Brochhausen legally revokes d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical. Mathias Brochhausen obsolete_legally transfers true is_specified_input_of A relation between an information content entity and a value specification that specifies its value. OBI has value specification BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. is-aggregate-of OBSOLETE 'organize' holds between an independent continuant and a planned process, iff the independent continuant particpates in the planned process and also participated in the creation of the plan specification that the planned process realizes. Mathias Brochhausen It would need further development, but it is not used by any other terms. obsolete organize true OBSOLETE This relation holds between two specifically dependent continuants, a and b, where b is of its nature such that it cannot exist unless a exists and where a is of its nature such that it cannot exist unless b exists. John Judkins Mathias Brochhausen http://ncor.buffalo.edu/2016/deontic-gainesville.pdf It would need further development, but it is no longer used by any other terms. It would need further development, but it is no longer used by any other terms. obsolete mutually specifically depends on true OBSOLETE A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Prescribing is what happens when an information content entity created, ratified, or issued by an entity with authority over the domain the ICE targets states actions or specifications or the omission of actions that are expected to be adhered to. Neil J. Otte It would need further development, but it is not used by any other terms. obsolete prescribes true x has policy y if x is an organization, y is a directive information entity that is the outcome of a document act, and y is meant to regulate the actions of either x or x’s members. Mathias Brochhausen S. Clint Dowland has policy x services geographical region y if x is an organization and y is a geographical region in which x is performing or organizing planned processes that benefit third parties. Mathias Brochhausen S. Clint Dowland services geographical region Inverse of 'has policy'. Mathias Brochhausen S. Clint Dowland policy of bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer_of has characteristic 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 http://purl.obolibrary.org/obo/ro.owl participates in 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 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. http://purl.obolibrary.org/obo/obi.owl is concretized as concretizes 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. http://purl.obolibrary.org/obo/obi.owl concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role 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 This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ location_of location of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ located_in http://www.obofoundry.org/ro/#OBO_REL:located_in located in This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation. the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. 2D_boundary_of boundary of is 2D boundary of is boundary of 2D boundary of my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. has boundary has_2D_boundary has 2D boundary before or simultaneous with simultaneous with x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/ro.owl http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent http://purl.obolibrary.org/obo/ro.owl has active participant temporally related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships http://purl.obolibrary.org/obo/ro.owl mereotopologically related to 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 http://purl.obolibrary.org/obo/ro.owl member of has member is a mereological relation between a collection and an item. SIO has member A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity. http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.owl condition ameliorated by DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information. DEPRECATED inheres in true DEPRECATED bearer of true has measurement value has x coordinate value has z coordinate value has y coordinate value has specified value 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 value my filling in an immigration form, a judge's signing and stamping a court order A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. Mathias Brochhausen obsolete_deontic document act true APOLLO_SV:00000008 A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development APOLLO_SV:00000032 A measurement datum that is the output of counting. A measurement datum that is the output of counting. Mathias Brochhausen A measurement datum that is the output of counting. It can be denoted as an arithmetic value or in form of a word, and is usually as a result of a process. count APOLLO_SV:00000033 A planned process that computes the totality of some material entity. The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting http://purl.obolibrary.org/obo/obib.owl The planned process of finding the number of elements in a finite set of objects. counting APOLLO_SV:00000114 A reproduction of a pathogen organism of a particular biological taxon in a tissue of a host organism from another taxon. William R. Hogan infection process process of infection http://purl.obolibrary.org/obo/hp.owl A process of reproduction of a particular pathogen species inside some tissue of a particular host species. M. Brochhausen infection is reproduction of a pathogen inside some tissue of a host. By associating infection with the classes latent period and infectious period, which are associated with specific pathogen species and host species, Apollo-SV defines infection further as reproduction of a particular pathogen taxon inside some tissue of a particular host taxon. infection APOLLO_SV:00000243 A measurement datum that quantifies a temporal region that is occupied by a processual entity. Mathias Brochhausen http://purl.obolibrary.org/obo/apollo_sv/releases/v2023-01-10/apollo_sv.owl A measurement datum that quantifies a temporal region that is occupied by a processual entity. Duration duration APOLLO_SV:00000522 software source code version control repository A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc. William R. Hogan Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based source code repository APOLLO_SV:00000524 process of compiling software A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions. William R. Hogan It's compiling "software" (scare quotes) and not "source code" because you can compile Java bytecode to machine code, and Java bytecode is not technically "source code". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.). Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code. compiling software APOLLO_SV:00000796 creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating 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 An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant 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 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] BFO:0000003 occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. 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 (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] 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]) 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 A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. 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 A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. 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 An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 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 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] 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]) ERO:0000007 Flow cytometry is a technique. A technique is a planned process used to accomplish a specific activity or task. PERSON: Melissa Haendel http://en.wikipedia.org/wiki/Technique http://purl.obolibrary.org/obo/ero.owl A method or skill used to accomplish a specific activity or task. Protocol is added to eagle-i temporarily until a relationship between the informatio entity "protocol" and these planned processes is created. This class refers to the axtual process not the document technique ERO:0001327 Rehabilitation for alcohol abuse. A technique that is performed to restore some or all of the patient's physical, sensory, and mental capabilities that were lost due to injury, illness, or disease. PERSON: Nicole Vasilevsky http://medical-dictionary.thefreedictionary.com/rehabilitation http://purl.obolibrary.org/obo/ero.owl rehabilitation FMA:49443 Anatomical cluster FMA:55457 vocal fold FMA:64854 Subdivision of larynx FMA:64989 Heterogeneous cluster FMA:67135 Anatomical structure FMA:67165 Material anatomical entity GEO:000000005 A subnational entity that is the primary organizational member of a nation, is subject to the full set of laws of the nation, enjoys all the privileges established under the laws of the nation, is not a member of any other geopolitical entity, and itself governs a part of the geographical region governed by the nation. Amanda Hicks William R. Hogan http://purl.obolibrary.org/obo/geo.owl examples: Northern Ireland, Florida major administrative subdivision GEO:000000370 geographical entity of astronomical body A material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface). Mathias Brochhausen Matt Diller William R. Hogan http://purl.obolibrary.org/obo/dev/geo.owl Includes atmosphere, crust, geographical regions (e.g., the geographical region over which the state of Florida has jurisdiction), bodies of water, mountains, etc. Generally, an individual organism is a distinct object that is not a part of the Earth, although this requires more thought. But the intent is definitely for this class to NOT subsume organism universally. Human beings are contained within, but not part of, the Earth, for example. Note that despite the word 'planetary' in 'planetary surface', it refers generally to surface of dwarf planets, asteroids, moons, etc. We note that not all planets have a surface per se (e.g., gas giants such as Jupiter and Saturn). So only planets, natural satellites, etc. with a planetary surface (with or without a planetary boundary layer) have geographical entities. We note that the term 'geography' is also applied to the Earth's moon, Mars, Venus, and possibly even other moons and planets in our own solar system and beyond. Thus, we are attempting to define things generally enough that they could be reused for the geographical entities/features on the Moon, Mars, other planets, exoplanets, other natural satellites (a.k.a moons), asteroids, etc. geographical entity GEO:000000372 A geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. François Modave Mathias Brochhausen Matt Diller William R. Hogan http://purl.obolibrary.org/obo/dev/geo.owl geographical region GEO:000000396 A governmental organization with a defined territory on which it exercises internal and external sovereignty, a permanent population, a government, and the capacity to enter into relations with other sovereign states. William R. Hogan de facto sovereign state de facto state nation nation state http://en.wikipedia.org/wiki/Sovereign_state http://purl.obolibrary.org/obo/geo.owl Per Wikipedia, the word 'nation' does not always refer to soverign states. For example, the "nation of Islam". sovereign state GO:0008150 biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl biological_process Any morphological abnormality of the skin. http://purl.obolibrary.org/obo/hp/releases/2024-07-01/hp.owl 2011-06-12T10:03:23Z Fyler:4133 UMLS:C4023528 Abnormal skin morphology Abnormal skin structure Abnormality of skin morphology HP:0011121 abnormal skin morphology HP:0011121 A lesion of the skin that is located in a specific region rather than being generalized. http://purl.obolibrary.org/obo/hp/releases/2024-07-01/hp.owl 2012-03-01T02:37:43Z UMLS:C0850826 Localised skin lesion Localized skin lesion HP:0011355 localized skin lesion HP:0011355 A type of ulcer that is caused when an area of skin is subject to pressure over a prolonged period of time, ranging in range in severity from patches of discolored skin to open wounds that expose the underlying bone or muscle. The most common sites are the sacrum, coccyx, heels and the hips. http://purl.obolibrary.org/obo/hp/releases/2024-07-01/hp.owl 2013-11-08T08:49:52Z SNOMEDCT_US:399912005 SNOMEDCT_US:420226006 UMLS:C0011127 Bedsore Decubitus Ulcer Pressure Sore Pressure ulcer HP:0012399 Pressure ulcers tend to affect persons with reduced mobility who are bedridden or wheelchair-bound. pressure ulcer HP:0012399 A discontinuity of the skin exhibiting complete loss of the epidermis and often portions of the dermis and even subcutaneous fat. http://purl.obolibrary.org/obo/hp/releases/2024-07-01/hp.owl 2010-06-18T02:17:00Z MEDDRA:10040943 SNOMEDCT_US:46742003 UMLS:C0037299 Open skin sore HP:0200042 skin ulcer HP:0200042 IAO:0000001 conditional specification A directive information entity that specifies what should happen if the trigger condition is fulfilled. PlanAndPlannedProcess Branch OBI branch derived OBI_0000349 conditional specification 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:0000006 narrative object Examples of narrative objects are reports, journal articles, and patents submission. A narrative object is an information content entity that is a set of propositions. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions person:Chris Stoeckert OBI_0000013 group:OBI narrative object 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:0000008 obsolete_artifact true 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:0000010 software Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software IAO:0000012 obsolete_digital entity A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digitial quality' person:Chris Stoeckert OBI_0000261 group:OBI obsolete2_digital entity true IAO:0000013 journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. A report that is published in a journal. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert OBI_0000159 group:OBI journal article IAO:0000015 information carrier In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case. A quality of an information bearer that imparts the information content 12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'. 2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it. PERSON: Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy information carrier IAO:0000017 model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers Person: Alan Ruttenberg model number IAO:0000018 obsolete_material_entity true IAO:0000019 binary digital entity MS Word document, ZIP file, DICOM file, JPEG file A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Superclass was 'digital entity' digital_entity person:Chris Stoeckert OBI_0000244 group:OBI obsolete2_binary digital entity true IAO:0000024 The length of a ruler. a unit of measure is the quality of some material entity compared to which another quality is some multiple of. Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy obsolete_unit of measure true IAO:0000025 programming language R, Perl, Java A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000058 group:OBI programming language IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 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:0000029 numeral A symbol that denotes a number. PERSON: Jonathan Rees numeral 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:0000031 integer numeral A numeral that denotes an integer PERSON: Jonathan Rees integer numeral 1 1 IAO:0000032 10 feet. 3 ml. A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum 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:0000034 time trigger PlanAndPlannedProcess Branch time trigger IAO:0000035 obsolete_study interpretation A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses 2009-03-16: definition was "A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application." 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. The obsoleting of narrative object required a modest change in the definition of this term. Circularity with "interpretation... interprets" has been removed, using "about the implications" instead. Lawrence Hunter PERSON: Alan Ruttenberg PERSON: Jennifer Fostel PERSON: Melanie Courtot conclusion OBI_0000005 obsolete_study interpretation true IAO:0000037 dot plot Dot plot of SSC-H and FSC-H. A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot IAO:0000038 graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph IAO:0000047 text based digital entity XML file, C++ source code file A text based digital entity is a digital entity that is encoded so that it only contains text characters. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital document' digital_entity person:Chris Stoeckert OBI_0000132 group:OBI obsolete2_text based digital entity true IAO:0000055 rule example to be added A rule is an executable which guides, defines, restricts actions. MSI PRS OBI_0500021 PRS rule IAO:0000057 contour plot Contour plot of SSC-H, FSC-H, and FL1-H. generically_dependent_continuants person:Allyson Lister person:Chris Stoeckert OBI_0000246 group:Flow Cytometry community contour plot IAO:0000059 report figure A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report Replaced by defined version of figure person:Alan Ruttenberg person:Allyson Lister OBI_0000027 group:OBI obsolete2_report figure true IAO:0000064 algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. Philippe Rocca-Serra PlanAndPlannedProcess Branch OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm IAO:0000065 software interpreter R program, Perl interpreter, Java virtual machine A software interpreter is a software application that executes some specified input software. Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter person:Alan Ruttenberg person:Chris Stoeckert OBI_0000199 group:OBI software interpreter IAO:0000078 curation status specification The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification IAO:0000079 density plot Density plot of SSC-H and FSC-H. A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. person:Allyson Lister person:Chris Stoeckert OBI_0000179 group:Flow Cytometry community density plot IAO:0000088 report Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record). 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI OBI_0000099 report IAO:0000091 report element A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page). 2009-03-16: needs some more work (clarify relations). 2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion Replaced by textual entity and figure There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text PERSON: Alan Ruttenberg PERSON: Allyson Lister PERSON: Melanie Courtot GROUP:OBI OBI_0000001 obsolete_report element true IAO:0000093 binary executable Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007) 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity' person:Jennifer Fostel OBI_0000222 group:OBI obsolete2_binary executable true IAO:0000096 source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module IAO:0000097 report table A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion person:Alan Ruttenberg person:Allyson Lister OBI_0000265 group:OBI obsolete_report table true IAO:0000098 data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification 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:0000101 image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image IAO:0000102 data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part 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, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland 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 https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 IAO:0000105 digital document A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file. 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity' person:Jennifer Fostel OBI_0000195 group:OBI obsolete2_digital document true 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:0000128 _identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final. obsolete_identifier true IAO:0000129 version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version GROUP: IAO version number IAO:0000131 serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) GROUP: IAO serial number IAO:0000132 lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number IAO:0000140 A settings datum is a datum that denotes some configuration of an instrument. 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. setting datum IAO:0000141 3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 Need to rework digital entity. Digital quality was suggested by Barry. obsolete_digital quality true IAO:0000144 conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still Person:Alan Ruttenberg conclusion textual entity IAO:0000178 material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer IAO:0000179 histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI histogram IAO:0000180 heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap IAO:0000181 Venn diagram A Venn diagram is a report graph showing all hypothetically possible logical relations between a finite collection of sets. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Venn_diagram Venn diagram IAO:0000182 obsolete_survival curve A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://www.graphpad.com/www/book/survive.htm obsolete_survival curve true IAO:0000183 dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram IAO:0000184 scatter plot Comparison of gene expression values in two samples can be displayed in a scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot IAO:0000185 A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc. PERSON:Alan Ruttenberg PERSON:Joanne Luciano PERSON:Melanie Courtot WEB: http://en.wiktionary.org/wiki/photograph photograph IAO:0000186 photographic print A photographic print is a material entity upon which a photograph generically depends. PERSON:Alan Ruttenberg PERSON:Melanie Courtot photographic print IAO:0000225 obsolescence reason specification The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification 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:0000301 citation Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183. A textual entity intended to identify a particular publication. PERSON: Lawrence Hunter citation IAO:0000302 author identification L. Hunter A textual entity intended to identify a particular author PERSON: Lawrence Hunter author identification IAO:0000303 institutional identification University of Colorado Denver School of Medicine A textual entity intended to identify a particular institution PERSON: Lawrence Hunter institutional identification IAO:0000304 caption Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool. A textual entity that describes a figure PERSON: Lawrence Hunter caption IAO:0000305 document title Textual characteristics of traditional and Open Access scientific journals are similar A textual entity that names a document PERSON: Lawrence Hunter document title IAO:0000306 table | T F --+----- T | T F F | F F A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table IAO:0000307 table of abbreviations IAO information artifact ontology OBI ontology of biomedical investiations GO gene ontology A table where the constituent texts are abbreviations and their expansions PERSON: Lawrence Hunter table of abbreviations IAO:0000308 figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure IAO:0000309 diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram 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:0000311 publication journal article, newspaper story, book, etc. A document that is the output of a publishing process. PERSON: Chris Stoeckert PERSON: Jie Zheng PERSON: Lawrence Hunter published document Revisit the term in Octorber 2020. Improve the defintion. publication IAO:0000312 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation IAO:0000313 patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent 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:0000315 abstract The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data. A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. PERSON: Lawrence Hunter precis abstract IAO:0000316 introduction to a publication about an investigation Section labelled 'introduction' of a typical scientific journal article A part of a publication about an investigation that is about the objective specification (why the investigation is being done) PERSON: Lawrence Hunter background introduction overview introduction to a publication about an investigation IAO:0000317 methods section The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article. A part of a publication about an investigation that is about the study design of the investigation PERSON: Lawrence Hunter experimental experimental methods experimental procedures experimental section method methodology methods methods section IAO:0000318 results section The section labelled 'results' in a typical scientific journal article A part of a publication about an investigation that is about a study design execution PERSON: Lawrence Hunter results results section IAO:0000319 discussion section of a publication about an investigation A part of a publication about an investigation that is about the study interpretation of the investigation PERSON: Lawrence Hunter discussion discussion section discussions discussion section of a publication about an investigation IAO:0000320 references section The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called "literature cited" or "bibliography" A part of a document that has citations as parts PERSON: Lawrence Hunter literature cited reference reference list references references section IAO:0000321 author list Lawrence Hunter and Kevin Brettonel Cohen A part of a document that enumerates the authors of the document PERSON: Lawrence Hunter author list IAO:0000322 institution list The University of Colorado Denver School of Medicine and the University of Colorado Boulder. A part of a document that has parts that are institution identifications associated with the authors of the document PERSON: Lawrence Hunter institution list IAO:0000323 author contributions section LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript. A part of a publication that is about the specific contributions of each author PERSON: Lawrence Hunter author contributions authors' contribution authors' contributions authors' roles contributions by the authors contributorship author contributions section IAO:0000324 acknowledgements section The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript Part of a publication that is about the contributions of people or institutions other than the authors. PERSON: Lawrence Hunter acknowledgement acknowledgements acknowledgment acknowledgments acknowledgements section IAO:0000325 footnote The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text. A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document. PERSON: Lawrence Hunter endnote footnotes footnote IAO:0000326 supplementary material to a document A part of a document that is segregated from the rest of the document due to its size PERSON: Lawrence Hunter additional file additional files additional information appendix electronic supplementary material electronic supplementary materials supplemental data supplemental information supplemental material supplementary data supplementary files supplementary information supplementary material supplementary materials supporting information supplementary material to a document IAO:0000327 table of contents A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of contents IAO:0000328 table of figures A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred). PERSON: Lawrence Hunter table of figures IAO:0000329 running title A shorter version of a document title PERSON: Lawrence Hunter running title IAO:0000330 copyright section This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License. A document part that describes legal restrictions on making or distributing copies of the document PERSON: Lawrence Hunter copyright section 1 IAO:0000400 A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 Alan Ruttenberg AR notes: We need to discuss whether it should include site. cartesian spatial coordinate datum http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 1 IAO:0000401 A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region Alan Ruttenberg one dimensional cartesian spatial coordinate datum 1 1 IAO:0000402 A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region Alan Ruttenberg two dimensional cartesian spatial coordinate datum 1 1 1 IAO:0000403 A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region Alan Ruttenberg three dimensional cartesian spatial coordinate datum IAO:0000408 A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg length measurement datum IAO:0000409 denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type IAO:0000414 A scalar measurement datum that is the result of measurement of mass quality 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg mass measurement datum IAO:0000415 hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 A textual entity that expresses an assertion that is intended to be tested. 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg hypothesis textual entity IAO:0000416 A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000422 A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59 postal address IAO:0000429 email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address IAO:0000442 author role A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name. PERSON: Alan Ruttenberg PERSON: Melanie Courtot author role IAO:0000443 A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing Person:Alan Ruttenberg data item extraction from journal article IAO:0000444 A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free. Person: Jie Zheng https://en.wikipedia.org/wiki/Publishing VEuPathDB publishing process IAO:0000445 A document that is in preparation for submission to be published. PERSON: Jie Zheng EFO_0001795 in preparation VEuPathDB document in preparation for publication IAO:0000572 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. A planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting IAO:0000573 line graph A line graph is a type of graph created by connecting a series of data points together with a line. PERSON:Chris Stoeckert PERSON:Melanie Courtot line chart GROUP:OBI WEB: http://en.wikipedia.org/wiki/Line_chart line graph IAO:0000574 A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned. A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity 2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry. Person:Alan Ruttenberg Person:Bjoern Peters Person:Melanie Courtot assigning a CRID assigning a centrally registered identifier IAO:0000575 Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. A planned process in which a CRID registry associates an information content entity with a CRID symbol PERSON:Alan Ruttenberg associating information with a CRID in the CRID registry associating information with a centrally registered identifier in its registry IAO:0000576 a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID. MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now. obsolete_establishing a CRID registry true 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 code set of PubMed identifiers associated with journal articles. A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process. Justin Whorton PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot CRID registry Original proposal from Bjoern, discussions at IAO calls https://github.com/information-artifact-ontology/IAO/issues/237 centrally registered identifier registry IAO:0000580 Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot looking up a CRID looking up a centrally registered identifier IAO:0000582 time stamped measurement datum IAO:0000584 pmid:20604925 - time-lapse live cell microscopy A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series time sampled measurement data set 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 IAO:0000591 A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software method IAO:0000592 A software module is software composed of a collection of software methods. PERSON: Melanei Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software module IAO:0000593 A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software library IAO:0000594 A software application is software that can be directly executed by some processing unit. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software application IAO:0000595 A software script is software whose instructions can be executed using a software interpreter. PERSON: Melanie Courtot PERSON: Michel Dumontier https://github.com/information-artifact-ontology/IAO/issues/80 software script IAO:0000605 abbreviation textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect. A textual entity listing abbreviations and their expansions that are used in a document. PERSON: Bill Baumgartner abbreviation textual entity IAO:0000606 abbreviations section The section labelled 'abbreviations' in a typical scientific journal article. A part of a document where abbreviations and their long-forms used within the document are listed. PERSON: Bill Baumgartner abbreviation and acronyms abbreviation list abbreviations abbreviations and acronyms abbreviations list abbreviations used definitions for abbreviations list of abbreviations list of abbreviations used non-standard abbreviations nonstandard abbreviations nonstandard abbreviations and acronyms abbreviations section IAO:0000607 author information section The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/) A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information authors’ information biographies contributor information author information section IAO:0000608 author information textual entity From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD. A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document. PERSON: Bill Baumgartner author information textual entity IAO:0000609 author summary section The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/) A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers. PERSON: Bill Baumgartner author summary summary synopsis Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines) author summary section IAO:0000610 author summary textual entity From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX. A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). PERSON: Bill Baumgartner Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines). author summary textual entity IAO:0000611 availability section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained. PERSON: Bill Baumgartner availability availability of data data archiving data availability data availability statement data sharing statement availability section IAO:0000612 availability textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): Project home page:http://krux.googlecode.com A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained. PERSON: Bill Baumgartner availability textual entity IAO:0000613 case report section The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/) A part of a document about the medical history of a specific patient as it relates to the topic of the document. PERSON: Bill Baumgartner case presentation case report case report section IAO:0000614 case report textual entity Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/): The patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension. A textual entity that expresses a detailed account of a portion of the medical history for a specific patient. PERSON: Bill Baumgartner case report textual entity IAO:0000615 conclusion section The section labelled 'conclusion' in a typical scientific journal article. A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document. PERSON: Bill Baumgartner concluding remarks conclusion conclusions findings summary conclusion section IAO:0000616 conflict of interest section The section labelled 'conflict of interest statement' in a typical scientific journal article. A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document. PERSON: Bill Baumgartner authors' disclosures of potential conflicts of interest competing financial interests competing interests conflict of interest conflict of interest statement conflict of interests conflicts of interest declaration of competing interest declaration of competing interests declaration of interest declaration of interests disclosure of conflict of interest disclosure of potential conflicts of interest duality of interest statement of interest conflict of interest section IAO:0000617 conflict of interest statement SD [an author] is a Merck employee and Merck is the sponsor of this study. [Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document. PERSON: Bill Baumgartner conflict of interest textual entity IAO:0000618 consent section The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/) A part of a document about the consent process that was used to enroll patients in a study. PERSON: Bill Baumgartner consent consent section IAO:0000619 consent textual entity From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): Written informed consent was obtained from the patient’s parents for publication of this Case report and any accompanying images. A copy of the written consent is available for review by the Editor-in chief of this journal. A textual entity that documents the consenting process used to enroll patients in a study. PERSON: Bill Baumgartner consent textual entity IAO:0000620 ethical approval section The section labelled 'ethical approval' in a typical scientific journal article. A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis. PERSON: Bill Baumgartner ethical approval ethical requirements ethics ethics statement ethical approval section IAO:0000621 ethical approval textual entity From McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review. A textual entity that documents the ethical approval of some study design. PERSON: Bill Baumgartner ethical approval textual entity IAO:0000622 figures section The section labelled 'figures' in a typical scientific journal article. A part of a document that contains one or more figures. PERSON: Bill Baumgartner figures figures section IAO:0000623 funding source declaration section The section labelled 'funding' in a typical scientific journal article. A part of a document used to detail information regarding the source of funding used in support of the generation of the document content. PERSON: Bill Baumgartner financial support funding funding information funding sources funding statement funding/support grants role of the funding source source of funding sources of funding study funding funding source declaration section IAO:0000624 funding souce declaration textual entity From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). The funding sources played no role in study design, data collection, analysis or interpretation, writing the report, or the decision to submit the paper for publication. A textual entity documenting the source of funding that supported some study. PERSON: Bill Baumgartner funding source declaration textual entity IAO:0000625 future directions section The section labelled 'future directions' in a typical scientific journal article. A part of a document detailing extensions of the described work that may be implemented at some future point in time. PERSON: Bill Baumgartner future challenges future considerations future developments future directions future outlook future perspectives future plans future prospects future research future research directions future studies future work outlook future directions section IAO:0000626 future directions textual entity Excerpt from Wang and Li. Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members. A textual entity expressing ideas regarding future work relevant to work described in a document that could be done. PERSON: Bill Baumgartner future directions textual entity IAO:0000627 genome announcement section The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/) A document part announcing the publication of a novel draft genome sequence. PERSON: Bill Baumgartner genome announcement genome announcement section IAO:0000628 genome announcement textual entity Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB). A textual entity that describes the generation and public release of a novel, draft genome sequence. PERSON: Bill Baumgartner genome announcement textual entity IAO:0000629 keyword textual entity From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303729/): Exon orthology; alternative splicing; exon duplication; intron-exon structure. A textual entity listing keywords indicating the major theme(s) of a document. PERSON: Bill Baumgartner keyword textual entity IAO:0000630 keywords section The section labelled 'keywords' in a typical scientific journal article. A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed. PERSON: Bill Baumgartner keywords keywords section IAO:0000631 study limitations section The section labelled 'limitations' in a typical scientific journal article. A part of a document about biases or short comings related to the study design and execution. PERSON: Bill Baumgartner limitations study limitations Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations section IAO:0000632 study limitations textual entity Excerpt from the Limitations section of Fermann et al 2015, Acad Emerg Med. 2015 Mar; 22(3): 299–307 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405051/). Owing to the nature of a post hoc study, any significant values must be interpreted with caution. In the current analysis, no multiple testing was conducted and p-values remain unadjusted. Moreover, a selection bias arising from the randomized open-label design of the original EINSTEIN PE study cannot be ruled out. A textual entity addressing a shortcoming or bias of a study design or execution. PERSON: Bill Baumgartner Author guidelines published by The Society for Academic Emergency Medicine. (http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html) study limitations textual entity IAO:0000633 materials section The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/) A part of a document about the materials required to reproduce the content of the document. PERSON: Bill Baumgartner materials materials section IAO:0000634 notes section The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc. PERSON: Bill Baumgartner notes notes section IAO:0000635 patients section The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/) A part of a document about the patients that participated in a study. PERSON: Bill Baumgartner patients section IAO:0000636 patients textual entity Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/): Between January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred. A textual entity expressing information regarding the patients used in a study. PERSON: Bill Baumgartner patients textual entity IAO:0000637 pre-publication history section The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/) A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors. PERSON: Bill Baumgartner notice of republication pre-publication history pre-publication history section IAO:0000638 pre-publication history textual entity From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/): The pre-publication history for this paper can be accessed here: http://www.biomedcentral.com/1471-2253/13/33/prepub A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information. PERSON: Bill Baumgartner pre-publication history textual entity IAO:0000639 related work section The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/) A part of a document about work in other publications that is relevant to the content of the document. PERSON: Bill Baumgartner related literature related work related work section IAO:0000640 related work textual entity Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/): Our work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015). A textual entity that discusses work from other publications and expresses their relevancy to the content of a document. PERSON: Bill Baumgartner related work textual entity IAO:0000641 requirements section The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/). A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource. PERSON: Bill Baumgartner requirements requirements section IAO:0000642 requirements textual entity From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): • Operating systems: Platform independent • Programming language: Matlab, R, Python • Other requirements: None • License: GNU GPL v3 • Any restrictions to use by non-academics: None A textual entity that expresses the requirements necessary to use a resource, e.g. software. PERSON: Bill Baumgartner requirements textual entity IAO:0000643 statistical analysis textual entity From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant. A textual entity documenting statistical analysis tools and techniques employed. PERSON: Bill Baumgartner statistical analysis textual entity IAO:0000644 statistical analysis section The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/) A part of the document used to describe the statistical methodologies employed in the work presented in the document. PERSON: Bill Baumgartner statistical analysis statistical analysis section IAO:0000645 tables section The section labelled 'tables' in a typical scientific journal article. A part of a document that contains one or more tables. PERSON: Bill Baumgartner tables tables section IAO:0000646 An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail. Mathias Brochhausen postal code IAO:0000647 A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region. Mathias Brochhausen Postal delivery route IAO:0000648 A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes. Mathias Brochhausen ZIP code zone improvement plan code IAO:0000650 database extract, transform, and load process A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second. Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output. PERSON:Alan Ruttenberg ETL WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load database extract, transform, and load process IAO:0000701 descriptive data section A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made. PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/prisma/ ONE ontology descriptive data section IAO:0000702 additional results section A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.) PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/consort/ https://www.equator-network.org/reporting-guidelines/prisma/ https://www.equator-network.org/reporting-guidelines/strobe/ ONE ontology additional results section IAO:0000703 research participants section A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.). PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/consort/ https://www.equator-network.org/reporting-guidelines/prisma/ https://www.equator-network.org/reporting-guidelines/strobe-nut/ ONE ontology research participants section IAO:0000704 measurement methods section A methods section that describes details of data assessment methods (data measurement). PERSON: Chen Yang PERSON: Jie Zheng https://www.equator-network.org/reporting-guidelines/strobe/ ONE ontology measurement methods section IAO:0000705 research settings section A document part that describes the physical/social/cultural conditions around a research trial. PERSON: Chen Yang PERSON: Jie Zheng https://www.ncbi.nlm.nih.gov/books/NBK262175/ ONE ontology research settings section IAO:0000706 study bias section A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others. PERSON: Chen Yang PERSON: Jie Zheng DOI: 10.1097/PRS.0b013e3181de24bc ONE ontology study bias section IAO:0000707 graphical abstract An abstract that is pictorial summary of the main findings described in the document. PERSON: Jie Zheng PERSON: Tim Beck visual abstract https://www.elsevier.com/authors/journal-authors/graphical-abstract Biomedical literature NLP project graphical abstract IAO:0000708 A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor. "You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors." [https://orcid.org/] This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25) http://orcid.org/0000-0002-1595-3213 ORCID ID ORCiD Open Researcher and Contributor ID Open Researcher and Contributor Identifier https://orcid.org/ https://github.com/information-artifact-ontology/IAO/issues/259 ORCID identifier IAO:0020000 identifier An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity. Justin Whorton Mathias Brochhausen Mathias Brochhausen proper name https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Sep 29, 2016: The current definition has been amended from the previous version: "A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." to more accuratly reflect the necessary and sufficient condition on the class. (MB) identifier IAO:0020001 alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems A grapheme is an information content entity that is a fundamental unit in a written language. An information content entity that is a fundamental unit in a written language. Justin Whorton http://en.wikipedia.org/wiki/Grapheme https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there. grapheme IAO:0020002 An utterance is an information content entity that is a complete unit of speech in spoken language. Mathias Brochhausen Wikipedia: http://en.wikipedia.org/wiki/Utterance Mathias Brochhausen utterance IAO:0020003 An attributive collection of qualities inhering in energy when transported through a medium in a wave. Mathias Brochhausen mechanical wave quality IAO:0020004 is a quality that is the concretization of graphemes and inheres in a material object. Mathias Brochhausen Mathias Brochhausen writing quality IAO:0020005 pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting, is a material information bearer that bears the concretization of graphemes. Mathias Brochhausen Mathias Brochhausen writing bearer IAO:0020006 portion of energy IAO:0020007 Energy that is transported in a sound wave. Mathias Brochhausen sound energy IAO:0020008 Sound energy bearing the concretization of an utterance and being the output of an uttering process. utterance energy IAO:0020009 Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states. http://en.wikipedia.org/wiki/Oscillation Mathias Brochhausen oscillating IAO:0020010 A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity. Justin Whorton Mathias Brochhausen Mathias Brochhausen dubbing process naming https://github.com/information-artifact-ontology/IAO/issues/237 Mathias Brochhausen identifier creating process IAO:0020011 is a planned process of making speech sounds which may or may not have an actual language involved. Mathias Brochhausen http://en.wiktionary.org/wiki/utter Mathias Brochhausen utterance process IAO:0020015 A personal name is a proper name identifying an individual person. An identifier referring to an individual entity that is ascribed personhood by the user of the identifier. Justin Whorton Mathias Brochhausen Mathias Brochhausen http://en.wikipedia.org/wiki/Personal_name https://github.com/information-artifact-ontology/IAO/issues/237 Personal names "today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names." (http://en.wikipedia.org/wiki/Personal_name) Personal names to not include names of fictional characters, e.g. Sherlock Holmes. Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB) personal name IAO:0020016 A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name Justin Whorton Mathias Brochhausen Mathias Brochhausen first name http://en.wikipedia.org/wiki/Given_name https://github.com/information-artifact-ontology/IAO/issues/237 given name IAO:0020017 A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children. Justin Whorton Mathias Brochhausen Mathias Brochhausen last name surname http://en.wikipedia.org/wiki/Family_name https://github.com/information-artifact-ontology/IAO/issues/237 family name IAO:0020020 An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate. An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things. Alan Ruttenberg Justin Whorton Mathias Brochhausen Mathias Brochhausen code map code system codeset coding system controlled vocabulary https://github.com/information-artifact-ontology/IAO/issues/237 Alan Ruttenberg Clint Dowland Matt Diller Sarah Bost William R. Hogan Code sets might include non-entities/things (e.g. missing thumbs). Does not imply absence vs. presence of any taxonomy. Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities. Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean). For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs). For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets. Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain. The information content entities do not denote each other. code set IAO:0020021 A document that denotes some identity and is concretized by the bearer of some credential role. Amanda Hicks identity document IAO:0020022 A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents. Amanda Hicks is an aggregate of ICEs also an ICE? yes Is part_of the appropriate relation to use for data items and documented identities? documented identity IAO:0020023 I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database. Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit). Amanda Hicks authentication IAO:0020024 A role that inheres in a concretization of an identity document and is realized by an authentication process. Amanda Hicks credential role IAO:0020025 obligor role Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla. A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. Mathias Brochhausen Sarah Bost duty holder role (IAO:210016) obsolete obligor role true IAO:0020026 obligee role Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money. A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. Mathias Brochhausen Sarah Bost claimant role (IAO:0021013) obsolete obligee role true IAO:0020027 Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role. Mathias Brochhausen OBIB/ICO community https://github.com/d-acts/d-acts/issues/29 owner role IAO:0021000 obsolete_claim true IAO:0021001 my filling in an immigration form, a judge's signing and stamping a court order A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. Mathias Brochhausen deontic document act IAO:0021002 my filling in an immigration form, a judge's signing and stamping a court order A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document. Mathias Brochhausen obsolete_document act true IAO:0021003 Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. Mathias Brochhausen The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. Thanks to W.R. Hogan for finding the Reinach quote. social act IAO:0021004 the claim of a piece of land, the obligation to pay rent to the owner of a rental property Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities. Mathias Brochhausen obsolete_socio-legal generically dependent continuant true IAO:0021005 deontic declaration my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract. A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document. Mathias Brochhausen declaration status function declaration obsolete_deontic declaration true IAO:0021006 A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. Mathias Brochhausen obsolete obligee role true IAO:0021007 A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification). Mathias Brochhausen document act input document IAO:0021008 A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave. Mathias Brochhausen Neil Otte deontic role IAO:0021009 A social act that creates or revokes a deontic role. Mathias Brochhausen deontic declaration IAO:0021010 obsolete_obligation true IAO:0021013 A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A. J. Neil Otte Mathias Brochhausen Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. https://plato.stanford.edu/entries/rights/ Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. https://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child. claimant role IAO:0021014 The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration. Mathias Brochhausen obsolete_declaration executive role true IAO:0021015 the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant. Mathias Brochhausen not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants. obsolete_document template creator role true IAO:0021016 A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B. J. Neil Otte Mathias Brochhausen Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. https://plato.stanford.edu/entries/rights/ duty holder role IAO:0021017 The role of a human being or an aggregate of human beings concretizing a claim. Mathias Brochhausen obsolete_claimant role true IAO:0021018 The role of a human being or an aggregate of human beings concretizing an obligation. Mathias Brochhausen obsolete_obligator role true IAO:0021019 A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C. J. Neil Otte Mathias Brochhausen Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. https://plato.stanford.edu/entries/rights/ privilege holder role IAO:0021020 me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act. Mathias Brochhausen obsolete_declaration target true IAO:0021021 The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act. Mathias Brochhausen document act template creator role IAO:0021022 A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration. Mathias Brochhausen declaration performer role deontic declaration performer role IAO:0021023 A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role. J. Neil Otte Mathias Brochhausen Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. https://plato.stanford.edu/entries/rights/ power role IAO:0021030 The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act. Mathias Brochhausen obsoleted_document act target true IAO:0021031 a judge's role of signing a court order A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act. Mathias Brochhausen document act performer role IAO:0021032 A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. Sarah Bost obsolete_obligee role true IAO:0021033 A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. Sarah Bost obsolete_obligor role true IAO:0021102 A social act that postulates a socio-legal fact for a specified group of people or organizations. Mathias Brochhausen enactment standing declaration IAO:0021300 A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. John Judkins Mathias Brochhausen obsolete obligor role true IAO:8000000 ontology module I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it. ontology file This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology. ontology module IAO:8000001 base ontology module An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies. base ontology module IAO:8000002 editors ontology module An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users. source ontology module editors ontology module IAO:8000003 main release ontology module An ontology module that is intended to be the primary release product and the one consumed by the majority of tools. TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module main release ontology module IAO:8000004 bridge ontology module An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module. bridge ontology module IAO:8000005 import ontology module A subset ontology module that is intended to be imported from another ontology. TODO: add axioms that indicate this is the output of a module extraction process. import file import ontology module IAO:8000006 subset ontology module An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms. ontology slim subset ontology subset ontology module IAO:8000007 curation subset ontology module A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation. curation subset ontology module IAO:8000008 analysis ontology module An ontology module that is intended for usage in analysis or discovery applications. analysis subset ontology module IAO:8000009 single layer ontology module A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint. ribbon subset single layer subset ontology module IAO:8000010 exclusion subset ontology module A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes. antislim exclusion subset ontology module IAO:8000011 external import ontology module An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach. external import external import ontology module IAO:8000012 species subset ontology module A subset ontology that is crafted to either include or exclude a taxonomic grouping of species. taxon subset species subset ontology module IAO:8000013 reasoned ontology module An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available. reasoned ontology module IAO:8000014 generated ontology module An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV. TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process generated ontology module IAO:8000015 template generated ontology module An ontology module that is automatically generated from a template specification and fillers for slots in that template. template generated ontology module IAO:8000016 taxonomic bridge ontology module taxonomic bridge ontology module IAO:8000017 ontology module subsetted by expressivity ontology module subsetted by expressivity IAO:8000018 obo basic subset ontology module A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). An ontology is OBO Basic if and only if it has the following characteristics: DAG Unidirectional No Dangling Clauses Fully Asserted Fully Labeled No equivalence axioms Singly labeled edges No qualifier lists No disjointness axioms No owl-axioms header No imports obo basic subset ontology module IAO:8000019 ontology module subsetted by OWL profile ontology module subsetted by OWL profile IAO:8000020 EL++ ontology module EL++ ontology module IDO:0000636 A process that is a systemic inflammatory response to infection. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl sepsis IDO:0000637 A sepsis that results in organ dysfunction, hypotension, or hypofusion of at least one organ. Albert Goldfain Alexander Diehl Lindsay Cowell http://purl.obolibrary.org/obo/ido/2017-11-03/ido.owl severe sepsis MAXO:0000001 A clinically prescribed procedure, therapy, intervention, or recommendation. http://purl.obolibrary.org/obo/hp.owl 2018-11-16T20:07:28Z OGMS:0000096 health care process medical action MAXO:0000002 All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state. http://purl.obolibrary.org/obo/hp.owl 2018-11-16T20:08:29Z NCIT:C25218 NCIT:C49236 OAE:0000094 OGMS:0000112 An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process. therapeutic procedure MAXO:0000034 All manners of treatment to relieve illness and injury of a particular body site or system. http://purl.obolibrary.org/obo/hp.owl http://purl.obolibrary.org/obo/maxo/releases/2023-12-01/maxo.owl 2023-03-20T19:58:58Z therapeutic procedure by site MAXO:0000499 All manners of treatment to bring respiratory system back to its normal state. http://purl.obolibrary.org/obo/maxo/releases/2023-12-01/maxo.owl http://orcid.org/0000-0001-7941-2961 2020-01-23T15:55:17Z NCIT:C15322 respiratory system therapeutic procedure respiratory therapy therapeutic procedure of respiratory system MAXO:0000500 A set of maneuvers or medical procedures performed to prevent and relieve airway obstruction. This ensures an open pathway for gas exchange between a patient's lungs and the atmosphere. http://purl.obolibrary.org/obo/maxo/releases/2023-12-01/maxo.owl 2020-01-23T15:56:57Z MeSH:D058109 PMID:18675024 airway management MAXO:0000503 Any method of artificial breathing that employs mechanical or non-mechanical means to force the air into and out of the lungs. Artificial respiration or ventilation is used in individuals who have stopped breathing or have respiratory insufficiency to increase their intake of oxygen (O2) and excretion of carbon dioxide (CO2). http://purl.obolibrary.org/obo/hp.owl 2020-01-23T16:34:17Z artificial ventilation mechanical ventilation artificial respiration A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:4 EFO:0000408 ICD9:799.9 MESH:D004194 NCIT:C2991 OGMS:0000031 Orphanet:377788 SCTID:64572001 UMLS:C0012634 condition disease disease or disorder disease or disorder, non-neoplastic diseases diseases and disorders disorder disorders medical condition other disease MONDO:0000001 DOID:4 EFO:0000408 MONDO:equivalentTo MONDO:i2s MONDO:relatedTo NCIT:C2991 disease MONDO:0000001 A disease involving the lower respiratory tract. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:0050161 ICD9:478.1 ICD9:478.19 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top SCTID:128272009 UMLS:C1290325 https://orcid.org/0000-0002-6601-2165 disease of lower respiratory tract disease or disorder of lower respiratory tract disorder of lower respiratory tract lower respiratory tract disease lower respiratory tract disease or disorder MONDO:0000270 DOID:0050161 MONDO:equivalentTo lower respiratory tract disorder MONDO:0000270 An impairment of the structure or function of the blood vessels which carry blood away from the heart. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:0050828 ICD9:447.8 ICD9:447.9 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C35317 SCTID:359557001 UMLS:C0852949 arterial disease arterial disorder arteriopathy artery disease artery disease or disorder disease of artery disease or disorder of artery disorder of artery MONDO:0000473 MONDO:equivalentTo NCIT:C35317 arterial disorder MONDO:0000473 Cessation of breathing and/or cardiac function. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:0060319 ICD10CM:I46 ICD9:427.5 MESH:D006323 NCIT:P378 SCTID:410429000 UMLS:C0018790 cardiopulmonary arrest circulatory arrest MONDO:0000745 DOID:0060319 MONDO:MEDGEN MONDO:equivalentTo MONDO:i2s cardiac arrest MONDO:0000745 An acute or chronic condition that is characterized by the inability of the kidneys to adequately filter the blood. http://purl.obolibrary.org/obo/mondo/releases/2024-06-04/mondo.owl DOID:1074 EFO:1002048 ICD9:404.12 ICD9:404.13 ICD9:586 MESH:D051437 NCIT:C4376 NCIT:P378 SCTID:42399005 UMLS:C0035078 UMLS:C1565489 failure, renal renal failure renal failure syndrome renal insufficiency MONDO:0001106 DOID:1074 MONDO:EFO MONDO:OTAR MONDO:equivalentTo MONDO:i2s MONDO:relatedTo NCIT:C4376 kidney failure MONDO:0001106 Life-threatening respiratory failure that develops rapidly. Causes include injury, sepsis, drug overdose, and pancreatitis. It manifests with dyspnea and cyanosis and may lead to cardiovascular shock. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl ICD9:518.81 MONDO:patterns/acute NCIT:C27043 SCTID:65710008 UMLS:C0264490 acute respiratory failure respiratory failure, acute MONDO:0001208 MONDO:equivalentTo MONDO:i2s NCIT:C27043 acute respiratory failure MONDO:0001208 A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia. http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl DOID:150 MESH:D001523 MFOMD:0000004 NCIT:C2893 SCTID:74732009 Psychiatric disease Psychiatric disorder disease of mental health mental disorder mental dysfunction mental illness MONDO:0002025 DOID:150 ISBN-13:978-1-259-64403-0 MONDO:OTAR MONDO:equivalentTo MONDO:relatedTo https://orcid.org/0000-0001-5208-3432 psychiatric disorder MONDO:0002025 A disease affects cognitive processes. http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl DOID:1561 ICD9:294.9 MEDGEN:40371 MESH:D019965 NCIT:C34870 NCIT:C92196 SCTID:443265004 UMLS:C0009241 https://orcid.org/0000-0002-6601-2165 cognitive disease cognitive disorder organic mental disorder MONDO:0002039 DOID:1561 MEDGEN:40371 MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo MONDO:exact-label-match MONDO:i2s MONDO:relatedTo cognitive disorder MONDO:0002039 A disease involving the renal system. http://purl.obolibrary.org/obo/mondo/releases/2024-06-04/mondo.owl DOID:18 EFO:0009690 ICD9:V47.4 MESH:D014570 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C27599 NCIT:C3430 SCTID:128606002 UMLS:C0042075 https://orcid.org/0000-0002-6601-2165 disease of renal system disease or disorder of renal system disease, urinary tract disease, urologic disease, urological diseases, urinary tract diseases, urologic diseases, urological disorder of renal system disorder of the urinary system disorder of urinary system non-neoplastic urinary tract disease renal system disease renal system disease or disorder urinary disease urinary system disease urinary system disorder urinary tract disease urinary tract diseases urinary tract disorder urologic disease urologic disorder urological disease urological diseases urological disorder urological disorders MONDO:0002118 MONDO:EFO MONDO:MEDGEN MONDO:OTAR MONDO:RelatedTo MONDO:equivalentTo MONDO:i2s urinary system disorder MONDO:0002118 Sudden and sustained deterioration of the kidney function characterized by decreased glomerular filtration rate, increased serum creatinine or oliguria. http://purl.obolibrary.org/obo/mondo/releases/2024-06-04/mondo.owl DOID:3021 ICD10CM:N17 MESH:D058186 MONDO:patterns/acute NCIT:C26808 AKI ARF acute kidney injury acute renal failure kidney failure, acute MONDO:0002492 MONDO:OTAR MONDO:equivalentTo acute kidney failure MONDO:0002492 A disease involving the cardiovascular system. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:1287 EFO:0000319 ICD9:390-459.99 ICD9:420-429.99 ICD9:423 ICD9:423.8 ICD9:424 ICD9:429 ICD9:429.2 ICD9:429.7 ICD9:429.8 ICD9:429.81 ICD9:429.89 ICD9:459.89 ICD9:459.9 MESH:D002318 MONDO:cjm MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C2931 SCTID:49601007 UMLS:C0007222 https://orcid.org/0000-0002-6601-2165 cardiovascular disease cardiovascular disease (CVD) cardiovascular disorder cardiovascular system disease cardiovascular system disease or disorder disease of cardiovascular system disease of subdivision of hemolymphoid system disease or disorder of cardiovascular system disorder of cardiovascular system circulatory system disease MONDO:0004995 DOID:1287 EFO:0000319 MONDO:equivalentTo MONDO:i2s MONDO:relatedTo NCIT:C2931 cardiovascular disorder MONDO:0004995 Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl myocardial infarction (disease) DOID:5844 EFO:0000612 HP:0001658 ICD10CM:I21 MESH:D009203 MONDO:ambiguous NCIT:C27996 SCTID:22298006 UMLS:C0027051 https://orcid.org/0000-0002-6601-2165 MI MI, myocardial infarction heart attack infarction (MI), myocardial myocardial infarct myocardial infarction myocardial infarction (disease) myocardial infarction, (MI) MONDO:0005068 DOID:5844 EFO:0000612 MONDO:equivalentTo MONDO:otherHierarchy NCIT:C27996 https://doi.org/10.1186/1472-6963-13-468 myocardial infarction MONDO:0005068 A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:1579 EFO:0000684 ICD10CM:J00-J99 ICD9:460-519.99 ICD9:500-508.99 ICD9:503 ICD9:508 ICD9:508.1 ICD9:508.8 ICD9:508.9 ICD9:510-519.99 ICD9:516 ICD9:516.8 ICD9:516.9 ICD9:517 ICD9:517.8 ICD9:519 ICD9:519.1 ICD9:519.3 ICD9:519.8 ICD9:519.9 ICD9:V12.60 ICD9:V47.2 MESH:D012140 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C26871 SCTID:50043002 disease of respiratory system disease or disorder of respiratory system disorder of respiratory system respiratory disease respiratory disorder respiratory system disease respiratory system disease or disorder respiratory system disorder MONDO:0005087 DOID:1579 EFO:0000684 MONDO:equivalentTo MONDO:i2s MONDO:relatedTo https://github.com/monarch-initiative/mondo/issues/4536 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-4142-7153 respiratory system disorder MONDO:0005087 A sudden loss of neurological function secondary to hemorrhage or ischemia in the brain parenchyma due to a vascular event. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl EFO:0000712 HP:0001297 MESH:D020521 NCIT:C3390 NIFSTD:birnlex_12783 SCTID:230690007 https://orcid.org/0000-0001-5208-3432 https://www.epilepsydiagnosis.org/etiology/stroke-overview.html CVA CVA, cerebrovascular accident cerebrovascular accident cerebrovascular accident, (CVA) stroke stroke syndrome syndrome, stroke undetermined stroke cerebral infarction MONDO:0005098 EFO:0000712 MONDO:equivalentTo Stroke includes two main types, hemorrhagic and ischemic. Both types of stroke can cause acute seizures at the time of the acute event, as well as epilepsy as a long-term complication. In the elderly, cerebrovascular disease and stroke are the most common cause of acute seizures and epilepsy. stroke disorder MONDO:0005098 A disease involving the kidney. http://purl.obolibrary.org/obo/mondo/releases/2024-06-04/mondo.owl DOID:557 EFO:0003086 ICD9:583.81 MESH:D007674 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C3149 SCTID:90708001 UMLS:C0022658 https://orcid.org/0000-0002-6601-2165 disease of kidney disease or disorder of kidney disorder of kidney kidney disease kidney disease or disorder kidney disorder renal disease renal disorder nephropathy MONDO:0005240 DOID:557 EFO:0003086 MONDO:EFO MONDO:OTAR MONDO:equivalentTo MONDO:i2s MONDO:relatedTo kidney disorder MONDO:0005240 An acute or chronic inflammation of the bone and its structures due to infection with pyogenic bacteria. http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl osteomyelitis (disease) DOID:1019 EFO:0003102 GARD:7286 HP:0002754 ICD9:730.0 ICD9:730.01 ICD9:730.1 ICD9:730.10 ICD9:730.11 ICD9:730.20 ICD9:730.28 ICD9:730.92 ICD9:730.93 ICD9:730.94 ICD9:730.96 ICD9:730.97 MEDGEN:10497 MESH:D010019 MONDO:ambiguous NCIT:C27577 NCIT:P378 SCTID:60168000 UMLS:C0029443 https://orcid.org/0000-0002-6601-2165 osteomyelitis osteomyelitis (disease) MONDO:0005246 DOID:1019 EFO:0003102 GARD:7286 MEDGEN:10497 MONDO:EFO MONDO:GARD MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo MONDO:i2s MONDO:otherHierarchy MONDO:relatedTo https://orcid.org/0000-0001-5208-3432 osteomyelitis MONDO:0005246 A bacterial infectious process affecting any part of the urinary tract, most commonly the bladder and the urethra. Symptoms include urinary urgency and frequency, burning sensation during urination, lower abdominal discomfort, and cloudy urine. http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl bacterial urinary tract infection (disease) UTI infection, urinary tract tract, infection of urinary urinary tract infection urinary tract infection (disease) urinary tract infectious disease ICD9:599.0 MEDGEN:675826 MONDO:ambiguous NCIT:C50791 NCIT:P378 SCTID:68566005 UMLS:C0729524 https://orcid.org/0000-0002-6601-2165 bacterial urinary tract infection (disease) MONDO:0005247 EFO:0003103 MEDGEN:675826 MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo MONDO:i2s bacterial urinary tract infection MONDO:0005247 An acute, acute and chronic, or chronic inflammation focally or diffusely affecting the lung parenchyma, caused by an infection in one or both of the lungs (by bacteria, viruses, fungi, or mycoplasma.). Symptoms include cough, shortness of breath, fevers, chills, chest pain, headache, sweating, and weakness. https://github.com/monarch-initiative/mondo/issues/3790 http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl DOID:552 EFO:0003106 ICD10CM:J15 ICD10CM:J18.9 ICD9:483 ICD9:483.8 ICD9:484.8 ICD9:486 MEDGEN:10813 MESH:D011014 NCIT:C3333 NCIT:P378 SCTID:233604007 UMLS:C0032285 acute pneumonia MONDO:0005249 DOID:552 EFO:0003106 MEDGEN:10813 MESH:D011014 MONDO:EFO MONDO:MEDGEN MONDO:OTAR MONDO:Redundant MONDO:equivalentTo MONDO:i2s MONDO:relatedTo NCIT:C3333/inferred https://orcid.org/0000-0001-5208-3432 pneumonia MONDO:0005249 A disease involving the heart and/or pericardium. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:114 EFO:0003777 ICD9:429.89 ICD9:429.9 ICD9:V47.2 MESH:D006331 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C3079 SCTID:56265001 UMLS:C0018799 https://github.com/monarch-initiative/mondo/issues/1189 https://orcid.org/0000-0002-6601-2165 cardiac disease disease of heart disease or disorder of heart disorder of heart disorder of heart/pericardium heart disease heart disease or disorder heart disorder heart trouble heart/pericardial disease heart/pericardial disease or disorder heart/pericardial disorder heart/pericardial trouble MONDO:0005267 DOID:114 EFO:0003777 MONDO:MEDGEN MONDO:equivalentTo MONDO:i2s MONDO:relatedTo NCIT:C3079 heart disorder MONDO:0005267 A disease involving the lung. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:850 EFO:0003818 ICD9:518.89 MESH:D008171 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C3198 SCTID:19829001 https://orcid.org/0000-0002-6601-2165 disease of lung disease or disorder of lung disorder of lung lung disease lung disease or disorder lung disorder lung disorders pulmonary disease pulmonary diseases pulmonary disorder pulmonary disorders MONDO:0005275 DOID:850 EFO:0003818 MONDO:equivalentTo MONDO:i2s MONDO:relatedTo lung disorder MONDO:0005275 The obstruction of the pulmonary artery or one of its branches by an embolus, sometimes associated with infarction of the lung. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl pulmonary embolism (disease) DOID:9477 EFO:0003827 HP:0002204 ICD9:415.19 MESH:D011655 MONDO:ambiguous NCIT:C50713 NCIT:P378 SCTID:59282003 UMLS:C0034065 https://orcid.org/0000-0002-6601-2165 embolism, pulmonary pulmonary artery embolism pulmonary embolism pulmonary embolism (disease) pulmonary embolus MONDO:0005279 DOID:9477 EFO:0003827 MONDO:equivalentTo MONDO:i2s MONDO:otherHierarchy MONDO:relatedTo NCIT:C50713 pulmonary embolism MONDO:0005279 A general term used to describe any disease affecting blood vessels]. It includes vascular abnormalities caused by degenerative, metabolic and inflammatory conditions, embolic diseases, coagulative disorders, and functional disorders such as posteri or reversible encephalopathy syndrome. https://github.com/monarch-initiative/mondo/issues/3602 http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:178 EFO:0004264 ICD10CM:I00-I99 ICD10CM:I70-I79 ICD9:442.9 MESH:D014652 MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C35117 SCTID:27550009 UMLS:C0042373 https://doi.org/10.1007/978-3-540-78785-3_7 https://orcid.org/0000-0002-0736-9199 disease of vasculature disease or disorder of vasculature disorder of vasculature vascular disorder vascular tissue disease vasculature disease vasculature disease or disorder vasculopathy MONDO:0005385 DOID:178 EFO:0004264 MONDO:equivalentTo NCIT:C35117 https://github.com/monarch-initiative/mondo/issues/4536 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-4142-7153 The etiology of vasculopathy is generally unknown and the condition is frequently not pathologically proven. Vasculitis, on the other hand, is a more specific term and is defined as inflammation of the wall of a blood vessel. However, the term vasculopathy is also used for “vasculitis” that has not been pathologically established. vascular disorder MONDO:0005385 A substance-specific organic brain syndrome that follows the discontinuation of administration or use, or reduction in intake of a substance (including alcohol, prescribed medications and recreational drugs). Syndrome manifests with diverse, often painful physical and psychological symptoms, which include but not limited to intense drug craving, anxiety, depression, insomnia, nausea, perspiration, body aches, tremors, hallucinations, and convulsions. https://github.com/monarch-initiative/mondo/issues/5544 http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl DOID:0060001 EFO:0005800 ICD9:292.0 MEDGEN:20990 MESH:D013375 MONDO:0000566 NCIT:C35046 SCTID:363101005 UMLS:C0038587 https://orcid.org/0000-0002-4142-7153 drug withdrawal drug withdrawal syndrome substance withdrawal substance withdrawal disorder substance withdrawal syndrome withdrawal syndrome withdrawal disorder MONDO:0005567 EFO:0005800 MEDGEN:20990 MONDO:EFO MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo MONDO:i2s https://orcid.org/0000-0001-5208-3432 substance withdrawal syndrome MONDO:0005567 Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. Cases of neonatal respiratory distress syndrome are not included in this definition. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:11394 EFO:1000637 GARD:0005698 ICD10CM:J80 MedDRA:10001052 NCIT:C3353 ARDS acute respiratory distress syndrome shock lung ALI Stiff lung acute lung injury increased-permeability pulmonary edema increased-permeability pulmonary oedema non-cardiogenic pulmonary edema non-cardiogenic pulmonary oedema MONDO:0006502 DOID:11394 EFO:1000637 MONDO:equivalentTo Orphanet:70578 Orphanet:70578/e This disease can present as a mild ARDS (PaO2/FiO2 of 201–300 mmHg) moderate ARDS (PaO2/FiO2 of 101–200 mmHg) and severe ARDS (PaO2/FiO2 ≤100 mmHg). [PMID:30872586] acute respiratory distress syndrome MONDO:0006502 An acute organic mental disorder induced by cessation or reduction in chronic alcohol consumption. Clinical characteristics include confusion; delusions; vivid hallucinations; tremor; agitation; insomnia; and signs of autonomic hyperactivity (e.g., elevated blood pressure and heart rate, dilated pupils, and diaphoresis). This condition may occasionally be fatal. It was formerly called delirium tremens. (From Adams et al., Principles of Neurology, 6th ed, p1175) http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl EFO:1000800 ICD9:291.0 MEDGEN:1398 MESH:D000430 MedDRA:10001610 SCTID:8635005 UMLS:C0001957 alcohol withdrawal associated autonomic hyperactivity alcohol withdrawal hallucinosis alcohol withdrawal induced delirium Tremens alcohol withdrawal-induced delirium Tremens autonomic hyperactivity, alcohol withdrawal associated delirium Tremens delirium Tremens, alcohol withdrawal induced delirium, alcohol withdrawal hallucinosis, alcohol withdrawal MONDO:0006642 EFO:1000800 MEDGEN:1398 MONDO:EFO MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo MONDO:i2s alcohol withdrawal delirium MONDO:0006642 Any variation from the normal rate or rhythm (which may include the origin of the impulse and/or its subsequent propagation) in the heart. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl EFO:0004269 ICD9:427.9 NCIT:C2881 NCIT:P378 SCTID:698247007 arrhythmia MONDO:0007263 EFO:0004269 MONDO:equivalentTo MONDO:i2s cardiac rhythm disease MONDO:0007263 A disorder resulting from inadequate blood flow in the vessels that supply the brain. Representative examples include cerebrovascular ischemia, cerebral embolism, and cerebral infarction. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:6713 EFO:0003763 ICD10CM:I60-I69 ICD9:430-438.99 ICD9:434.91 ICD9:437.8 ICD9:437.9 ISBN-13:978-1-259-64403-0 MESH:D002561 NCIT:C2938 OMIM:601367 SCTID:62914000 UMLS:C0007820 cerebrovascular disease cerebrovascular disorder CVA CVA (cerebral vascular accident) cerebral infarction cerebrovascular accident stroke MONDO:0011057 DOID:6713 EFO:0003763 MONDO:equivalentTo MONDO:i2s MONDO:relatedTo NCIT:C2938 https://github.com/monarch-initiative/mondo/issues/4536 https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-4142-7153 cerebrovascular disorder MONDO:0011057 The significant impairment of gas exchange within the lungs resulting in hypoxia, hypercarbia, or both, to the extent that organ tissue perfusion is severely compromised. Causes include chronic obstructive pulmonary disease, asthma, emphysema, acute respiratory distress syndrome, pneumonia, pulmonary edema, pneumothorax, and congestive heart failure. Treatment requires intubation and mechanical ventilation until the time the lungs recover sufficient function. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl DOID:11162 ICD9:518.81 ICD9:518.83 ICD9CM:518.84 MESH:D012131 NCIT:C26872 NCIT:C27043 SCTID:39871006 UMLS:C1145670 failure, respiratory respiratory failure respiratory insufficiency/failure acute respiratory failure chronic respiratory failure acute and chronic respiratory failure acute-on-chronic respiratory failure MONDO:0021113 DOID:11162 MONDO:equivalentTo MONDO:i2s NCIT:C26872 respiratory failure MONDO:0021113 A disorder that affects the muscle tissue of the heart. Representative examples include myocardial infarction, myocarditis, and cardiomyopathy. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl MONDO:design_pattern MONDO:patterns/location MONDO:patterns/location_top NCIT:C35544 SCTID:57809008 disease of myocardium disease or disorder of myocardium disorder of myocardium myocardial disease myocardial disorder myocardium disease myocardium disease or disorder disorder of heart muscle MONDO:0024643 MONDO:equivalentTo myocardial disorder MONDO:0024643 A disorder of the nervous system related to a vascular etiology. http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl MONDO:design_pattern MONDO:patterns/location NCIT:C117007 UMLS:C3898144 disease of nervous system vasculature nervous system disorder of vasculature neurovascular disorder vasculature nervous system disorder MONDO:0043218 MONDO:equivalentTo NCIT:C117007 neurovascular disorder MONDO:0043218 An inflammatory process affecting the lung parenchyma. It is a milder form of lung inflammation compared to pneumonia. http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl EFO:1001991 MEDGEN:811420 MONDO:patterns/inflammatory_disease_by_site NCIT:C113159 SCTID:205237003 UMLS:C3714636 inflammation of lung parenchyma lung parenchyma inflammation pneumonitis MONDO:0043905 MEDGEN:811420 MONDO:EFO MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo Pneumonitis typically refers to non-infectious inflammation, whereas pneumonia refers to infectious pneumonitis MONDO:0043905 A disorder characterized by confusion; inattentiveness; disorientation; illusions; hallucinations; agitation; and in some instances autonomic nervous system overactivity. It may result from toxic/metabolic conditions or structural brain lesions. (From Adams et al., Principles of Neurology, 6th ed, pp411-2) http://purl.obolibrary.org/obo/mondo/releases/2024-07-02/mondo.owl EFO:0009267 ICD9:293.0 MEDGEN:41445 MESH:D003693 NCIT:C2981 PMID:15876360 SCTID:2776000 UMLS:C0011206 OBS syndrome organic brain syndrome MONDO:0045057 MEDGEN:41445 MONDO:EFO MONDO:MEDGEN MONDO:OTAR MONDO:equivalentTo delirium MONDO:0045057 https://github.com/monarch-initiative/mondo/issues/5858 http://purl.obolibrary.org/obo/mondo/releases/2024-01-03/mondo.owl https://orcid.org/0000-0001-5208-3432 human disease or disorder MONDO:0700096 human disease MONDO:0700096 NCBITaxon:9606 Homo sapiens human being Homo sapiens NCIT:C122590 A hollow tube that is inserted into a vein. http://purl.obolibrary.org/obo/go.owl C122590 Medical Device Venous Catheter C0745442 NICHD Venous Catheter Venous Catheter NCIT:C13717 Named locations of or within the body. http://purl.obolibrary.org/obo/hp.owl C13717 Body Location or Region Anatomic Site C1515974 CPTAC ICDC Anatomic_Sites Anatomic Location Anatomic Site Anatomic Sites Anatomical Location Anatomical_Location CDISC Location Site Topographic (Anatomic) Site Topographic Site Anatomic Site NCIT:C164323 The anatomical site on which surgery was performed. http://purl.obolibrary.org/obo/hp.owl C164323 Spatial Concept Surgical Site C0332850 ICDC PCDC PROCEDURE_SITE Surgical Site anatomical site of surgery anatomical_site_of_surgery Surgical Site NCIT:C17612 A venous catheter positioned with the tip in the proximal third of the superior vena cava, the right atrium, or the inferior vena cava. http://purl.obolibrary.org/obo/go.owl C17612 Medical Device Central Venous Access Catheter C1145640 CPTAC NICHD A tube surgically placed into a blood vessel for the purpose of giving intravenous fluid and drugs. It also can be used to obtain blood samples. This device avoids the need for separate needle insertions for each infusion or blood test. Examples of these devices include Hickman catheters, which require clamps to make sure the valve is closed, and Groshong catheters, which have a valve that opens as fluid is withdrawn or infused and remains closed when not in use. Central_Venous_Access_Catheter Central Line Catheter Central Venous Access Catheter Central Venous Access Catheters central venous access catheter Central Venous Access Catheter OBIB:0000716 mastectomy / craniotomy / liver resection e.t.c. A planned process that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, or to help improve bodily function or appearance. http://en.wikipedia.org/wiki/Surgery http://purl.obolibrary.org/obo/obib/2023-04-05/obib.owl surgical procedure OBI:0000011 planned process A process that realizes a plan which is the concretization of a plan specification. planned process OBI:0000066 investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation OBI:0000070 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived http://purl.obolibrary.org/obo/obi.owl study assay any method assay OBI:0000181 population PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population. a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area 1/28/2013, BP, on the call it was raised that we may want to switch to an external ontology for all populatin terms: http://code.google.com/p/popcomm-ontology/ PERSON: Philippe Rocca-Serra adapted from Oxford English Dictionnary rem1: collection somehow always involve a selection process http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl population OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000471 study design execution a planned process that carries out a study design study design execution OBI:0000679 average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl average value OBI:0000968 device A voltmeter is a measurement device which is intended to perform some measure function. An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure. A material entity that is designed to perform a function in a scientific investigation, but is not a reagent. 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. http://purl.obolibrary.org/obo/aeo.owl device 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. value specification OBI:0002830 catheter A catheter left inside the body, either temporarily or permanently, may be referred to as an indwelling catheter. A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body. https://orcid.org/0000-0002-8844-9165 http://purl.bioontology.org/ontology/MESH/D057785 http://purl.obolibrary.org/obo/obi/2024-06-10/obi.owl catheter 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:0200000 data transformation A planned process that produces output data from input data. data transformation OBI:0500000 study design A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. study design OBI:1110122 pathologic process abnormal, harmful processes caused by or associated with a disease IEDB IEDB http://purl.obolibrary.org/obo/obi/2023-09-20/obi.owl pathologic process 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 http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl clinical finding OGMS:0000096 A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl A process involving a patient and a healthcare professional that focuses on the assessment, diagnosis, treatment and consultation for a disease or injury, or for prevention of a subsequent injury. health care process OGMS:0000097 A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl health care encounter OGMS:0000098 TODO Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl 09/16/2020 Is this same as admission? Is this the same as inpatient encounter? hospitalization OGMS:0000100 A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl inpatient encounter OGMS:0000102 A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure. At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 creation date: 2011-09-20T09:57:44Z http://purl.obolibrary.org/obo/ogms.owl Damage to a person's tissues, bones, or organ systems with the potential for dysfunction and caused by mechanical, thermal, or radiation mechanisms injury 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 http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl clinical data item OMRSE:00000001 A social role inhering in a human being. Mathias Brochhausen William R. Hogan http://purl.obolibrary.org/obo/omrse.owl human social role OMRSE:00000010 A role in human social processes that is realized by health care processes such as seeking or providing treatment for disease and injury, diagnosing disease and injury, and undergoing diagnosis. William R. Hogan health care role http://purl.obolibrary.org/obo/omrse.owl Mathias Brochhausen human health care role OMRSE:00000011 A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen patient CAFE domain expert working group. http://purl.obolibrary.org/obo/omrse.owl A person who presents to a healthcare provider for clinical care. In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. patient role OMRSE:00000012 A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism. Mathias Brochhausen http://purl.obolibrary.org/obo/omrse.owl A healthcare provider with responsibility for the care of ill and injured patients. William R. Hogan health care provider role OMRSE:00000013 A health care role borne by a human being and realized by promoting, maintaining, or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. Mathias Brochhausen physician http://en.wikipedia.org/wiki/Physician http://purl.obolibrary.org/obo/omrse.owl A credentialled health professional graduate of a school of medicine who provides medical care by promoting, maintaining, or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments. physician role OMRSE:00000014 A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. Mathias Brochhausen nurse based on: http://en.wikipedia.org/wiki/Nursing http://purl.obolibrary.org/obo/omrse.owl A health professional graduate of a school of nursing who provides nursing care to promote the attainment, maintenance, or recovery of optimal health and quality of life for individuals, families, and communities. nurse role OMRSE:00000015 http://purl.obolibrary.org/obo/omrse.owl Definition needed, but the idea is that we want to differentiate between provider and payer organizations. Some organizaitons have both roles (e.g., UPMC has a Hospital Division, a Physician Divison, and an Insurance Division). health care provider organization role OMRSE:00000022 An object aggregate of organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. collection of organisms OMRSE:00000023 An object aggregate all of whose components are human beings. collection of humans OMRSE:00000024 A role inhering in an entity realized by social interactions in human society. Mathias Brochhausen http://purl.obolibrary.org/obo/omrse.owl Previous definition: A role played by an entity in human social processes. role in human social processes OMRSE:00000025 A role in human social processes that inheres in an organization. William R. Hogan http://purl.obolibrary.org/obo/omrse.owl Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. organization social role OMRSE:00000026 A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen http://purl.obolibrary.org/obo/omrse.owl Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. Ditto for its current descendants. Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. Previous definition: A role in human social processes played by an organism. organism social role OMRSE:00000027 An organization social role that is realized by a health care process. http://purl.obolibrary.org/obo/omrse.owl An organization that has a role in the healthcare delivery process. Previous definition: An organization social role played by an organization in health care processes. organization health care role OMRSE:00000033 An aggregate of organizations that have some feature in common, but is not itself an organization. An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common William R. Hogan William R. Hogan Amanda Hicks http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations OMRSE:00000038 A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. An individual(s) with authority and rights and duties enforceable by law. legal person role OMRSE:00000054 A healthcare provider role that inheres in an organization and is realized by providing inpatient and outpatient care. Mathias Brochhausen http://purl.obolibrary.org/obo/omrse.owl A healthcare facility that provides inpatient and outpatient care. hospital role OMRSE:00000067 A patient role that inheres an organism suffering one or more injuries. Amanda Hicks injured patient The following definition for 'injured patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering one or more injuries. http://purl.obolibrary.org/obo/omrse.owl An individual with one or more injuries that requires treatment. injured patient role OMRSE:00000074 A material entity that has as parts one or more sites large enough to contain humans, has as part one or more material entities that separates it from other sites, and bears a residence function. Amanda Hicks https://github.com/ufbmi/OMRSE/wiki/Housing-unit-and-Household http://purl.obolibrary.org/obo/aeo.owl Housing units are individuated by their residence functions. housing unit OMRSE:00000077 OMRSE:00000085 A role that concretizes a socio-lega generically dependent continuant Amanda Hicks http://purl.obolibrary.org/obo/omrse.owl socio-legal human social role OMRSE:00000086 A socio-legal human social role that concretizes a socio-legally generically dependent continuat that was created by a declaration performed by an organization. Amanda Hicks http://purl.obolibrary.org/obo/omrse.owl human role within an organization OMRSE:00000087 http://purl.obolibrary.org/obo/omrse.owl employer role OMRSE:00000126 A deontic document act that concludes an inpatient encounter. Amanda Hicks discharge process http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl patient discharge OMRSE:00000129 A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon. http://purl.obolibrary.org/obo/omrse.owl US physician assistant role OMRSE:00000130 A physician role that, if it is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or providing airway management or by making decisions independently of a supervising physician regarding the adminstration of such medication. Jonathan Bona Mathias Brochhausen http://purl.obolibrary.org/obo/omrse.owl A physician with responsibility for managing complex airways, and administering anesthesia or making decisions about anethesthic medications to be administered in collaboration with the attending physician. anesthesiologist role OMRSE:00000201 A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter. Amanda Hicks http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl admission process OMRSE:00002072 A role that inheres in some entity that is realized in a social act. Matthew Diller http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes OOSTT:00000000 A healthcare provider representing their specialty in the multidisciplinary peer review committee. Mathias Brochhausen obsolete_specialty liaison true OOSTT:00000001 A role borne by a physician that, if realized, is realized by making the diagnostic and therapeutic decision during a trauma resuscitation. Mathias Brochhausen trauma team lead role OOSTT:00000002 An organization that is the bearer of a trauma center role. Mathias Brochhausen trauma center OOSTT:00000003 A professional organization of healthcare providers and trauma facilitites aiming to improve trauma care, the trauma system, and/or to conduct trauma research. Mathias Brochhausen A group of health professionals and trauma facilities with a formal mission focused on improving trauma care, the trauma system, and/or trauma research. trauma professional organization OOSTT:00000004 A role that inheres in a healthcare provider and, if realized, is realized by the bearer representing their speciality in the multidisciplinary peer review committee. Mathias Brochhausen specialty liaison role OOSTT:00000005 A plan specification specifying the monitoring, evaluating, and improving of the quality of care for trauma patients and of a trauma service as whole. Mathias Brochhausen Sarah Bost A plan aiming towards the improvement of quality of care by monitoring and evaluating care and patient safety for individual trauma patients and the trauma service overall. trauma quality improvement and patient safety program OOSTT:00000006 A committee with members from multiple specialties that engages in case review of trauma cases. Mathias Brochhausen A committee with members from multiple specialties that engages in case review of trauma cases. trauma multidisciplinary peer review committee OOSTT:00000007 A performance improvement committee that is part of a trauma program and reviews the system of care within that trauma center. Mathias Brochhausen A performance improvement committee that reviews the system, processes, and efficiencies of care within a trauma service. trauma program operational review committee OOSTT:00000008 A role appointed by a legislature that, if realized, grants the bearer authority to plan, coordinate, and monitor trauma systems. Mathias Brochhausen Sarah Bost The agency statutorily responsible for trauma systems planning, program coordination, and monitoring within the state, region or county. trauma lead agency role OOSTT:00000009 An organization in a defined geographic area that ensures optimal trauma care, which includes injury prevention, access to care, prehospital care, acute hospital care, and rehabilitation. Mathias Brochhausen Sarah Bost A systematic approach within a geographic region to assure and improve the process of trauma care, including prehospital care and rehabilitation, by establishing guidelines and monitoring performance and outcomes of care for the region's population and visitors. regional trauma system OOSTT:00000010 A conditional specification that guides prehospital providers in determining the most appropriate facility to care for the injured patient. Mathias Brochhausen Sarah Bost A decision tool "to help prehospital providers determine the most appropriate facility to care for the injured patient" developed by a medical direction authority [PMID: 22626915]. field triage guideline OOSTT:00000011 The planned process of alerting the trauma team members that a trauma patient is enroute or has arrived. Mathias Brochhausen Sarah Bost Notification of the appropriate pre-defined trauma team, to match the severity of anticipated injuries, to assemble and prepare to evaluate and treat a patient after notification that the patient is enroute or has arrived at the emergency department. trauma team activation OOSTT:00000012 The planned process of trauma team members arriving to treat the patient. Mathias Brochhausen Assembling of the appropriate trauma team (surgeon, nurses, emergency physician, anesthesia specialist, X-ray technicians, and others as indicated) to match the patient's injury or physiological severity. trauma team response OOSTT:00000013 A healthcare provider who is bearing a trauma team lead role. Mathias Brochhausen trauma team lead OOSTT:00000014 An organization that has statutory authority from the legislature to develop and oversee a trauma system. Mathias Brochhausen Sarah Bost trauma systems agency The agency legally responsible for trauma-EMS systems planning, program coordination, and monitoring within the state, region or county. trauma lead agency OOSTT:00000015 An organization of organizations and healthcare providers to facilitate and coordinate a multidisciplinary response to severe injury. Mathias Brochhausen Sarah Bost An organized and regulated local, state, provincial, regional, or national approach to facilitating and coordinating a multidisciplinary medical system response to severely injured patients. trauma system OOSTT:00000016 A statute or a set of statutes specifying an agency that holds authority for the creation and operation of a trauma system. Mathias Brochhausen A statute or multiple statutes that identifies a lead agency and authorizes the creation, operation, and evaluation of a state, regional or local trauma system. enabling legislation OOSTT:00000017 The organization that bears a trauma program role and is part of a healthcare provider organization. Mathias Brochhausen trauma service The organizational unit of a healthcare facility that is designated to provide and coordinate care for injured patients. trauma program OOSTT:00000018 A role borne by a human healthcare provider that, if realized is realized by managing the operation of the trauma service, including: supervision of trauma registry, trauma case managers, and support staff; coordination with hospital administration and medical staff; coordination of trauma quality improvement functions; preparation of trauma designation/verification applications, documentation and required reporting; and trauma-specific education and training. Mathias Brochhausen Sarah Bost TPM role The individual responsible for managing the day-to-day operation of the trauma program, including: supervision of trauma registry, trauma case managers, and support staff; coordination with hospital administration and medical staff; coordination of trauma quality improvement functions; preparation of trauma designation/verification applications, documentation and required reporting; and trauma-specific education and training. The individual responsible for managing the operation of the trauma service, including: supervision of trauma registry, trauma case managers, and support staff; coordination with hospital administration and medical staff; coordination of trauma quality improvement functions; preparation of trauma designation/verification applications, documentation and required reporting; and trauma-specific education and training. trauma program manager role OOSTT:00000019 A planned process that comprehensively determines whether a facility meets the established criteria (state or national) regarding procedures, resources, and capabilities for the level of trauma service requested by the facility. Mathias Brochhausen A process that comprehensively determines whether a facility meets the established criteria of a verification body (e.g. the American College of Surgeons) regarding procedures, resources, personnel and capabilities required to be a designated trauma facility. trauma center verification OOSTT:00000020 A deontic document act that creates the role of a trauma center based on meeting the criteria by a designated organization. Mathias Brochhausen Sarah Bost A state, regional, provincial, or national recognition process in which a facility is awarded a trauma center role after a formal review of the hospital's organization, capacity, personnel, and resources by a verifying agency. trauma center designation OOSTT:00000021 A human health care role borne by a physician that, if realized, is realized by having the authority to direct and oversee the management all aspects of the trauma service. Mathias Brochhausen TMD role The role borne by a physician having the authority to manage all aspects of a trauma service. trauma medical director role OOSTT:00000022 An individual who abstracts, records, and validates data in an electronic trauma registry; assists with data analysis; and runs reports. Jonathan Bona Mathias Brochhausen Sarah Bost An individual who abstracts and records data into an electronic trauma registry and runs reports. trauma registrar role OOSTT:00000023 A performance improvement committee tasked to evaluate trauma care within a region or state. Mathias Brochhausen The CAFE Domain Expert Group trauma system operational process performance improvement committee OOSTT:00000024 An organization of healthcare professionals from multiple disciplines who collectively work together on the assessment and treatment of those who are potentially severely injured. Mathias Brochhausen A multidisciplinary team of healthcare professionals who collectively work together on the initial assessment and treatment of individuals who are potentially severely injured. The term "potentially" was added both to the definition and the OOSTT user-centered description to acount for overtriage. Trauma resiscitation teams assess patients that are deemed to be severly injured by prehsopital healthcare providers. trauma resuscitation team OOSTT:00000025 A Level I trauma center role is a trauma center role that is borne by a hospital and that is the specified output of a Level I trauma center designation. If realized, it is realized by providing trauma care and education in accordance with the requirements for Level I trauma centers by the designating organization. Mathias Brochhausen Sarah Bost level I trauma center role https://en.wikipedia.org/w/index.php?title=Trauma_center&oldid=685886443 An example of the requirements for a Level I trauma center can be found on page 17 in Resources for Optimal Care of the Injured Patient, 6th edition: https://www.facs.org/~/media/files/quality%20programs/trauma/vrc%20resources/resources%20for%20optimal%20care.ashx level 1 trauma center role OOSTT:00000026 A Level II trauma center role is a trauma center role that is borne by a hospital and that is the specified output of a Level II trauma center designation. If realized, it is realized by providing trauma care and education in accordance with the requirements for Level II trauma centers by the designating organization. Mathias Brochhausen Sarah Bost level II trauma center role https://en.wikipedia.org/w/index.php?title=Trauma_center&oldid=685886443 An example of the requirements for a Level II trauma center can be found on page 18 in Resources for Optimal Care of the Injured Patient, 6th edition: https://www.facs.org/~/media/files/quality%20programs/trauma/vrc%20resources/resources%20for%20optimal%20care.ashx level 2 trauma center role OOSTT:00000027 A Level III trauma center role is a trauma center role that is borne by a hospital and that is the specified output of a Level III trauma center designation. If realized, it is realized by providing trauma care and education in accordance with the requirements for Level III trauma centers by the designating organization. Mathias Brochhausen Sarah Bost level III trauma center role https://en.wikipedia.org/w/index.php?title=Trauma_center&oldid=685886443 An example of the requirements for a Level III trauma center can be found on page 19 in Resources for Optimal Care of the Injured Patient, 6th edition: https://www.facs.org/~/media/files/quality%20programs/trauma/vrc%20resources/resources%20for%20optimal%20care.ashx level 3 trauma center role OOSTT:00000028 A trauma lead agency responsible for implementing rules and financing. Jonathan Bona Mathias Brochhausen The entity given authority by the government to implement rules and financing. jurisdictional lead agency OOSTT:00000029 A role that is borne by a hospital or clinic and, if realized, is realized by its bearer providing emergency trauma care through specially trained personnel. The role is the specified outcome of a trauma center designation. Mathias Brochhausen A formally recognized acute care hospital or clinic that meets the standards and established criteria for trauma center designation and provides stabilization or definitive care to trauma patients. trauma center role OOSTT:00000031 A Level IV trauma center role is a trauma center role that is borne by a hospital and that is the specified output of a Level IV trauma center designation. If realized, it is realized by providing trauma care and education in accordance with the requirements for Level IV trauma centers by the designating organization. Mathias Brochhausen Sarah Bost level IV trauma center role https://en.wikipedia.org/w/index.php?title=Trauma_center&oldid=685886443 An example of the requirements for a Level IV trauma center can be found on page 20 in Resources for Optimal Care of the Injured Patient, 6th edition: https://www.facs.org/~/media/files/quality%20programs/trauma/vrc%20resources/resources%20for%20optimal%20care.ashx level 4 trauma center role OOSTT:00000032 A pediatric trauma center role is a trauma center role that is borne by a hospital and that is the specified output of a pediatric trauma center designation. If realized, it is realized by providing pediatric trauma care and education in accordance with the requirements for pediatric trauma centers by the designating organization. Mathias Brochhausen Sarah Bost https://en.wikipedia.org/w/index.php?title=Trauma_center&oldid=685886443 A trauma center role that is borne by a hospital that is organized to provide trauma care to injured infants, children, and adolescents. Its bearer has a full range of pediatric specialists and equipment available 24 hours a day and admits a minimum required annual volume of severely injured patients established by the designating agency. The facility has transfer agreements with referring facilities, and provides performance improvement and education outreach to those facilities. The role is created by a pediatric Trauma Center designation. pediatric trauma center role OOSTT:00000033 A Level V trauma center role is a trauma center role that is borne by a hospital or clinic and that is the specified output of a Level V trauma center designation. If realized, it is realized by providing trauma care and education in accordance with the requirements for Level V trauma centers by the designating organization. Mathias Brochhausen Sarah Bost level V trauma center role https://en.wikipedia.org/w/index.php?title=Trauma_center&oldid=685886443 level 5 trauma center role OOSTT:00000034 A trauma center verifcation that has a designated trauma center as specified input. Designated trauma centers need to go through the process of reverification in a specified time interval. Mathias Brochhausen A process to determine whether a verified trauma center continues to meet the verification standards of the American College of Surgeons or a similar process in a particular trauma system or jurisdiction within a specified time period. trauma center reverification OOSTT:00000035 A planned process providing an assessment of a hospital regarding the feasibility of it becoming a designated trauma center. Mathias Brochhausen A planned process providing an assessment of a hospital's organization, capacity, personnel, and resources regarding the feasibility of it becoming a verified or designated trauma center. trauma center consultation OOSTT:00000036 A healthcare provider organization role that is borne by a part of a healthcare provider organization and, if realized, is realized by providing and coordinating care for injured patients. Mathias Brochhausen A program within a healthcare facility that provides and coordinates care for injured patients. trauma program role OOSTT:00000037 A plan specification that specifies which members of trauma personnel are supposed to be ready for trauma team activation during which time periods. John Judkins Mathias Brochhausen trauma panel The plan specifying which trauma personnel are required to respond to trauma team activations for given time periods. trauma on call plan specification OOSTT:00000038 A trauma professional organization focusing its mission on a specified region within a nation. John Judkins Mathias Brochhausen A professional organization focusing its mission on the improvement of trauma care within the region. regional trauma professional organization OOSTT:00000039 A trauma professional organization focusing its mission on a national level. John Judkins Mathias Brochhausen A professional organization focusing its mission on the improvement of trauma care across the nation, with potential impacts at state, regional, and local levels. national trauma professional organization OOSTT:00000040 A plan specification specifying the organization of meetings of representatives of all medical specialities involved in trauma care to review the performance from a peer perspective. Mathias Brochhausen Sarah Bost Guidelines for organization of the trauma peer review committee meetings with an intended outcome of reviewing the performance of trauma care from a peer perspective. trauma peer review committee meeting plan specification OOSTT:00000041 A planned process that realizes the concretization of a trauma peer review committee meeting plan specification. This meeting is inteded to to review the performance from a representatives of all medical specialities involved in trauma care by their peers. Mathias Brochhausen The scheduled time at which the members of the trauma peer review committee meet to evaluate and provide feedback to individual care providers regarding provided trauma care. trauma peer review committee meeting OOSTT:00000043 A role that is borne by a person that also bears a emergency medicine physician role and, if realized, is realized by providing management and leadership for the clinical department that providie emergency care to ill and injured patients. Mathias Brochhausen director of emergency medicine head of emergency medicine department role http://www.acep.org/workarea/DownloadAsset.aspx?id=29878 A emergency physician who provides management and leadership for the physicians providing emergency care to ill and injured patients. head of emergency medicine role OOSTT:00000044 A human health care role borne by a nurse and if realized, relized by managing a team of healthcare professionals, provide continuing education or providing input to healthcare policies in their organization Mathias Brochhausen A qualified nurse leader who has authority to manage and oversee nursing care provided within the healthcare facility, including provision of input to the facility's healthcare policies. nurse executive role OOSTT:00000046 A role that is the specified outcome of a social act and that is mutually specifically dependent on a reportee role and that, if realized, is realized by the bearer of the role reporting activities and results to the bearer of the depending reportee role. John Judkins Mathias Brochhausen An individual who provides key information to another individual. reporter role OOSTT:00000047 A role that is the specified outcome of a social act and that is mutually specifically dependent on a reporter role and that, if realized, is realized by the bearer of the role receiving reports on activities and results by the bearer of the depending reporter role. John Judkins Mathias Brochhausen An individual who receives key information from another individual. reportee role OOSTT:00000048 A specialty liaison role borne by a human being, which is also bearing an health care provider role, and if realized, is realized by the bearer representing anesthesiology in the multidisciplinary peer review committee. John Judkins Mathias Brochhausen A physician or CRNA who represents anesthesia in the multidisciplinary peer review committee. anesthesiology liaison role OOSTT:00000049 A plan specification that has continuing medical education objective specifications as parts and that when concretized, is realized in processes that help maintain competence and learn about new and developing areas of medicine or the medical speciality of its bearer. John Judkins Mathias Brochhausen A description of the continuing medical education offering that includes content, methodology, and evaluation with emphasis on helping health professionals maintain continued competency or learn new concepts in medical care. continuing medical education plan specification OOSTT:00000050 An objective specification that describes the endpoint of processes to maintain competency and learn new and developing areas in medicine or one of its specialities. John Judkins Mathias Brochhausen Sarah Bost https://en.wikipedia.org/w/index.php?title=Continuing_medical_education&oldid=708782251 The description of content and expected learning for health professionals that is necessary to maintain continued competency and to learn new and developing concepts in medical care. Note that these are represented in OOST merely to define continuing medical education plan specifications. (JB & MB 29 June 2017) continuing medical education objective specification OOSTT:00000051 A role that inheres in an organization and, if realized, is realized by the bearer providing direction and overseeing the operations of a hospital. John Judkins Mathias Brochhausen obsolete_hospital governing body role true OOSTT:00000052 A committee with members from multiple specialties that engages in case review of trauma cases. Mathias Brochhausen trauma multidisciplinary peer review committee (OOSTT_00000006) A committee with members from multiple specialties that engages in case review of trauma cases. obsolete_trauma peer review committee true OOSTT:00000053 obsoleted_preshospital continuing education true OOSTT:00000054 A planned process that has prehospital protocols as its specified output. Mathias Brochhausen A planned process overseen by an authorized person or committee for development of prehospital practice guidelines regarding the assessment, management, and transport of patients with emergency conditions. prehospital protocol development OOSTT:00000055 An organization that is part of the bearer of a health care provider organization role and that has members that all bearer of a healthcare provider role within that organization. Mathias Brochhausen All healtcare providers who have been credentialed by a healthcare organization to provide care to patients or to perform administrative functions, including oversight of patient care. medical staff OOSTT:00000056 obsolete_resolution of support document true OOSTT:00000057 obsoleted_subordinate role true OOSTT:00000058 obsolete_authority role true OOSTT:00000059 A plan specification that specifies planned income and expenses for a person or an organization for a specified period of time. John Judkins Mathias Brochhausen A detailed plan identifying the sources of revenue and allocation of funds for a designated period of time. budget OOSTT:00000060 A collection of humans that is part of a trauma program and whose members bear a trauma leadership role. John Judkins Mathias Brochhausen The individuals who provide oversight, direction, coordination, and management for the facility's trauma program. trauma program leadership OOSTT:00000061 A deontic role borne by the bearer of a healthcare provider role that, if realized, is realized by developing, overseeing and improving medical care for injured patients in a healthcare provider organization. John Judkins Mathias Brochhausen Sarah Bost The entity with the power to develop, oversee, improve medical care, and implement corrective actions following a performance improvement process for injured patients in the healthcare facility. The definition is intended to include rehabilitation as one part of medical care. authority over trauma care OOSTT:00000062 A role that inheres in an organization and that, if realized, is realized by its bearer overseeing the overall operation of a hospital. Mathias Brochhausen hospital board role A group of individuals appointed to a hospital's board of directors who provide governance, direction and oversight of the overall operation of a hospital. hospital governing body role OOSTT:00000063 A role that is borne by a human being and that, if realized, is realized by managing an organization as the final decision maker for day to day operations and the bearer of which is held accountable for the organizations performance. Mathias Brochhausen managing director The qualified person with the authority to make final day-to-day decisions for an organization, and who is accountable for the organization's performance. chief executive officer role OOSTT:00000064 A role that inheres in a human being and that, if realized, is realized by managing and overseeing the delivering of medical care at a hospital. Mathias Brochhausen A qualified physician who has authority to manage and oversee medical care provided within the healthcare facility. chief medical officer role OOSTT:00000065 A role that inheres in a human being and that, if realized, is realized by by its bearer managing nursing staff at a hospital and ensuring that standards of care are met. Mathias Brochhausen The chief nursing officer in a healthcare facility. head of clinical services role OOSTT:00000066 A specialty liaison role borne by a human being, which is also bearing a health care provider role, and if realized, is realized by the bearer representing emergency medicine in the multidisciplinary peer review committee. Mathias Brochhausen emergency medicine liaison role OOSTT:00000067 A specialty liaison role borne by a human being, which is also bearing a health care provider role, and if realized, is realized by the bearer representing orthopedic surgery in the multidisciplinary peer review committee. Mathias Brochhausen Sarah Bost A orthopedic surgeon who formally represents orthopedic surgery in the multidisciplinary peer review committee. orthopedic surgery liaison role OOSTT:00000068 A specialty liaison role borne by a human being, which is also bearing a health care provider role, and if realized, is realized by the bearer representing neurosurgery in the multidisciplinary peer review committee. Mathias Brochhausen neurosurgery liaison role OOSTT:00000069 A specialty liaison role borne by a human being, which is also bearing an health care provider role, and if realized, is realized by the bearer representing critical care in the multidisciplinary peer review committee. Mathias Brochhausen An critical care physician who serves as the formal representative for the critical care process on the multidisciplinary peer review committee. critical care liaison role OOSTT:00000070 A specialty liaison role borne by a human being, which is also bearing a health care provider role, and if realized, is realized by the bearer representing radiology in the multidisciplinary peer review committee. Mathias Brochhausen A radiologist who formally represents the imaging department in the multidisciplinary peer review committee. radiology liaison role OOSTT:00000071 A healthcare process involving a injured patient focusing on their trauma-caused condition. A healthcare process focused on the assessment and management of an injured patient. trauma care process OOSTT:00000072 A plan specification that prescribes educational processes to identify, monitor, and address potential opportunities to improve trauma care. J. Neil Otte John Judkins Mathias Brochhausen trauma QI/PI plan specification A plan that prescribes the processes to identify, monitor, and address potential opportunities to improve trauma care. trauma quality improvement and performance improvement plan specification OOSTT:00000073 A planned process that realizes the concretization of a trauma quality improvemement and performance improvement plan specification. J. Neil Otte John Judkins Mathias Brochhausen trauma QI/PI process The process for implementing measures to improve trauma patient outcomes and trauma care workflows. trauma quality improvement and performance improvement process OOSTT:00000074 An information content entity that is the specified outcome of and documents the sucessful completion of a tertiary education program. John Judkins Mathias Brochhausen Recognized degree awarded after successful completion of a college or post-graduate porgram. academic degree OOSTT:00000075 A healthcare provider role borne by a human being and that, if realized, realized by providing assessment and treatment to develop, recover, or maintain the daily living and work skills of people with a physical, mental, or cognitive disorder. Mathias Brochhausen A healthcare professional who specializes in providing assessment and treatment to develop, recover, or maintain the daily living functioning and work-related skills of a person with a disability. occupational therapist role OOSTT:00000076 A health care provider role borne by a human being and, if realized, is realized by providing assessment and treatment to remediate impairments or promote mobility, function, and quality of by interventions that use mechanical force and movements. Mathias Brochhausen A healthcare professional who specializes in providing assessment and treatment to remediate impairments or promote mobility, function, and quality of life by interventions that use mechanical force, movements, massage, or electrical stimulation. physical therapist role OOSTT:00000077 A healthcare provider role borne by a human being and if realized, is realized by providing assessment and treatment that follows surgery, or treatment of a disease or of an injury, and which restores a patient's preferable functionality. Mathias Brochhausen A health professional (physiatrist, PT, OT, speech/language therapist) who promotes return to or improvement in functional status after a debilitating illness or injury event. rehabilitation specialist role OOSTT:00000078 A university (Latin: universitas, "a whole") is an institution of higher (or tertiary) education and research which grants academic degrees in various subjects and typically provides undergraduate education and postgraduate education. https://en.wikipedia.org/w/index.php?title=University&oldid=714964422 university OOSTT:00000079 A planned process that realizes a plan that concretizes a prehospital training plan specification and that relays information to members of the prehospital care providers and exercises the application of that information. Mathias Brochhausen Sarah Bost A training process with the primary objective of teaching prehospital care providers the assessment and management of care for patients with urgent and emergent conditions before and during transport to the hospital. prehospital provider training OOSTT:00000080 obsolete_emergency medical services operation true OOSTT:00000081 An academic degree awarded by colleges and universities upon completion of a program of study lasting two years. John Judkins Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Associate_degree&oldid=723897149 Recognition awarded after completion of a specific curriculum from an accredited tertiary education provider that falls between high school and bachelor's degree program. associate degree OOSTT:00000082 An academic degree awarded by universities upon completion of a course of study demonstrating a mastery or high-order overview of a specific field of study or area of professional practice.[1] Within the area studied, graduates are posited to possess advanced knowledge of a specialized body of theoretical and applied topics; high order skills in analysis, critical evaluation, or professional application; and the ability to solve complex problems and think rigorously and independently. John Judkins Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Master%27s_degree&oldid=726036185 master's degree OOSTT:00000083 An academic degree awarded by colleges and universities upon completion of a course of study lasting three to seven years. John Judkins Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Bachelor%27s_degree&oldid=725713923 bachelor's degree OOSTT:00000084 An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a bachelor's of nursing program. John Judkins Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Bachelor_of_Science_in_Nursing&oldid=725962822 bachelor's of nursing degree OOSTT:00000085 An academic degree granted by an accredited tertiary education provider after the successful completion of an associate of nursing program. John Judkins Mathias Brochhausen associate of science in nursing OOSTT:00000086 An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a master's of nursing program. John Judkins Mathias Brochhausen An advanced academic degree in the principles and practices of nursing, with a focus on administration, education, or advanced nursing practice, granted by an accredited college or university after the successful completion of a master's of nursing program. master's in the science of nursing degree OOSTT:00000087 An objective specification that describes the endpoint of processes to maintain competency and learn new and developing areas in trauma medicine. John Judkins Mathias Brochhausen Sarah Bost The description of content and expected learning for health professionals participating in the care of injured patients that is necessary to maintain continued competency and to learn new and developing concepts in trauma care management. Note that these are represented in OOST merely to define continuing trauma education plan specifications. (JB & MB 29 June 2017) continuing trauma education objective specification OOSTT:00000088 A plan specification that has a continuing trauma education objective specification as parts. John Judkins Mathias Brochhausen continuing trauma education plan A description of the continuing medical education offering that includes content, methodology, and evaluation with emphasis on helping health professionals participating in the care of injured patients to maintain continued competency or learn new concepts in trauma care. continuing trauma education plan continuing trauma education plan specification OOSTT:00000089 A physician role borne by a human being and that, if realized, is being realized by its bearer using operative manual and instrumental techniques on a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A physician who specializes in performing operative manual and instrumental techniques on a patient to investigate or treat a pathological condition such as disease or injury or congenital defect, to help improve bodily function or appearance, or to repair ruptured areas. term requested in OMRSE. Do not use outside the CAFE application! surgeon role OOSTT:00000090 A surgeon role borne by a human being and, that, if realized, is realized by its bearer using operative manual or instrumental techniques on the musculoskeletal system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A surgeon who specializes in performing operative manual and instrumental techniques on the musculoskeletal system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair ruptured areas. term requested in OMRSE. Do not use outside the CAFE application! orthopedic surgeon role OOSTT:00000091 A physician role borne by a human being and that, if realized, is being realized by its bearer using operative manual and instrumental techniques on preadult patients to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. A surgeon who specializes in performing operative manual and instrumental techniques on infants, children, and adolescents to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair ruptured areas. term requested in OMRSE. Do not use outside the CAFE application! pediatric surgeon role OOSTT:00000092 An organization that provides prehospital care or transport to the sick and wounded. Mathias Brochhausen EMS ambulance service ems agency Stedman's Medical Dictionary for the Health Professions and Nursing. 7th edition. This term class is different from http://purl.obolibrary.org/obo/ARG_2000136 (emergency medical services). The latter seems to be inteded to represent a medical speciality, while this class represents an organization. obsolete_emergency medical service agency true OOSTT:00000093 A planned process that involves a physiscian and an agency providing prehospital care or transport of the sick and wounded and the physisican provides input regarding patient care and planning and operation of the service from a medical perspective. Mathias Brochhausen A planned process that involves a physiscian and an organization providing prehospital care and transport of the sick and wounded in which the physician provides input regarding patient care and evaluating performance of the service and individual providers of care . medical direction to emergency medical services OOSTT:00000094 A plan specification that specifies how the organizational structures interact to coordinate, manage and provide trauma care in a specified geographical region. John Judkins Mathias Brochhausen trauma system plan trauma system plan specification OOSTT:00000095 A healthcare provider role that, if realized, is realized by planning, organizing and overseeing planned processes that realize the concretization of a trauma quality improvement and patient safety program. Mathias Brochhausen The role of a healthcare provider that ensures trauma quality improvement and patient safety within the trauma program. trauma quality improvement and patient safety program lead role OOSTT:00000096 A surgeon role borne by a human being and, that, if realized, is realized by its bearer using operative and non-operative manual or instrumental techniques on a patient to investigate or treat an injury or other pathological situation that are caused by an injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen Sarah Bost A surgeon with oversight responsibility for the emergent, urgent, and restorative care of the injured patient, who specializes in performing operative and non-operative manual and instrumental techniques on a patient to investigate or treat an injury to help improve bodily function or appearance, or to repair ruptured areas. trauma surgeon role OOSTT:00000097 A role that, if realized, is realized by its bearer providing an assessment of processes carried out by another entity (person, organization, computer system) regarding their compliance with specifications and their quality. Mathias Brochhausen Role borne by an individual or organization to assess and ensure that a facility or person is compliant with policies, procedures, or guidelines. performance evaluator role OOSTT:00000098 A role that, if realized, is realized by its bearer undergoing an assessment of its actions carried out by a person or an organization regarding the compliance with specifications and the quality of those actions. Mathias Brochhausen The individual or facility being assessed by an individual, committee, or external organzation. performance evaluatee role OOSTT:00000099 A deontic role that, if realized, is realized by its bearer providing a document that lists the minimum qualifications of a person to become a member of the trauma service. Mathias Brochhausen Sarah Bost The power to establish minimum qualifications to be a member of the trauma service. authority to specify criteria for trauma service membership OOSTT:00000100 A socio-legal generically dependent continuant that is concretized in a role within an organizational context and which legally, normatively, or ethically permits some action. J. Neil Otte authority OOSTT:00000101 Authority prescribed by some enabling legislation J. Neil Otte Authority prescribed by enabling legislation, rules, or regulations statutory authority OOSTT:00000102 A deontic role that, if realized, is realized by its bearer actively participating in a document act that has a trauma service member role as its specified output. Mathias Brochhausen Sarah Bost The power to appoint members to the trauma service. authority to appoint members to the trauma service OOSTT:00000103 An organization healthcare role that is borne by a hospital and that, if realized, is realized by directly organizing and controlling prehospital providers. Mathias Brochhausen Stedman's Medical Dictionary for the Health Professions and Nursing. 7th Edition. 2012. emergency medical services base station role OOSTT:00000104 A document that is about a trauma registrar role and specifies the extent of work and the rights and obligations that are associated with that role. Mathias Brochhausen Sarah Bost The description of job requirements and expectations of the individual assigned to abstract and record patient data and run reports for the trauma registry. It is important to note that this is not the rights and obligations or the professional role itself. This is a descriptive information content entity, not a directive one or a conglomerate of socio=legal entities. trauma registrar job description OOSTT:00000105 A deontic role that, if realized, is realized by its bearer participating in a document act that revokes a trauma service member role. Mathias Brochhausen Sarah Bost The power to revoke membership on the trauma service. authority to remove members from the trauma service OOSTT:00000106 An obligee role that, if realized, is realized by its bearer participating in continuing trauma eduction for an amount of time specified in their program or country. Sarah Bost continuing trauma education obligor role The obligation to participate in continuing trauma eduction for an amount of time specified in the partcipant's program or country. continuing trauma education obsolete_continuing trauma education obligee role true OOSTT:00000107 A planned process that is scattered over multiple temporal regions that fulfills an obligation for continuing medical education in the area of trauma care. Mathias Brochhausen trauma education verifiable for continuing medical education requirement OOSTT:00000108 A role that is borne by a member of an emergency department that has been authorized by department leadership and that, if realized, is realized by its bearer representing the emergency department. Mathias Brochhausen emergency department representative role OOSTT:00000109 A plan specification that specifies which orthopedic surgeon to call, if the primary on-call orthopedic surgeon is not available due to already taking care of other trauma patients. Jonathan Bona Mathias Brochhausen The identification of the orthopaedic surgeon scheduled to respond to a trauma patient when the primary oncall orthopaedic surgeon is unavailable due to extenuating circimstances. orthopedic surgeon backup call schedule OOSTT:00000110 A governmental organization that has the authority to create, amend, fund, and repeal laws. J. Neil Otte legislature OOSTT:00000111 An organization that is a part of some government. J. Neil Otte government organization Derived from 18 U.S. Code § 2711. Accessed 12.4.2022 at https://www.law.cornell.edu/uscode/text/18/2711#4 governmental organization OOSTT:00000112 Government is the means by which policy within a community are enforced, as well as the mechanism for determining the policy of the community. J. Neil Otte https://en.wikipedia.org/w/index.php?title=Government&oldid=727121222 government (http://www.ontologyrepository.com/CommonCoreOntologies/Government) the community may be local, regional, state, or national (Comment provided by J. Ball, N. Sanddal, S. Bowman) - 2017-07-18 obsolete_government true OOSTT:00000114 An organization consisting of persons who bear committee member role where that organization is appointed by an organization or members of an organization to realize a role. J. Neil Otte A group of individuals appointed by an organization or organization leader to complete a specific task or to fulfill a specific set of responsibilities. Dec 10, 2016: The definition originally stated that the committee was realizing a function. After review of the BFO definition of function I decided to change it to "role". M. Brochhausen committee OOSTT:00000115 A committee whose function is to evaluate the system of care within a trauma center. J. Neil Otte Sarah Bost A committee whose function is to evaluate and recommend improvements to the quality of the system of care within a trauma center or trauma system. performance improvement committee OOSTT:00000116 A role that inheres in a homo sapiens that, if realized, is realized by preparing, keeping, and overseeing records made in a register. Jonathan Bona Neil J. Otte An individual who abstract(s) and record(s) data into an electronic registry . registrar role OOSTT:00000117 A role that, if realized, is realized in the organization context of a committee. Neil J Otte The duties and responsibilities assigned to the member(s) of a committee. committee member role OOSTT:00000118 A disposition realized in process profiles that have participants the biological qualities of patients and the practices and instruments of medical professionals. Neil J. Otte An organizational approach to patient care that reduces or mitigates the risk for untoward patient outcomes. patient safety OOSTT:00000119 An organization whose purpose is to serve the goals of a particular profession or whose members bear roles within a single profession. J. Neil Otte professional organization OOSTT:00000120 A medical residency in the medical speciality that focuses on the care for undifferentiated and unscheduled patients with illnesses and injuries requiring immediate medical attention. Mathias Brochhausen Sarah Bost https://en.wikipedia.org/w/index.php?title=Emergency_medicine&oldid=746479802 A formal process for new physicians who choose emergency medicine as a specialty to obtain education, training, and practice experience under the supervision of a board-certified emergency physician. emergency medicine residency program OOSTT:00000121 A medical residency in the medical specialty that focuses on using operative manual or instrumental techniques on the musculoskeletal system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen Sarah Bost A formal process for surgeons who choose orthopedic surgery as a specialty to obtain education, training, and practice experience under the supervision of a board-certified orthopedic surgeon. orthopedic surgery residency program OOSTT:00000122 A medical residency in the medical specialty that focuses on using operative manual and instrumental techniques on the nervous system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen Sarah Bost A formal process for new physicians who choose neurosurgery as a specialty to obtain education, training, and practice experience under the supervision of a board-certified neurosurgeon. neurosurgery residency program OOSTT:00000124 A continuous coverage policy to ensure availability of a general surgeon. Jonathan Bona Mathias Brochhausen A healthcare facility policy that specifies the requirement for general surgeon availability 24 hours a day, 7 days a week. continuous general surgery coverage policy OOSTT:00000125 A plan specification that specifies which surgeon to call, if the on-call trauma surgeons is not available due to already taking care of other trauma patients. Jonathan Bona Mathias Brochhausen The identification of the surgeon scheduled to respond to a trauma patient when the primary oncall surgeon is unavailable due to extenuating circumstances. trauma surgeon backup call schedule OOSTT:00000126 An organization with a specific responsibility that is a part of a larger organization with a specific responsibility. http://en.wikipedia.org/wiki/Department A formal subdivision of an organization with a specific responsibility. This class does not contain governmental departments. Governmental department is to be found here: http://purl.obolibrary.org/obo/OOSTT_00000274 MB, Jan 4, 2017 department OOSTT:00000127 A department that is part of a healthcare provider organization and that specialzes in the care for undifferentiated and unscheduled patients with illnesses and injuries requiring immediate medical attention. Mathias Brochhausen A formal subdivision of a healthcare facility that specializes in the care of unscheduled patients with urgent and emergent health conditions. emergency department OOSTT:00000128 A plan specification that specifies which neurosurgeon to call, if the primary on-call neurosurgeon is not available due to already taking care of other trauma patients. Jonathan Bona Mathias Brochhausen neurosurgeon backup call schedule OOSTT:00000129 A neurosurgeon backup call schedule that has been approved by the trauma medical director. Mathias Brochhausen TMD-approved neurosurgeon backup call schedule OOSTT:00000130 A planned process in which a person, an aggregate of persons or an organization reviews a plan specification and decides whether or not the plan specification is appropriate to achieve its objective and whether it is congruent with pre-existing plans and procedures. Mathias Brochhausen A formal review and approval process conducted by a committee or organization which is authorized to determine if a plan, policy, or procedure is appropriate to achieve organizational objectives. plan specification approval process OOSTT:00000131 A orthopedic surgeon backup call schedule that has been approved by the trauma medical director. Mathias Brochhausen TMD-approved orthopedic surgeon backup call schedule OOSTT:00000132 A role that inheres in a person, who is a member in a trauma program, and, if realized, is realized by acting us the contact point of the trauma program regarding nursing care in the emergency department. Mathias Brochhausen obsolete_emergency department nursing liaison of trauma program true OOSTT:00000133 A plan specification that specifies on which schedule and to which extent anesthesia services are provided within a healthcare provider organization. Mathias Brochhausen anesthesia services availability plan specification (OOSTT_00000375) A plan that specifies the schedule for ensuring adequate numbers of anesthesia care providers are readily available 24 hours a day 7 days a week within a trauma center. obsolete_anesthesia services availability plan specification true OOSTT:00000134 A planned process that realizes the concretization of an anesthesia services availability plan specification. Mathias Brochhausen Implementation of an anesthesia services availability plan that includes continuous monitoring to ensure that anesthesia services are readily available 24 hours a day 7 days a week and to identify variations in the plan that need corrective action in a performance improvement process. anesthesia services availability plan execution OOSTT:00000135 A continuous coverage policy to ensure availability of an orthopedic surgeon. Jonathan Bona Mathias Brochhausen Sarah Bost A healthcare facility policy that specifies the requirement for orthopedic surgeon availability 24 hours a day, 7 days a week. continuous orthopedic surgery coverage policy OOSTT:00000136 A continuous coverage policy to ensure availability of a neurosurgeon. Jonathan Bona Mathias Brochhausen A healthcare facility policy that specifies the requirement for neurosurgeon availability 24 hours a day, 7 days a week. continuous neurosurgery coverage policy OOSTT:00000137 A health care process that has as participant a patient who is not scheduled for medical treatment and requires immediate medical treatment John Judkins A healthcare process in which a patient needs and is provided urgent or emergent care. emergency health care process OOSTT:00000138 A continuous coverage policy that specifies procedures to ensure that anesthesiology services are available at a healthcare provider organization 24 hours, 7 days a week. Mathias Brochhausen Sarah Bost A healthcare facility policy that specifies the requirement for availability of anesthesiology services 24 hours a day, 7 days a week. continuous anesthesiology coverage policy OOSTT:00000139 A medical fellowship that provides education in providing surgical treatment to patients that experienced musculoskeletal trauma. Mathias Brochhausen A planned process that is part of medical training and is aimed at surgeons to provide advanced preparation in the diagnosis and treatment of musculosketel diseases and injury. orthopedic surgery fellowship program OOSTT:00000140 A planned process that is part of medical training and is aimed at physicians to provide training in one of the medical specialities. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Fellowship_(medicine)&oldid=748253626 medical fellowship program OOSTT:00000141 A role that inheres in an organization and, if realized, is realized by the bearer organizing the provision of operative manual and instrumental techniques on a patient, either to remodel body parts to change their appearance or to restore the appearance and sometimes the function of body parts affected by trauma, previous surgery, or congenital defect. John Judkins An association of plastic surgeons with the role of sharing information and establishing guidelines for the diagnosis, treatment, and surgical techniques to remodel body parts to change their appearance or to restore the appearance and sometimes the function of body parts affected by trauma, previous surgery, or congenital defect plastic surgery provider organization role OOSTT:00000142 A role that inheres in an organization and, if realized, is realized by the bearer organizing the provision of operative manual and instrumental techniques on a patient's hand to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. John Judkins An group or association of hand surgeons with the role of sharing information and establishing guidelines for the diagnosis, treatment, and surgical techniques on a patient's hand and upper extremities. hand surgery provider organization role OOSTT:00000143 A role that inheres in an organization and, if realized, is realized by the bearer organizing the provision of operative manual and instrumental techniques to join or repair blood vessels too small to view unaided by microscopy, in order to provide blood circulation to a body part that is being surgically attached or reconstructed John Judkins An organization that provides specialized operative manual and instrumental techniques to join or repair blood vessels too small to view unaided by microscopy, in order to provide blood circulation to a body part that is being surgically attached or reconstructed This is not a representation of a professional organization of microvascular sugery providers, but an organization that provides microvascular surgery. microvascular surgery provider organization role OOSTT:00000144 A role that inheres in an organization and, if realized, is realized by the bearer organizing the provision of operative manual and instrumental techniques on a patient's spine to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. John Judkins A group or association of neurosurgical or orthopedic spine surgeons with the role of sharing information and establishing guidelines for the diagnosis, treatment, and surgical techniques on a patient's spine and spinal cord. spinal surgery provider organization role OOSTT:00000146 An aggregate of organizations whose members are all bearer of a level 1 trauma center role. Mathias Brochhausen A group of healthcare facilities that are all ACS verified or state designated as level 1 trauma centers. aggregate of level 1 trauma centers OOSTT:00000147 A role that inheres in a human being and, if realized, is realized by representing an emergency department in the quality improvement program of organization providing pre-hospital care and services. John Judkins Mathias Brochhausen The health professional who represents the emergency department at a prehospital provider agency QI program. representative from emergency department to pre-hospital provider QI program OOSTT:00000148 A health care provider role that inheres in a human being and, if realized, is realized by a process of providing health care to a patient before and during transport of the patient to the hospital or from the initial hospital to the another healthcare provider organization. John Judkins A healthcare provider who cares for patients with urgent conditions before and during transport to the initial hospital or between the initial hospital and referral facility. based on the comments from our expert team, this class is modeled to include air medical provides (not to include pilots) and not to include dispatchers. prehospital care provider role OOSTT:00000149 A coverage policy that specifies that a emergency physician who is certified by an official agency or correspondent authority is present in the emergency department 24 hours, 7 days a week. Mathias Brochhausen A healthcare facility policy that specifies the requirement for an emergency physician who is certified by an official agency or correspondent authority availability 24 hours a day, 7 days a week. continuous board certified emergency physician staffing policy OOSTT:00000150 An information content entity that documents the participants of continuing trauma care education. Mathias Brochhausen The record verifying the completion of continuing trauma education requirements by trauma center physicians, nurses, and advance practice providers. record of participation in continuing trauma care education OOSTT:00000151 A role that is borne by a human being that is part of an emergency medical service agency, and that is realized by that person serving as the point of contact for a trauma program to the emergency medical service provider. Mathias Brochhausen EMS liaison to trauma program A formally designated EMS provider that serves as a conduit for two-way information sharing between the EMS agency and the trauma program. emergency medical services liaison to trauma program OOSTT:00000152 A role that is borne by an emergency physician who is a member of the emergency department and that is realized by its bearer serving as the point of contact for all quality improvement-related communication between to the emergency department and the trauma medical director. Mathias Brochhausen Sarah Bost An emergency physician who serves as the formal point of contact for the trauma medical director for all quality improvement-related issues regarding trauma care within the ED. obsolete_emergency department quality improvement liaison to TMD role true OOSTT:00000153 A physician role that, if it is realized, is realized by providing treatment for undifferentiated and unscheduled patients with illnesses and injuries requiring immediate medical attention. Mathias Brochhausen A physician who provides treatment to the ill and injured needing urgent and emergent care. emergency physician role OOSTT:00000154 An obligee role that if realized is realized by its bearer evaluating the nursing care provided to trauma patients. Mathias Brochhausen trauma nursing evaluator obligor role The individual with authority and responsibility for evaluating the nursing care provided to trauma patients. trauma nursing evaluator obsolete_trauma nursing evaluator obligee role true OOSTT:00000155 An obligee role that, if realized, is realized by its bearer organizing and overseeing the trauma quality improvement and patient safety program. Mathias Brochhausen Sarah Bost tqip coordinator obligor role A health professional role that results in the oversight and management of the trauma center's quality improvement and patient safety program as specified by the American College of Surgeons. tqip coordinator obsolete_tqip coordinator obligee role true OOSTT:00000156 A collection of humans that only has as members bearers of an anesthesiologist role. Mathias Brochhausen Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of anesthesiologists OOSTT:00000157 An objective specification that specifies the intended outcome of educating members of prehospital providers and conducting exercises that apply the learned material. Mathias Brochhausen prehospital training objective The specified outcome of the prehospital training process that includes the practical application of learned material to assess and manage patient care. prehospital provider training objective specification OOSTT:00000158 A plan specification that specifies the content and intended outcome of relying information about best practice in prehospital care to members of a prehospital care provider. Mathias Brochhausen Sarah Bost A description of the prehospital training process that includes content, methodology, and evaluation with emphasis on methods for assessing and managing the patient with an urgent or emergent illness or injury before and during transport to the hospital. prehospital provider training plan specification OOSTT:00000159 A plan specification that specifies standards and procedures for care provided to emergency patients before they reach the emergency department. Mathias Brochhausen A practice guideline that specifies the standards and procedures for the assessment and management of care provided to emergency patients before reaching the initial hospital or between the initial hospital and referral facility. prehospital protocol OOSTT:00000160 A physician role that, if it is realized, is realized by diagnosing and managing life-threatening conditions requiring sophisticated organ support and invasive monitoring. Jonathan Bona Mathias Brochhausen A physician with responsibility for diagnosing, managing, and treating life-threatening conditions in collaboration with other health professionals and the patient's family. critical care physician role OOSTT:00000161 An aggregate of organizations whose members are all bearer of a level 2 trauma center role. Mathias Brochhausen A group of healthcare facilities that are all ACS verified or state designated as level 2 trauma centers. aggregate of level 2 trauma centers OOSTT:00000162 An information content entity that is about a person and affirms that they have attended at least 50% of trauma quality improvement meetings. Mathias Brochhausen The record verifying that each specified member participates in the trauma quality improvement committee and attends the minimum number of meetings as required by the designating agency. record of participation in majority of trauma quality improvement meetings OOSTT:00000163 A role that inheres in a nurse and, if realized, is realized by its bearer to act as contact for all matter relating to nursing in the emergency room. Mathias Brochhausen An emergency nurse manager who serves as the point of contact for all matters related to nursing in the ED. emergency department nursing liaison OOSTT:00000164 A planned process that has members of an emergency medical service agency as participants and that aims to improve patient outcomes of prehospital care. Mathias Brochhausen A process that is designed to improve the quality of prehospital care that may involve individual EMS providers, an entire EMS agency, or a system-wide effort. emergency medical services quality improvement process OOSTT:00000165 A collection of humans that only has bearers of an emergency physician role as members. Mathias Brochhausen Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of emergency physicians OOSTT:00000166 An information content entity that is the specified outcome of an advanced advanced trauma life support. Jonathan Bona Mathias Brochhausen A record confirming the individuals who successfully complete an ATLS course. documentation of successful completion of ATLS course information successful completion of ATLS course information content entity OOSTT:00000167 A planned process aims to provide training for medical providers in the management of acute trauma cases, developed by the American College of Surgeons. Mathias Brochhausen Sarah Bost An educational program developed and overseen by the American College of Surgeons that provides health care professionals with knowldege and skills for the management of acute trauma patients. advanced trauma life support course OOSTT:00000168 A collection of emergency physicians that has successfully completed the advanced life support course. Mathias Brochhausen Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of emergency physicians with ATLS training OOSTT:00000169 A successful completion of ATLS course information that is not older than specified time before ATLS knowledge is no longer deemed current. Mathias Brochhausen A successful completion of the ATLS course that is not older than specified time before ATLS knowledge is no longer deemed current. documentation of current successful ATLS completion current successful ATLS completion information content entity OOSTT:00000170 A collection of emergency physicians with ATLS training for which the training has not been more than the time specified before their knowledge is no longer deemed current. Mathias Brochhausen Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of emergency physicians current in ATLS OOSTT:00000171 An emergency physician role that is the specified output of a board certification process and that, if realized, is realized by providing treatment for undifferentiated and unscheduled patients with illnesses and injuries requiring immediate medical attention. Mathias Brochhausen A physician who has completed an emergency medicine residency program and achieved board certification in the country of intended practice. board certified emergency physician role OOSTT:00000172 Board certification is the process by which a healthcare provider (physician, nurse, or other) in the United States demonstrates a mastery of basic knowledge and skills in a speciality of their occupation through written, practical, or simulator-based testing. Mathias Brochhausen Board certification is the process by which a healthcare provider (physician, nurse, or other) in the United States demonstrates a mastery of basic knowledge and skills in a speciality of their occupation through written, practical, or simulator-based testing. Health professionals from other countries go through a similar process as consistent with their country's requirements. medical board certification OOSTT:00000173 An emergency medicine physician role that is the outcome of fullfilling all obligations to be allowed to take a board certification exam in emergency medicine. Mathias Brochhausen An emergency physician who has completed all training requirements and is eligible to take the board certification examination in the country of intended practice. board eligible emergency physician role OOSTT:00000174 A collection of emergency physicians that only has members, which are board certified in emergency medicine or or have met all requirements for that subspecialty in their country of practice. All emergency physicians credentialed to practice in a healthcare facility who are either board certified or have met all requirements for that subspecialty in their country of practice. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of board certified emergency physicians OOSTT:00000175 A collection of emergency physicians that fulfil all criteria to sit a board certification exam, but that either have not taken one or have failed. Mathias Brochhausen All emergency physicians who have completed all training requirements and are eligible to sit for the emergency physician or pediatric emergency physician board certification exam in the country of intended practice. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of board eligible emergency physicians OOSTT:00000176 A collection of emergency physicians that all successfully took the board certification exam in emergency medicine and that have had ATLS training. Mathias Brochhausen All board certified emergency physicians who have successfully completed the ATLS course. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of board certified emergency physicians current in ATLS OOSTT:00000177 A plan specification that specifies the job requirements for the trauma surgeon positions in an institution and how those trauma surgeons will be used within the organization. Jonathan Bona Mathias Brochhausen institution-specific trauma surgeon profile Position description that is custom tailored to a particular medical facility and the role expected for trauma surgeon at that location. institute-specific trauma surgeon job description OOSTT:00000178 An institution-specific trauma surgeon profile that has been approved by the trauma medical director. Mathias Brochhausen TMD approved institution-specific trauma surgeon profile Institution-specific trauma surgeon qualification criteria approved by the trauma medical director. TMD-approved institution-specific trauma surgeon job description OOSTT:00000179 A plan specification that specifies the job requirements for the emergency medicine physician positions in an institution and how those emergency medicine physicians will be used within the organization. Jonathan Bona Mathias Brochhausen institution-specific emergency medicine physician job description An institution-specific job description of an emergency medicine physician. institution-specific emergency medicine physician job description institution-specific emergency medicine physician role description OOSTT:00000180 The qualification criteria for a physician to become a member of the emergency department that have been approved by the trauma medical director of the institution the department is a part of. Mathias Brochhausen TMD approved institution-specific emergency medicine physician profile OOSTT:00000181 An trauma surgeon role that is the outcome of fullfilling all obligations to be allowed to take a board certification exam in surgical critical care. Mathias Brochhausen Sarah Bost A surgeon who has completed all training requirements and is eligible to take the surgical critical care board certification examination in the country of intended practice. obsolete_board eligible trauma surgeon role true OOSTT:00000182 An emergency physician role that is the specified output of a board certification process and that, if realized, is realized by its bearer using operative manual or instrumental techniques on a patient to investigate or treat an injury or other pathological situation that are caused by an injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A physician who is board certified in surgery and credentialed by the trauma program within the hospital to provide emergency surgical care of trauma patients and to oversee the patient care process. obsolete_board certified trauma surgeon role true OOSTT:00000183 An information content entity that is about the bearer of a healthcare provider role and that affirms that they fulfilled all requirements to receive state licensure in their healthcare provider role for the state they practice in. The assurance that a healthcare provider is licensed for their health care role. documentation of compliance with state licensure requirement compliance with state licensure requirement information content entity OOSTT:00000184 A collection of humans that only consists of surgeons that are mentioned in a trauma on call plan specification and that are subject to a performance review by the trauma medical director. Mathias Brochhausen Sarah Bost Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of trauma service surgeons reviewed by the TMD OOSTT:00000185 An obligee role that is realized by its bearer organizing and managing a trauma quality improvement and patient safety program. Mathias Brochhausen Sarah Bost coordination of trauma quality improvement and patient safety obligor role The obligation to organize and managing the formal process to ensure performance improvement and patient safety in a facility. coordination of trauma quality improvement and patient safety obsolete_coordination of trauma quality improvement and patient safety obligee role true OOSTT:00000186 A plan specification that specifies that content, methodology, and testing of educational programs for nurses teaching standardized diagnostic and therapeutic procedures with trauma patients in a hospital setting. Mathias Brochhausen ATNC course plan specification https://de.wikipedia.org/w/index.php?title=Advanced_Trauma_Care_for_Nurse&oldid=148554154 A description of the advanced trauma care for nurses education program that includes content, methodology, and testing processes with emphasis on standardized diagnostic and therapeutic procedures to care for trauma patients in the hospital setting. advanced trauma care for nurses course plan specification OOSTT:00000187 An information content entity that is a specific output of a person participating in an advanced trauma care for nurses program and that certifies successful completion of the program. Mathias Brochhausen ATNC certificate Recognition awarded after successfully completing the advanced trauma care for nurses education program. advanced trauma care for nurses certificate OOSTT:00000188 A plan specification that specifies the content, methodology, evaluation of a course aimed at nurses and providing cognitive knowledge and psychomotoric skills that help optimizing trauma patient care in a hospital setting. Mathias Brochhausen A description of the Trauma Nurse Core Curriculum course that includes content, methodology, and evaluation with emphasis on providing nurses with cognitive knowledge and psychomotor skills that focus on assessing and managing the patient with serious or life-threatening injuries. trauma nursing core course plan specification OOSTT:00000189 An information content entity that is a specified output of a person participating in an trauma nursing core course and that certifies successful completion of that course. Documentation that a nurse has successfully completed the Trauma Nurse Core Curriculum program. trauma nursing core course certificate OOSTT:00000190 A deontic document act that creates a mutally dependent employee and employer role. Mathias Brochhausen A contract specifying the relationship between an employee and employer that outlines specific role responsibilities and expectations. JPB (20 March 2017): should output employee role and employer role employment contract document act OOSTT:00000191 An employee role that is the specified output of an employment contract document act and that, if realized, is realized by its bearer providing services for the amount of type regarded full time under the specific labor administration. Mathias Brochhausen An employee who provides services full time as specified in the employment agreement. full time employee role OOSTT:00000192 A plan specification that specifies the content, methodology, and evaluation of a training course teaching the Abbreviated Injury Scale (AIS), informs about coding rules and conventions, and discusses methods for assessing the multiple injury patient. Mathias Brochhausen AAAM course plan specification A description of the AIS training process that includes content, methodology, and evaluation with emphasis on coding rules and conventions, and methods for assessing the patient with multiple injuries. abbreviated injury scale training course plan specification OOSTT:00000193 A planned process that realizes the concretization of an abbreviated injury scale training course plan specification. Mathias Brochhausen AAAM course A training process with the primary objective of teaching AIS scoring. abbreviated injury scale training course OOSTT:00000194 A collection of general surgeons that has successfully completed the advanced life support course. Mathias Brochhausen All surgeons serving who have successfully completed the Advanced Trauma Life Support program at some point in time. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of general surgeons with ATLS training OOSTT:00000195 A physician role borne by a human being and that, if realized, is being realized by its bearer using operative manual and instrumental techniques on a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas without the bearer of the role specializing into any particular field of surgery. Mathias Brochhausen A surgeon without specialization who performs operative manual and instrumental techniques on a patient to investigate or treat a disease or injury, to help improve bodily function or appearance, or to repair unwanted ruptured areas . general surgeon role OOSTT:00000196 A collection of general surgeons with ATLS training for which the training has not been more than the time specified before their knowledge is no longer deemed current. Mathias Brochhausen All surgeons serving on the trauma panel who have successfully completed the Advanced Trauma Life Support program at some point in time. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of general surgeons current in ATLS OOSTT:00000197 A deontic role that is the specified outcome of a document act between the chair of a surgery department and the bearer of a surgeon role that, of realized, is realized by its bearer admitting, evaluating, diagnosing, consulting, and providing pre-, intra and post-operative care, and performing surgical procedures, to patients of all ages, to correct or treat various conditions, diseases, disorders, and injuries of the alimentary tract, abdomen and its contents, extremities, breast, skin and soft tissue, head and neck, and endocrine systems. Mathias Brochhausen https://www.umc.edu/uploadedFiles/UMCedu/Content/Administration/Business_Services/Medical_Staff_Services/New_Faculty/SUR%20-%20General%20Surgery%20Clinical%20Privileges_rev07032013.pdf A general surgeon who is credentialed by a healthcare facility to admit, evaluate, diagnose, consult, and provide pre-, intra and post-operative care, and perform surgical procedures, to patients of all ages, to correct or treat various conditions, diseases, disorders, and injuries of the various body systems. general surgery privileges role OOSTT:00000198 A collection of humans that consists only of bearers of a trauma surgeon role that are also bearing a general surgery privileges role. Mathias Brochhausen Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of trauma surgeons with general surgery privileges OOSTT:00000199 A collection of humans that consists only of bearers of a trauma surgeon role that are mentioned in a trauma on call plan specification and that particpates in trauma education verifiable for 18 hours over 3 years. Mathias Brochhausen Sarah Bost Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of trauma surgeons on trauma service fulfilling CME requirement OOSTT:00000200 A plan specification that specifies the content, methodology, and evaluation of a course that aims to teach students about a subject through the experience of solving an open-ended problem found in trigger material. Mathias Brochhausen practice-based learning course plan https://en.wikipedia.org/w/index.php?title=Problem-based_learning&oldid=751054692 A description of the education offering that includes content, methodology, evaluation, and definition of competencies with emphasis on training on open-ended problems. practice-based learning course plan practice-based learning course plan specification OOSTT:00000201 A collection of humans that consists only of bearers of a trauma surgeon role that are mentioned in a trauma on call plan specification and that particpates in practice based training course organized by a trauma program. Mathias Brochhausen Sarah Bost All trauma surgeons participating in the trauma service who have completed a trauma program sponsored simulation-based training program. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of trauma surgeons on trauma service with practice-based learning course OOSTT:00000202 A collection of trauma surgeons that fulfil all criteria to sit a board certification exam, but that either have not taken one or have failed. Mathias Brochhausen All surgeons who have completed all training requirements and are eligible to take the acute care and trauma surgery board certification examination in the country of intended practice. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of board eligible trauma surgeons OOSTT:00000203 A collection of trauma surgeons that only has members which are board certified in trauma surgery. Mathias Brochhausen All board certified trauma surgeons. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of board certified trauma surgeons OOSTT:00000204 An information content entity that is a specific output of a person participating in an internal trauma program course using a practice based learning approach and that certifies successful completion of the course. Mathias Brochhausen Recognition awarded after successful completion of a trauma practice-based learning course approved by the trauma program. trauma program internal practice-based learning course certificate OOSTT:00000205 A practice-based learning course plan specification that aims to improve the quality of patient outcomes in trauma medicine. Mathias Brochhausen A description of the education offering that includes content, methodology, and evaluation with emphasis on practice-based learning techniques for treatment of injured patients. practice-based learning trauma care course plan specification OOSTT:00000207 A collection of humans that consists exclusively of trauma surgeons that are listed on the trauma on call plan specification. Mathias Brochhausen All trauma surgeons participating on the trauma service. This class already follows the strategy of not fully defining collections (using universal restrictions) due to the reasoning load it creates. We only represent which properties the affirmed members of this class have using a necessary existential restriction collection of trauma surgeons on a trauma service OOSTT:00000208 An obligee role that inheres in a human being mentioned in an on call plan specification and that, if realized, is realized by its bearer participating a planned process realizing the concretization of the plan specification and being on call exclusively for the organization at specified times that is the contractual partner in the document act that created this role. Mathias Brochhausen Sarah Bost on call exclusivity obligor role A healthcare professional who has a primary obligation to a single facility while on call, however, in certain subspecialty instances, the individual may be on call at more than one facility, in which case a back up call schedule is required. on call exclusivity obsolete_on call exclusivity obligee role true OOSTT:00000209 A collection of trauma surgeons who are members of the trauma service of an organization and are exclusively on call for that organization. Mathias Brochhausen Sarah Bost All trauma surgeons who are members of the trauma service and exclusively serve one trauma center during a specific time period. collection of trauma surgeons with on call exclusivity OOSTT:00000210 A plan specification that specifies the content, methodology, evaluation of a course to relay information and exercise procedures relevant to optimize critical care. Mathias Brochhausen A description of the critical care certificate training process that includes content, methodology, and evaluation with emphasis on methods for assessing and treating the patient with critical or life/limb-threatening injuries and illnesses. critical care certificate course plan specfication OOSTT:00000211 A planned process that is the realization of the concretization of a critical care certificate course plan specification. Mathias Brochhausen A training process with the primary objective of teaching care of patients who are critically ill or injured. critical care certificate course OOSTT:00000212 An information content entity that is the specified output of a critical care certificate course. Mathias Brochhausen Sarah Bost Recognition awarded after successful completion of education and training in any aspect of critical care meeting standards established under the authority of a governing board or agency. critical care certificate OOSTT:00000213 A collection of trauma surgeons that are part of the on call list of an organization and are certified in critical care. Mathias Brochhausen collection of trauma surgeons certified for critical care OOSTT:00000214 A medical fellowship that provides education in using operative manual or instrumental techniques on a patient to investigate or treat an injury or other pathological situation that are caused by an injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen Sarah Bost A credentialed program of medical training for general surgeons to provide advanced preparation and certification in trauma surgery and management of injured patients. Some programs also include critical care. trauma surgery fellowship program OOSTT:00000215 An information content entity that is the specified output of a person successfully fulfilling the evaluation criteria at the end of a a trauma-focused post-residency training that lasts a minimum of one year and provides additional knowledge and experience in the management of injured patients. Jonathan Bona Mathias Brochhausen Sarah Bost A record confirming that a physician successfully fulfilled the evaluation criteria at the end of a trauma-focused post-residency training that lasts a minimum of one year and provides additional knowledge and experience in the management of injured patients. documentation of successful completion of trauma surgery fellowship successful completion of trauma surgery fellowship information content entity OOSTT:00000216 A collection of trauma surgeons that are part of the on call list of an organization and for whom exists information about successfully finishing a trauma surgery fellowship program. Mathias Brochhausen obsolete_collection of fellowship-trained trauma surgeons on a trauma panel true OOSTT:00000217 A collection of humans that consists only of bearers of a trauma surgeon role an that are mentioned in a trauma on call plan specification. Mathias Brochhausen Sarah Bost collection of orthopedic surgeons on trauma service OOSTT:00000218 A collection of humans that consists only of bearers of a orthopedic surgeon role an that are mentioned in the trauma panel and that particpates in trauma education verifiable for 18 hours over 3 years. Mathias Brochhausen Sarah Bost All orthopedic surgeons participating in the trauma service who are current in fulfilling requirements for trauma-related continuing medical education. collection of orthopedic surgeons on trauma service fulfilling CME requirement OOSTT:00000219 An orthopedic surgeon role that is the outcome of fullfilling all obligations to be allowed to take a board certification exam in orthopedic surgery. Mathias Brochhausen An orthopeadic surgeon who has completed all requisite training requirements and is eligible to take the board certification examination in the country of intended practice. board eligible orthopedic surgeon role OOSTT:00000220 An orthopedic surgeon role that is the specified output of a board certification process and that, if realized, is realized by its bearer using operative manual or instrumental techniques on the musculoskeletal system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A physician who has completed an orthopedic surgery residency program and achieved board certification. board certified orthopedic surgeon role OOSTT:00000221 A collection of orthopedic surgeons mentioned on the trauma on call plan specification that fulfil all criteria to sit a board certification exam, but that either have not taken one or have failed. Mathias Brochhausen Sarah Bost All orthopedic surgeons who have completed all training requirements, are eligible to sit for the orthopedic surgery board certification exam, practicing in a healthcare facility, and participating in the trauma service. collection of board eligible orthopedic surgeons on trauma service OOSTT:00000222 A collection of orthopedic surgeons that are mentioned in the trauma on call plan specification and that are board certified in orthopedic surgery. Mathias Brochhausen Sarah Bost collection of board certified orthopedic surgeons on trauma service OOSTT:00000223 A deontic role that is the specified outcome of a document act between the head of a orthopedic surgery and the bearer of a orthopedic surgeon role that, of realized, is realized by its bearer admitting, evaluating, diagnosing, consulting, and providing pre-, intra and post-operative care, and performing orthopedic surgical procedures, to patients of all ages, to correct or treat various conditions, diseases, disorders, and injuries of the musculoskeletal system. Mathias Brochhausen An orthopaedic surgeon who is credentialed by a healthcare facility to provide services that include assessment, diagnosis, management, and treatment of various conditions and injuries of the musculosekeletal system. general orthopedic surgery privileges role OOSTT:00000224 A collection of humans that consists only of bearers of a orthopedic surgeon role that are mentioned in the trauma on call plan specification and that are also bearing a general orthopedic surgery privileges role. Mathias Brochhausen obsolete_collection of orthopedic surgeons on trauma panel with general orthopedic surgery privileges true OOSTT:00000225 A plan specification that specifies under which circumstances and with which neurological injuries patients admitted to one hospital will be triaged to another healthcare provider organization when no neurosurgical coverage is available at the first hospital. Jonathan Bona Mathias Brochhausen A plan specifying the healthcare facility destination of a patient with neurologic injuries when neurosurgical coverage or resources (e.g, neuro ICU) are not available at the first facility. hospital neurological injury triage plan specification OOSTT:00000226 A plan specification that specifies under which circumstances and with which neurological injuries patients will be triaged from the emergency department to another healthcare provider organization when limited or no neurosurgical coverage is available and that is the specified output of an approval process through the trauma medical director. Mathias Brochhausen Sarah Bost A hospital's neurologic injury triage plan identifying the destination of patients with specified injuries, or based on injury severity, approved by the trauma medical director. TMD-approved hospital neurological injury triage plan specification OOSTT:00000227 A collection of humans that consists only of bearers of a neurosurgeon role that are mentioned in a trauma on call plan specification. Mathias Brochhausen Sarah Bost collection of neurosurgeons on trauma service OOSTT:00000228 A collection of orthopedic surgeons who are members of the trauma service of an organization and are exclusively on call for that organization. Mathias Brochhausen Sarah Bost All orthopedic surgeons who are members of the trauma service and exclusively serve one trauma center during a specific time period. collection of orthopedic surgeons with on call exclusivity OOSTT:00000229 A collection of neurosurgeons that are members of the trauma service of an organization and are exclusively on call for that organization. Mathias Brochhausen Sarah Bost All neurosurgeons who are members of the trauma service and exclusively serve one trauma center during a specific time period. collection of neurosurgeons with on call exclusivity OOSTT:00000230 A collection of humans that consists only of bearers of a neurosurgeon role that are mentioned in a trauma on call plan specification and that particpates in trauma education verifiable for 18 hours over 3 years. Mathias Brochhausen Sarah Bost All neurosurgeons participating in the trauma service who are current in fulfilling requirements for trauma-related continuing medical education. collection of neurosurgeons on trauma service fulfilling CME requirement OOSTT:00000231 A collection of humans that consists only of bearers of an anesthesiologist role that are mentioned in a trauma on call plan specification. Mathias Brochhausen collection of anesthesiologists on trauma service OOSTT:00000232 A medical residency in the medical speciality that focuses on the administration of medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or on making decisions regarding the administration of such medication. Mathias Brochhausen Sarah Bost A formal process for new physicians who choose anesthesiology as a specialty to obtain education, training, and practice experience under the supervision of a board-certified anesthesiologist. anesthesiology residency program OOSTT:00000233 An information content entity that is the specified output of a person successfully fulfilling the evaluation criteria at the end of an anesthesiology residency program. Jonathan Bona Mathias Brochhausen Sarah Bost Information confirming that a physician successfully fulfilled the evaluation criteria at the end of an anesthesiology residency program. documentation of successful completion of anesthesiology residency successful completion of anesthesiology residency information content entity OOSTT:00000234 A collection of humans that consists only of bearers of an anesthesiologist role and that have successfully completed an anesthesiology residency and that are mentioned in a trauma on call plan specification. Mathias Brochhausen Sarah Bost collection of anesthesiologists with anesthesiology residency on trauma service OOSTT:00000235 A nurse role that is the specified output of post-graduate education in nursing and that is realized by using extended and expanded skills, experience and knowledge in assessment, planning, implementation, diagnosis and evaluation of the care required. Mathias Brochhausen Sarah Bost A nurse with, at minimum, a Master's degree in nursing who uses expanded knowledge and skills in assessment, diagnosis, planning, implementation, and evaluation of patient care. advanced practice registered nurse role OOSTT:00000236 An advanced practice registered nurse role that is the specified outcome of an accredition process with the Council of Accreditation in the United States of American and depends on graduate level education and board certification in anesthesiology. Mathias Brochhausen CRNA role A nurse with advanced education and training in anesthesiology who has successfully completed a national certification examination process, and is credentialed to practice by a healthcare facility. certified registered nurse anesthetist role OOSTT:00000237 A collection of humans that only has bearers of an certified registered nurse anesthetist role as members. Mathias Brochhausen All nurses with advanced education in anesthesiology who have successfully completed a national certification examination process, and is credentialed to practice by a healthcare facility. collection of certified registered nurse anesthetist OOSTT:00000238 A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on the genitourinary system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen Sarah Bost urologist A surgeon with special training in genitourinary surgery operative techniques who investigates and treats patients with diseases and injuries to the kidneys and genitorurinary tract. genitourinary surgeon role OOSTT:00000239 A physician role that, if realized, is realized by the study and identification of the cause and pathway of diseases through examination of the whole body, tissue, cells, and body fluids. Mathias Brochhausen A physician who specializes in determining the cause and pathway of diseases and death through examination of the whole body, tissue, cells, and body fluids. pathologist role OOSTT:00000240 A physician role that, if realized, is realized by providing diagnosis and treatment of diseases of the heart and the blood vessels. Mathias Brochhausen A physician with speciialized training in cardiology who diagnoses and treats patients with dysrhythmias and diseases of the heart and blood vessels. cardiologist role OOSTT:00000241 A physician role that, if realized, is realized by providing diagnosis and treatment of diseases of the kidney, including renal replacement therapy (dialysis and renal transplants). Mathias Brochhausen A physician that specializes in the diagnosis and treatment of diseases of and injuries to the kidney, including renal replacement therapy (dialysis and renal transplants). nephrologist role OOSTT:00000242 A physician role that, if realized, is realized by providing diagnosis and treatment of diseases of the lung and the respiratory tract. Mathias Brochhausen A physician who provides diagnosis and treatment of diseases of the lungs and the respiratory tract in association with the healthcare team managing an injured patient. pulmonologist role OOSTT:00000243 A physician role that, if realized, is realized by providing minimally invasive image-guided diagnosis and treatment of diseases in every organ system. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Interventional_radiology&oldid=752183885 A physician radiologist credentialed in providing minimally invasive image-guided diagnosis and treatment of diseases and vascular injuries. interventional radiologist role OOSTT:00000244 A physician role that, if realized, is realized by providing diagnosis and medical treatment for infants, children, and adolescents. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Pediatrics&oldid=752810576 A physician who specializes in providing diagnosis and medical treatment for infants, children, and adolescents. pediatrician role OOSTT:00000245 A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on the heart and the great blood vessels of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A surgeon with special training in cardiac surgery operative techniques who investigates and treats patients with diseases and injuries of the heart and great vessels. cardiac surgeon role OOSTT:00000246 A physician role that, if realized, is realized by providing diagnosis and treatment, including surgical procedures, on the eyeball. Mathias Brochhausen A physician who specializes in providing diagnosis and treatment, including surgical procedures on the eye and appendages (muscles, lids, sockets) ophthalmologist role OOSTT:00000247 A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques for the restoration, reconstruction, or alteration of the human body. Mathias Brochhausen A surgeon who specializes in performing operative manual and instrumental techniques to remodel body parts to change their appearance or to restore the appearance and sometimes the function of body parts affected by trauma, previous surgery, or congenital defect. plastic surgeon role OOSTT:00000248 A physician role that, if it is realized, is realized by providing treatment for diseases of and injuries to the female reproductive system. Jonathan Bona Mathias Brochhausen A physician or surgeon with specialty in obstretrics and gynecology with responsibility for managing diseases and injuries to the female reproductive tract. gynecologist role OOSTT:00000249 A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on the hard and soft tissue of the oral and maxillofacial anatomy of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A surgeon who specializes in performing operative manual and instrumental techniques on the hard and soft tissue of the oral and maxillofacial anatomy of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair ruptured areas. oral and maxillofacial surgeon role OOSTT:00000250 A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on the hand and upper extremeties of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Mathias Brochhausen A surgeon who performs specialized operative manual and instrumental techniques on a patient to investigate or treat a disease or musculoskeletal injuries of the hand and wrist. hand surgeon role OOSTT:00000251 An organizational social role that is the output of an accreditation process and that, if realized, is realized by its bearer providing education and evaluation for students seeking degrees allowing them to work as medical professionals. Mathias Brochhausen An organizational social role that is the output of an accreditation process and that, if realized, is realized by its bearer providing education and evaluation for students seeking degrees allowing them to work as allopathic or osteopathic physicians. medical school role OOSTT:00000252 A hospital role that, if realized, is realized by its bearer provides clinical education and training for future and current health professionals. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Teaching_hospital&oldid=751897752 A hospital with an academic affiliation that provides clinical education and training for future and current health professionals. teaching hospital role OOSTT:00000253 An objective specification to bring about the existence of an organization of organizations and healthcare providers to facilitate and coordinate a multidisciplinary response to severe injury. Mathias Brochhausen trauma system creation objective An information item specifying the aim to bring together participating organizations to coordinate a multidisciplinary response for patients with severe injury. trauma system creation objective specification OOSTT:00000254 A plan specification that has a trauma system creation objective as a part and that specifies the necessary processes to achieve that objective. Mathias Brochhausen Sarah Bost The plan describing the process for creation of a trauma system. trauma system creation plan specification OOSTT:00000255 A planned process that realizes the concretization of a trauma system creation plan specification. Mathias Brochhausen The authority and process used to create a trauma system for an area or region. trauma system creation OOSTT:00000256 An organization that brings together human beings or organizations from different backgrounds with shared idealistic or financial interest in some process and its outcomes to counsel and evaluate that process and its outcomes. Mathias Brochhausen Sarah Bost An assembly of individuals and organization representatives with different perspectives and responsibilities who collaborate to improve the trauma care process and its outcomes. multidisciplinary stakeholder group OOSTT:00000257 A planned process that realizes the concretization of a trauma system plan specification. Mathias Brochhausen trauma system operation OOSTT:00000258 An organization that has hospitals as members and that aims to represent the interests of hospitals. Mathias Brochhausen hospital association OOSTT:00000259 A professional organization consisting of physicians and that aims to represent the interests of physicians. Mathias Brochhausen medical association OOSTT:00000260 A professional organization consisting of nurses and that aims to represent the interests of nurses. Mathias Brochhausen A professional organization of nurses that focuses its mission on the improvement of nursing care at the national, state, regional, or local level. nurses association OOSTT:00000261 An organization that has emergency medical service agencies as members and that aims to represent the interests of emergency medical service agencies. Mathias Brochhausen Sarah Bost An association of EMS agencies that any agency may join voluntarily to share information or collaborate on issues of local, state, regional, or national importance. emergency medical services agency association OOSTT:00000263 An organization that EMS agencies as members and that aims to represent the interests of these agencies. Mathias Brochhausen An association of EMS agencies that any agency may join voluntarily to share information or collaborate on issues of state or national importance. obsolete_EMS agency organization true OOSTT:00000264 A healthcare provider role that, if realized, is realized by its bearer providing out-of-hospital acute care and transport to definitive care, to patients with illnesses and injuries which the patient believes constitute a medical emergency. Mathias Brochhausen https://www.ems.gov/whatisems.html A healthcare provider who treats illnesses and injuries that require an urgent medical response, providing out-of-hospital treatment and transport to definitive care. emergency medical service provider role OOSTT:00000265 A professional organization consisting of emergency medical service providers and that aims to represent the interests of emergency medical service providers. Mathias Brochhausen Sarah Bost An association of EMS providers that any provider may join voluntarily to share information or to collaborate on or advocate for issues of local, state, or national importance. emergency medical services provider association OOSTT:00000266 A plan specification that specifies the times of meeting for which the multidisciplinary stakeholder group will convene. Mathias Brochhausen multidisciplinary stakeholder group meeting schedule OOSTT:00000267 A planned process by an individual or organization to assess and ensure that a facility or person is compliant with policies, procedures, or guidelines, and that outcomes are comparable to established benchmarks. Mathias Brochhausen performance review process OOSTT:00000268 A role inhering in a human being or an organization that, if realized, is realized its bearer being the active participant of a performance review process. Mathias Brochhausen obsolete_performance reviewer role true OOSTT:00000269 A committee that is the bearer of a performance reviewer role. Mathias Brochhausen obsolete_performance review committee true OOSTT:00000270 An organization that consists of organizations and human beings bearing specific roles in the process of enforcing policies within a community. The members of the machinery of government receive their authority through the government. Mathias Brochhausen A network of organizations enforcing policies within a local, regional, state or national jurisdiction by authorized members of the government. machinery of government OOSTT:00000271 An organization that is part of the machinery of government and that is responsible for the oversight and administration of specific functions. The governmental agencies are given the authority to fulfill those responsibilities by the government. government agency governmental agency OOSTT:00000272 An organization that is not a governmental agency, not an organizational member of the machinery of government, and not part of the government. Mathias Brochhausen non-government organization non-governmental organization OOSTT:00000273 A governmental agency that is not reporting to any specific departmental part of government. Mathias Brochhausen free-standing government agency free-standing governmental agency OOSTT:00000274 the US State Department, the German Bundesgesundheitsministerium, the UK Her Mayesty's Treasury An organization that is part of the government and that is responsible for managing a specific sector of government. government department ministry https://en.wikipedia.org/w/index.php?title=Ministry_(government_department)&oldid=755317373 governmental department OOSTT:00000275 A governmental department that manages aspects of prevention, healthcare, healthcare administration, and public health. Mathias Brochhausen department of health OOSTT:00000276 A governmental department that manages the government of the travel of goods and people in the governed area and the infrastructure related to travel. Mathias Brochhausen department of transportation OOSTT:00000277 A governmental department that manages the government of means to prevent and fight fires and, in some cases, other accidental events and natural disasters. Mathias Brochhausen department of fire administration OOSTT:00000279 A deontic document act that has as specified its output duty holder roles that are borne a trauma system or its organizational members and that are specified in a directive information content entity that is policy of that trauma system. Mathias Brochhausen ratifying regulations for trauma system OOSTT:00000280 A deontic role that if realised is realised by its bearer being the active participant in a document act ratifying regulations for trauma systems. Mathias Brochhausen authority to create regulation for trauma system OOSTT:00000281 A plan specification that is part of a budget and that specified the availability and usage of funds. Mathias Brochhausen spending plan OOSTT:00000282 A role borne by a human healthcare provider that, if realized is realized by managing and coordinating the operations a trauma system and its evaluation. Mathias Brochhausen trauma system manager role OOSTT:00000283 A human health care role that, if realized, is realized by its bearer keeping hospitals up-to-date on requirements, health practices, and staff needs to ensure patient safety and provide reports, analyses and benchmarking based on outcome and performance data. Mathias Brochhausen performance improvement coordinator role OOSTT:00000284 A plan specification that specifies the trauma system design with adopted standards of care for prehospital and hospital personnel and a process to regularly review the plan over time. Mathias Brochhausen https://www.facs.org/~/media/files/quality%20programs/trauma/tsepc/pdfs/regionaltraumasystems.ashx obsolete_trauma system plan true OOSTT:00000285 A trauma system plan that has been signed of by the lead health officer of its region. Mathias Brochhausen obsolete_signed-off trauma system plan true OOSTT:00000286 A plan specification approval process that has a trauma system plan as specified input and part of the government or part of the machinery of government as an active agent expressing their agreement with the trauma system plan. Mathias Brochhausen trauma system plan government approval process The part of goverment or part of the governmental machinery can be national, state, or regional. trauma system plan governmental approval process OOSTT:00000287 A trauma system plan specification that is the specified output of a governmental approval process. Mathias Brochhausen Approval is given on the appropriate level: national, state, or regional. government-approved trauma system plan specification OOSTT:00000288 An information content entity that is the specified output of some training process, and that certifies that the recipient has completed that process. Jonathan Bona training certificate OOSTT:00000289 A plan specification that specifies procedures to ensure that a physician in a particular role is available at a healthcare provider organization 24 hours, 7 days a week. Jonathan Bona continuous coverage policy OOSTT:00000290 A healthcare provider representing their specialty in the multidisciplinary peer review committee. Mathias Brochhausen Sarah Bost A physician or other qualified healthcare professional representing their specialty in the multidisciplinary peer review committee who is also responsible for providing specialty input on issues, carrying opportunities for improvement back to their specialty, and assisting with formation, implementation, and auditing of corrective action plans. specialty liaison to multidisciplinary peer review committee role OOSTT:00000291 A plan specification that is about a trauma system plan specification and specifies procedures to evolve and revise the trauma system plan specification. Mathias Brochhausen trauma system plan development policy OOSTT:00000292 An emergency medical service agency that provides transport to the sick and wounded. Mathias Brochhausen EMS transporting agency emergency medical service transportation agency OOSTT:00000293 An information content entity that is part of an action specfication and that lists planned participants for the processes specified. Mathias Brochhausen list of planned participants OOSTT:00000294 A trauma system that is designed to care for all injured patients and that involves all acute care facilities. Mathias Brochhausen PMID: 16531850 inclusive trauma system OOSTT:00000295 A trauma system that has relatively few high-level centers that deliver definitive care. Mathias Brochhausen PMID: 16531850 exclusive trauma system OOSTT:00000296 An aggregate of emergency medical services agencies that provide transport for the sick and injured. Mathias Brochhausen aggregate of emergency medical service transporting agency OOSTT:00000297 An aggregate of emergency medical services agencies that do not provide transport for the sick and injured. Mathias Brochhausen aggregate of emergency medical services non-transporting agencies OOSTT:00000298 An organization that has other organizations as parts and that rovides emergency medical care. Once it is activated through the report of an incident that causes serious illness or injury, the focus of EMS is emergency medical care of the patient. Mathias Brochhausen EMS ambulance services paramedic services https://www.ems.gov/whatisems.html emergency medical services system OOSTT:00000299 An organization that intends to provide care or transport to the sick and injured as part of an emergency medical services system. Mathias Brochhausen EMS agency emergency medical services An organization that responds to emergency calls to care for the ill and injured that may additionally involve transport to an emergency facility. emergency medical services agency OOSTT:00000300 An emergency medical service transporting agency providing air transportation to move patients to and from healthcare facilities or accident scenes. Mathias Brochhausen air ambulance https://en.wikipedia.org/w/index.php?title=Air_medical_services&oldid=782277605 air medical services agency OOSTT:00000301 An emergency medical service transportation agency that specializes on pediatric patients. Mathias Brochhausen emergency medical service pediatric transportation agency OOSTT:00000302 An emergency medical services pediatric transportation agency that provides ground transportation. Mathias Brochhausen emergency medical services pediatric ground transportation agency OOSTT:00000303 An emergency medical services pediatric transportation agency that provides air transportation. Mathias Brochhausen emergency medical services pediatric air transportation agency OOSTT:00000304 An aggregate of organization that consists only of emergency medical service pediatric ground transportation agencies. Mathias Brochhausen aggregate of emergency medical services pediatric ground transportation agencies OOSTT:00000305 An aggregate of organization that consists only of emergency medical service pediatric air transportation agencies. Mathias Brochhausen aggregate of emergency medical services pediatric air transportation agencies OOSTT:00000306 A healthcare provider organization role that is borne by a hospital and that gets assigned based on an evaluation process. If realized, the role is realized by the hospital providing a burns managment team and providing state-of-the-art burn treatment and recovery to patients. Mathias Brochhausen burn center role OOSTT:00000307 An aggregate of organizations that has bearers of a burn center role as parts. Mathias Brochhausen aggregate of burn centers OOSTT:00000308 A healthcare provider organization role that is borne by a hospital and that gets assigned based on an evaluation process. If realized, the role is realized by the hospital providing a burns managment team and providing state-of-the-art specialized pediatric burn treatment and recovery. Mathias Brochhausen pediatric burn center role OOSTT:00000309 A role borne by a hospital and realized by providing specialized care for patients with traumatic brain injuries. Mathias Brochhausen center for traumatic brain injury role OOSTT:00000310 An aggregate of organizations that has bearers of a center for traumatic brain injuries role as parts. Mathias Brochhausen aggregate of centers for traumatic brain injuries OOSTT:00000311 A role borne by an organization and realized by providing specialized rehabilitation for patients with traumatic brain injuries. Mathias Brochhausen traumatic brain injury rehabilitation organization role OOSTT:00000312 An aggregate of organizations that has bearers of a traumatic brain injury rehabilitation facility role as parts. Mathias Brochhausen aggregate of traumatic brain injury rehabilitation organizations OOSTT:00000313 A role borne by a hospital and realized by providing specialized care for patients with spinal cord injuries. Mathias Brochhausen spinal cord injury center role OOSTT:00000314 A role borne by an organization and realized by providing specialized rehabilitation for patients with spinal cord injuries. Mathias Brochhausen spinal cord injury rehabilitation organization role OOSTT:00000315 An aggregate of organizations that has bearers of a spinal cord injury center role as parts. Mathias Brochhausen aggregate of spinal cord injury centers OOSTT:00000316 An aggregate of organizations that has bearers of a spinal cord injury rehabilitation facility role as parts. Mathias Brochhausen aggregate of spinal cord injury rehabilitation organizations OOSTT:00000317 A governmental agency that evaluates healthcare provider organizations, which are candidates for acquiring a trauma center role, and reports as an outcome whether the organization is fit to be a trauma center. Mathias Brochhausen trauma center verification government agency trauma center verification governmental agency OOSTT:00000318 A plan specification that specifies how members of emergency medical services agenies are supposed to acquire medical direction, when direct communication with medical providers is not available. Mathias Brochhausen emergency medical services offline medical direction protocol OOSTT:00000319 A plan specification that specifies when members of emergency medical services agenies are required to try to set up direct conversation with other healthcare providers to give medical direction. Mathias Brochhausen emergency medical services online medical direction guideline OOSTT:00000320 A trauma system participation incentive plan specification that specifies the availability of funding the local, regional, state or national government for trauma centers joining a trauma system. Mathias Brochhausen trauma system participation direct incentive plan specification OOSTT:00000321 A trauma system participation incentive plan specification that specifies indirect incentives to motivate trauma centers to participate in a trauma system. Examples of such incentives are additional billing codes, remuneration for trauma team response, and availability of training opportunities. Mathias Brochhausen trauma system participation indirect incentive plan specification OOSTT:00000322 A plan specification that specifies resources that become available to trauma centers if they participate in a trauma system. Mathias Brochhausen trauma system participation incentive plan specification OOSTT:00000323 A nurse role that is the specified output of nursing licensing act as specified by a country, state, province or similar licensing body ensureing that the bearer of the role meets the requirements specified in their jursidiction to obtain a nursing license. Mathias Brochhausen https://en.wikipedia.org/w/index.php?title=Registered_nurse&oldid=783787566 registered nurse role OOSTT:00000325 A role that is borne by a human being and that, if realized, is realized by its bearer providing direction to the a trauma program and coordinate the activities of the program as organizational members. Mathias Brochhausen trauma program leadership role OOSTT:00000326 An anesthesiologist role that is the outcome of fullfilling all obligations to be allowed to take a board certification exam in anesthesiology. Mathias Brochhausen board eligible anesthesiologist role OOSTT:00000327 An emergency physician role that is the specified output of a board certification process and that, if realized is realized, is realized either by administering medication for the temporary general or local suppression of sensory or motor nerve function during some health care encounter or providing airway management or by making decisions independently of a supervising physician regarding the adminstration of such medication. Mathias Brochhausen board certified anesthesiologist role OOSTT:00000328 A collection of humans that consists only of bearers of a board certified anesthesiologist role. Mathias Brochhausen Sarah Bost collection of board certified anesthesiologists on trauma service OOSTT:00000329 A collection of humans that consists only of bearers of a board certified neurosurgeon role. Mathias Brochhausen obsolete_collection of board certified neurosurgeons true OOSTT:00000330 An advanced practice registered nurse role that if realized is realized by its bearer assessing patient needs, ordering and interpreting diagnostic and laboratory tests, diagnosing illness and disease, prescribing medication and formulating treatment plans. Mathias Brochhausen NP role https://en.wikipedia.org/w/index.php?title=Nurse_practitioner&oldid=889394537 nurse practitioner role OOSTT:00000331 A role that is borne by a member of the medical team of an emergency department and that, if realized, is realized by its bearer serving as the point of contact for all quality improvement-related communication between the emergency department and the trauma program. Mathias Brochhausen Sarah Bost An member of the medical team of an emergency department who serves as the formal point of contact for the trauma program for all quality improvement-related issues regarding trauma care within the ED. emergency department quality improvement liaison to trauma program role OOSTT:00000332 A general surgeon role that is the specified output of a board certification process and that, if realized, is realized by its bearer using operative manual and instrumental techniques on a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas without the bearer of the role specializing into any particular field of surgery. Sarah Bost A physician who has completed a general surgery residency program and achieved board certification. board certified general surgeon role OOSTT:00000333 A general surgeon role that is the outcome of fullfilling all obligations to be allowed to take a board certification exam in general surgery. Sarah Bost A general surgeon who has completed all requisite training requirements and is eligible to take the board certification examination in the country of intended practice. board eligible general surgeon role OOSTT:00000334 A board certified general surgeon with additional training, experience, and career focus in the care of injured patients. Sarah Bost board certified general surgeon with trauma concentration OOSTT:00000335 A plan specification that specifies which anesthesiologist to call, if the primary on-call anesthesiologist is not available due to already taking care of other trauma patients. Mathias Brochhausen anesthesiologist backup call schedule OOSTT:00000336 A duration that specifies the temporal extension of a hospital stay. Mathias Brochhausen length of stay hospitalization duration OOSTT:00000337 A clinical finding that occurs during the course of, or because of, another disease, treatment, or procedure. [Definition Source: NCI] Mathias Brochhausen http://purl.obolibrary.org/obo/NCIT_C2959 complication finding OOSTT:00000338 An information content entity that is a measurement of time used to describe a lifetime. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf age unit OOSTT:00000339 A human disease that is borne by an organism and, if realized, is realized by the formation of a blood clot in the veins. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf deep vein thrombosis OOSTT:00000340 A planned process that results in a drug report about an individual. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf drug screening OOSTT:00000341 A data item that specifies when an individual is released from the emergency department of a hospital. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf emergency department discharge date OOSTT:00000342 An information content entity that describes if an individual does not have a zip/postal code specifying their place of residence. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf homeless status OOSTT:00000343 An data item that is the outcome of an oxygen saturation measurement process that takes place no more than 30 minutes after admission to a healthcare provider. Diya Mehta initial oxygen saturation American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf initial oxygen saturation information after admission OOSTT:00000344 A data item that is the outcome of a temperature measurement process that takes place no more than 30 minutes after admission to a healthcare provider. Diya Mehta initial temperature American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf initial temperature at admission OOSTT:00000345 An information content entity that is about an injury borne by a patient and that has an ICD code as a part. Diya Mehta ICD-10 injury diagnosis American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf international classification of diseases tenth revision injury diagnosis OOSTT:00000346 An information content entity that is the outcome of a person stating how they wish to compensate a due amount. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf primary payment method information OOSTT:00000347 A postal address that is about a residence a person is living in for a short period of time. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf temporary address OOSTT:00000348 A data item that specifies when a trauma surgeon arrived at the patient's bedside. Diya Mehta American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2021. Accessed July 7, 2023 https://www.facs.org/media/ouzftbad/ntds_data_dictionary_2021.pdf trauma surgeon arrival time OOSTT:00000349 A data item that provides the cumulative amount of time a patient spent in the ICU during one hospitalization measured in whole day increments. Mathias Brochhausen American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary. 2024 Admissions. American College of Surgeons (ACS), Chicago, IL, 2023. Total ICU length of stay Each partial or full day must be measured as one calendar day. total intensive care unit length of stay data item OOSTT:00000350 A value specification that specifies the situation to which a patient is discharged after hospilaization, including the information that the patient passed away during hospitalization. Mathias Brochhausen American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary. 2024 Admissions. American College of Surgeons (ACS), Chicago, IL, 2023. hospital discharge disposition patient discharge disposition information OOSTT:00000351 A planned process consisting of chest compressions often combined with artificial ventilation, or mouth to mouth in an effort to manually preserve intact brain function until further measures are taken to restore spontaneous blood circulation and breathing in a person who is in cardiac arrest. Mathias Brochhausen CPR https://en.wikipedia.org/w/index.php?title=Cardiopulmonary_resuscitation&oldid=1193977417 cardiopulmonary resuscitation OOSTT:00000352 A bloodstream infection that is associated with the placing of a central line or an umbilical catheter in an organism. Emma Chappell American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf Central venous access catheter is equivalent to central line central line associated bloodstream infection OOSTT:00000353 An surgical procedure that was not part of the initial treatment plan. Mathias Brochhausen unplanned visit to the OR unplanned surgical procedure OOSTT:00000354 An admission process through which a patient is admitted to the intensive care unit. Mathias Brochhausen ICU admission intensive care unit admission process OOSTT:00000355 An intensive care unit admission process that was not part of the initial treatment plan. Mathias Brochhausen unplanned ICU admission unplanned intensive care unit admission process OOSTT:00000356 A population of all human beings receiving healthcare from one healthcare provider during a specified time. Mathias Brochhausen patient population OOSTT:00000357 The average value (arithmetic mean) of the length of stay data of the patient population of an inpatient healthcare provider. Mathias Brochhausen mean length of stay OOSTT:00000358 An information content entity that is about a person that is living in a country they are not a citizen of without legal immigration or VISA paperwork. Diya Mehta undocumented person status OOSTT:00000359 An information content identity that denotes the age of a patient at the time of the specific injury. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf age at injury OOSTT:00000360 A governmental organization that exists within a major administrative subdivision that is occupied by other settlements and governs those settlements while also being governed by their respective major administrative subdivision. Emma Chappell minor administrative subdivision OOSTT:00000361 A governmental organization administers a settlement of human beings with defined boundaries. Emma Chappell city town village This term includes cities of any population, not limited to large or urban cities municipality OOSTT:00000362 An information content entity that is about the biological qualities and characteristics most commonly found between the female, male, and intersex categories. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf sex information content entity OOSTT:00000364 A trauma surgeon backup call schedule that has been approved by the trauma medical director. Joseph Utecht TMD-approved trauma surgeon backup call schedule OOSTT:00000365 A physician who has completed an neurosurgery residency program and achieved board certification. Joseph Utecht A physician who has completed an neurosurgery residency program and achieved board certification. board certified neurosurgeon role OOSTT:00000366 A neurosurgeon role that is the outcome of fullfilling all obligations to be allowed to take a board certification exam in neurosurgery. Joseph Utecht Sarah Bost A neurosurgeon who has completed all training requirements and is eligible to take the board certification examination in the country of intended practice. board eligible neurosurgeon role OOSTT:00000367 A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on the nervous system of a patient to investigate or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. A surgeon who specializes in performing operative manual and instrumental techniques on the nervous system of a patient to investigate or treat a disease or injury, to help improve bodily function or appearance, or to repair compromised areas. neurosurgeon role OOSTT:00000368 A collection of humans that consists only of bearers of a neurosurgeon role that are mentioned in a trauma on call plan specification and that are board certified in neurosurgery. Mathias Brochhausen Sarah Bost collection of board certified neurosurgeons on trauma service OOSTT:00000369 A collection of humans that consists only of bearers of a neurosurgeon role that are mentioned in a trauma on call plan specification and that are eligible for board certification in neurosurgery. Mathias Brochhausen Sarah Bost collection of board eligible neurosurgeons on trauma service OOSTT:00000370 A duty holder role that, if realized, is realized by its bearer participating in continuing trauma eduction for an amount of time specified in their program or country. Sarah Bost The obligation to participate in continuing trauma eduction for an amount of time specified in the partcipant's program or country. continuing trauma education continuing trauma education obligor role OOSTT:00000371 A duty holder role that is realized by its bearer organizing and managing a trauma quality improvement and patient safety program. Mathias Brochhausen Sarah Bost The obligation to organize and managing the formal process to ensure performance improvement and patient safety in a facility. coordination of trauma quality improvement and patient safety coordination of trauma quality improvement and patient safety obligor role OOSTT:00000372 A duty holder role that inheres in a human being mentioned in an on call plan specification and that, if realized, is realized by its bearer participating a planned process realizing the concretization of the plan specification and being on call exclusively for the organization at specified times that is the contractual partner in the document act that created this role. Mathias Brochhausen Sarah Bost A healthcare professional who has a primary obligation to a single facility while on call, however, in certain subspecialty instances, the individual may be on call at more than one facility, in which case a back up call schedule is required. on call exclusivity on call exclusivity obligor role OOSTT:00000373 A duty holder role that, if realized, is realized by its bearer organizing and overseeing the trauma quality improvement and patient safety program. Mathias Brochhausen Sarah Bost A health professional role that results in the oversight and management of the trauma center's quality improvement and patient safety program as specified by the American College of Surgeons. tqip coordinator tqip coordinator obligor role OOSTT:00000374 A duty holder role that if realized is realized by its bearer evaluating the nursing care provided to trauma patients. Mathias Brochhausen Sarah Bost The individual with authority and responsibility for evaluating the nursing care provided to trauma patients. trauma nursing evaluator trauma nursing evaluator obligor role OOSTT:00000375 A plan specification that specifies on which schedule and to which extent anesthesia services are provided within a healthcare provider organization. Mathias Brochhausen A plan that specifies the schedule for ensuring adequate numbers of anesthesia care providers are readily available 24 hours a day 7 days a week within a trauma center. anesthesia services availability plan specification OOSTT:00000376 An information content entity that indicates whether an individual is injured while they are being compensated for their service Emma Chappell work related injury information American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf work related injury information content entity OOSTT:00000377 An information content identity that denotes the field where an individual is compensated for their service Emma Chappell American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf occupational industry information OOSTT:00000378 An information content identity that describes an individuals method of receiving an income by their contributions of labor or services to society or themselves Emma Chappell American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf occupation information OOSTT:00000379 An identifier that denotes the external factor that caused injury or the main reason a patient is admitted to the hospital. Emma Chappell ICD-10 primary external cause code American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf international classification of diseases tenth revision primary external cause code OOSTT:00000380 An iidentifier that denotes the location of the traumatic injury through a code Emma Chappell ICD-10 place of occurrence external cause code American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf international classification of diseases tenth revision place of occurrence external cause code OOSTT:00000381 An identifier that denotes one or more external causes in addition to the primary external cause of an injury where necessary using an ICD-10 code. Emma Chappell ICD-10 additional external cause code American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf international classification of diseases tenth revision additional external cause code OOSTT:00000382 An object used in order to prevent injury to a child. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf child protective device OOSTT:00000383 An information content entity that indicates whether the safety device that inflates rapidly was utilized during a motor vehicle crash. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf deployed airbag information content entity OOSTT:00000384 An information content entity that reports a patient's injuries assessing nine body regions and scoring injuries on a six point scale. Emma Chappell AIS code American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf abbreviated injury scale code OOSTT:00000385 An identifier specifying the name and version of a software that calculates abbreviated injury scale severity codes. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf AIS Version abbreviated injury scale version identifier OOSTT:00000386 A data item that denotes the total amount of time a patient has spent on a machine that moves oxygen in and out of their lungs. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf total length of ventilator use OOSTT:00000387 A process that leads to intense physical injury to the body. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf trauma incident OOSTT:00000388 An information content entity that is about the categorization of an individual's background as it is connected to a geographic region and the shared cultural practices of that region Emma Chappell ethnic category information OOSTT:00000389 A pathological process that is the realization of cardiac arrest after hospital arrival and the individual undergoing cardiac arrest receives cardiopulmonary resuscitation. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf cardiac arrest with cardiopulmonary resuscitation OOSTT:00000390 A bacterial urinary tract infection that is caused when an organism has a catheter in place. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf catheter related urinary tract infection OOSTT:00000391 An infection that occurs at a surgical site within a specified period of time. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf http://purl.obolibrary.org/obo/NCIT_C112019 Inspired by the NCIT definition surgical site infection OOSTT:00000392 A surgical site infection that occurs below the incision made during the procedure in the area of the muscles and the tissues that surround the muscles and occurs within a specified period of time. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf https://www.hopkinsmedicine.org/health/conditions-and-diseases/surgical-site-infections#:~:text=Deep%20incisional%20SSI.,was%20involved%20in%20the%20surgery. deep surgical site infection OOSTT:00000393 A surgical site infection that involves any part of the body deeper than the fascial/muscle layers, that was handled during the surgery and occurs within a specified period of time. Emma Chappell American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf https://www.hopkinsmedicine.org/health/conditions-and-diseases/surgical-site-infections#:~:text=Deep%20incisional%20SSI.,was%20involved%20in%20the%20surgery. organ/space surgical site infection OOSTT:00000394 A surgical site infection that occurs on area of the skin where the incision was made and occurs within a specified period of time. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf https://www.hopkinsmedicine.org/health/conditions-and-diseases/surgical-site-infections#:~:text=Deep%20incisional%20SSI.,was%20involved%20in%20the%20surgery. superficial incisional surgical site infection OOSTT:00000395 An infection that is caused by bacteria or fungi being present in the bloodstream. Emma Chappell American College of Surgeons TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871637/#:~:text=Bloodstream%20infections%20(BSI)%20are%20infectious,the%20alteration%20of%20clinical%2C%20laboratory bloodstream infection OOSTT:00000396 A pneumonia that may be caused when an individual is on mechanical ventilation for at least 48 hours. Emma Chappell American College of Surgions TCOT. National Trauma Data Standard Data Dictionary [Internet]. 2024. https://www.facs.org/media/k4wnvapp/final_2024-data-dictionary-830.pdf ventilator associated pneumonia OOSTT:00000398 An information content identity that describes a social categorization of human beings by assumptions based on physical characteristics or their assumed lineage Emma Chappell racial category information PATO:0000051 morphology A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. morphology PATO:0000122 length A 1-D extent quality which is equal to the distance between two points. length PATO:0000125 mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. mass PATO:0001018 physical quality A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. physical quality PATO:0001025 quality pressure PATO:0001241 physical object quality A quality which inheres in a continuant. physical object quality STATO:0000184 A ratio is a data item which is formed with two numbers r and s is written r/s, where r is the numerator and s is the denominator. The ratio of r to s is equivalent to the quotient r/s. review formal definition as both numerator and denominator should be of the same type, not just some data item Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra adapted from Wolfram Alpha: https://www.wolframalpha.com/share/clip?f=d41d8cd98f00b204e9800998ecf8427efdcsig76g7 http://purl.obolibrary.org/obo/stato.owl ratio STATO:0000414 mortality is a ratio formed by the number of deaths due to a disease divided by the total population size. Philippe Rocca-Serra adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm http://purl.obolibrary.org/obo/stato.owl mortality A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. http://purl.obolibrary.org/obo/uberon/releases/2024-08-07/uberon.owl A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] 2012-06-20 2012-08-14 2012-09-17 AAO:0000046 TAO:0000007 VHOG:0000224 AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 TAO:0000007 UMLS:C0005767 VHOG:0000224 Wikipedia:Blood XAO:0000124 ZFA:0000007 galen:Blood http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 portion of blood vertebrate blood uberon whole blood UBERON:0000178 AAO TAO VHOG AAO:LAP DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ZFIN:curator http://bgee.unil.ch/ ncithesaurus:Blood blood UBERON:0000178 The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. http://purl.obolibrary.org/obo/uberon/releases/2024-08-07/uberon.owl An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans 2012-06-20 2012-09-17 AAO:0010257 VHOG:0000723 excretory system AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 DOI:10.1371/journal.pone.0099864 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 GO:0072001 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 SCTID:362204003 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 Wikipedia:Excretory_system XAO:0000143 ZFA:0000163 galen:UrinaryTract systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 AAO VHOG AAO:BJB DOI:10.1371/journal.pone.0099864 GO ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 Wikipedia Wikipedia:Acoelomorpha http://bgee.unil.ch/ ncithesaurus:Urinary_System EDITOR_NOTE In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here renal system UBERON:0001008 Anatomical system that is involved in the production of hematopoietic cells. http://purl.obolibrary.org/obo/uberon/releases/2024-08-07/uberon.owl Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes 2012-06-20 2012-09-17 AAO:0011002 VHOG:0001624 AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 SCTID:362587009 TAO:0005023 UMLS:C0018957 VHOG:0001624 Wikipedia:Haematopoiesis XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 AAO VHOG AAO:EJS DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) WP http://bgee.unil.ch/ ncithesaurus:Hematopoietic_System hematopoietic system UBERON:0002390 An anatomical system that eliminates waste products that arise as a result of metabolic activity. http://purl.obolibrary.org/obo/uberon/releases/2024-08-07/uberon.owl http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z BTO:0006338 GO:0007588 uberon UBERON:8450002 excretory system UBERON:8450002 https://github.com/biopragmatics/biomappings UO:0000001 length unit length unit UO:0000002 mass unit mass unit UO:0000003 time unit time unit A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. Sarah Bost obsolete obligee role true A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. Sarah Bost obsolete obligor role true A collection of humans, all of which bear both an orthopedic surgeon role and an orthopedic board eligibility role and participate in a trauma care process John Judkins Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. obsolete_collection of board eligible orthopedic surgeons in trauma care true A role that inheres in a human being and is acquired by successfully completing an orthopedic residency. John Judkins Mathias Brochhausen orthopedic board eligibility role A collection of humans, all of which bear a neurosurgeon role and are designated as part of the trauma on call plan specification John Judkins Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. obsolete_collection of trauma panel neurosurgeons true An information content entity that is about a person and that affirms that they have attended at the number of meeting of the trauma peer review committee meetings as required by the designating or verifying agency. John Judkins Mathias Brochhausen The record verifying that each specified member participates in the trauma quality improvement committee and attends the majority of meetings as required by the designating or verifying agency. Whether this requirement is fulfilled depends on the PIPS attendance record. record of participation in majority of trauma peer review committee meetings A collection of humans, all of which bear a trauma surgeon role and, while on call, participate in emergency health care processes that are not trauma related. John Judkins Mathias Brochhausen All trauma surgeons who participate in acute care non-trauma-related surgery while on call for the trauma panel. Initially, we used the SubClass restriction, with 'only' after 'is aggregate of' as an equivalent to restriction, which fully defines this set. However, given the number of collections in OOSTT this negatively affected reasoning time. For our data management purposes having the restriction as an existential restriction is totally sufficient, so we go with this. collection of trauma surgeons providing non-trauma emergency care on call A plan specification that describes means of relaying information about changes to workflows of providing care for injured patients to the members of the trauma program. John Judkins Mathias Brochhausen The policy that describes the method of sharing information about the care of injured patients to the collective or individual members of the trauma program, e.g., change in protocol or procedures and rationale. trauma program communication policy about changes to trauma process Residency is a stage of graduate medical training. A part of graduate education where the graduate from a medical program practices medicine under the supervision of an attending physician. (OOSTT editor comment created by M. Brochhausen, Nov 9, 2016) http://vivoweb.org/sites/vivoweb.org/files/vivo-isf-public-1.6.owl Medical Residency The point in time at which an individual was born. Helen Parkinson http://www.ebi.ac.uk/efo/releases/v3.70.0/efo.owl SNOMEDCT:184099003 date of birth oboInOwl:ObsoleteClass An Organization that exercises executive, legislative, or judicial authority over a Geopolitical Entity. https://en.wikipedia.org/wiki/Government is curated in ontology: http://www.ontologyrepository.com/CommonCoreOntologies/Mid/AgentOntology Imported 8.30.2018 BSD 3-Clause License Copyright (c) 2017, CUBRC, Inc. All rights reserved. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. government owl:Thing example to be eventually removed example to be eventually removed failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job Person:Alan Ruttenberg failed exploratory term metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolete_core true placeholder removed placeholder removed terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason. We expect to be able to mine these new reasons and add instances as required. obsolete_other true universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. Alan Ruttenberg A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. Alan Ruttenberg defined class named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions Alan Ruttenberg named class expression to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. Alan Ruttenberg group:OBI to be replaced with external ontology term requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI requires discussion The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. https://github.com/information-artifact-ontology/ontology-metadata/issues/77 https://orcid.org/0000-0001-5208-3432 out of scope A professional organization that is the scientific and educational association of surgeons and is dedicated to improving the care of the surgical patient and to safeguarding standards of care in an optimal and ethical practice environment. Mathias Brochhausen https://www.facs.org/about-acs american college of surgeons A professional organization that is the scientific and educational association of emergency physicians and is that is dedicated to improving emergency care and to advocate for emergency physicians and their patients. Mathias Brochhausen american college of emergency physicians release version - 2025-01-24 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 http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ 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 occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1's jurisdiction falls within the relevant jurisdiction of G2. http://purl.obolibrary.org/obo/geo.owl 'is subordinate authority of' Domain: governing organization Range: governing organization Formal properties: transitive, anti-symmetric, irreflexive Natural language definition: A governing organization G1 is subordinate to another governing organization G2 iff there is some authority possessed by G2 that is not possessed by G1 and G1 falls within the relevant jurisdiction of G2. is subordinate authority of has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about Inverse of the relation 'mentions' 2022-01-28T07:20:08Z mentioned by A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. Alan Ruttenberg is quality measurement of has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_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 has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of 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 is_specified_output_of Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization. is member of organization has organization member Relating an organization to a legal person or organization. See tracker: https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178 Person: Jie Zheng http://purl.obolibrary.org/obo/obi.owl has organization member inheres in this fragility is a characteristic of this vase this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of 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 has_participant relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. http://purl.obolibrary.org/obo/ro/releases/2024-04-24/ro.owl https://en.wikipedia.org/wiki/Causality causally related to en Adam Goldstein Alan Ruttenberg Albert Goldfain Barry Smith Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Christian A. Boelling Clint Dowland Darren Natale David Osumi-Sutherland Gwen Frishkoff Holger Stenzhorn James A. Overton James Malone Jennifer Fostel Jie Zheng Jonathan Rees Larisa Soldatova Lawrence Hunter Mathias Brochhausen Matt Brush Melanie Courtot Michel Dumontier Paolo Ciccarese Pat Hayes Philippe Rocca-Serra Randy Dipert Ron Rudnicki Satya Sahoo Sivaram Arabandi Werner Ceusters William Duncan William Hogan Yongqun (Oliver) He The Information Artifact Ontology (IAO) is an ontology of information entities, originally driven by work by the OBI digital entity and realizable information entity branch. Information Artifact Ontology (IAO) An information artifact is, loosely, a dependent continuant or its bearer that is created as the result of one or more intentional processes. Examples: uniprot, the english language, the contents of this document or a printout of it, the temperature measurements from a weather balloon. For more information, see the project home page at https://github.com/information-artifact-ontology/IAO IDs allocated to related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS: IAO_0021000-IAO_0021999 IDs allocated to subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl: IAO_0021000-IAO_0021999 2022-11-07 Amanda Hicks Diya Mehta Emma Chappell J. Neil Otte Jane Ball John Judkins Jonathan Bona Mihail Eduard Tudoreanu Nels D. Sanddal Robert J. Winchell Robert T. Maxson Rohit Pradhan Rosemary Nabaweesi S. Clint Dowland Sarah Bost Stephen M. Bowman William R. Hogan Mathias Brochhausen The Ontology of Organizational Structures of Trauma centers and Trauma systems (OOSTT) is a representation of the components of trauma centers and trauma systems coded in Web Ontology Language (OWL2). Ontology of Organizational Structures of Trauma centers and Trauma Systems Development of this ontology is funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health. release version - 2025-01-24 IAO_0020000-IAO_0020999 William R. Hogan Mathias Brochhausen PNO http://creativecommons.org/licenses/by/4.0/ proper name ontology release version 2021-06-11 IAO_0021000-IAO_0021999 Cooper Stansbury J. Neil Otte Matthew Diller S. Clint Dowland Sarah Bost William R. Hogan Amanda Hicks Laura Slaughter Mathias Brochhausen Mauricio B. Almeida The ontology is based on a theory of document acts proposed by Barry Smith and Reinach's theory of social acts and legal entities: Reinach, A. (1989), Sämtliche Werke. Texkritische Ausgabe, Edited by Karl Schuhmann and Barry Smith, München: Philosophia Verlag. Smith, B. (2008) “Searle and de Soto: The new ontology of the social world”, The Mystery of Capital and the Construction of Social Reality, B. Smith, D.M. Mark and I. Ehrlich, United States, Open Court., 35-52. Smith, B. (2012) "How to Do Things With Documents", Rivista di estetica, 50 (2/2012), LII: 179-198. However, there are some amendments from our side which are to be found in the documentation. document act ontology http://creativecommons.org/licenses/by/3.0/ development version 2022-07-05