http://orcid.org/0000-0002-4366-3088 https://orcid.org/0000-0001-8815-0078 David Osumi-Sutherland Jie Zheng Pier Luigi Buttigieg Ramona Walls The Population and Community Ontology (PCO) describes material entities, qualities, and processes related to collections of interacting organisms such as populations and communities. It is taxon neutral, and can be used for any species, including humans. The classes in the PCO are useful for describing evolutionary processes, organismal interactions, and ecological experiments. Practical applications of the PCO include community health care, plant pathology, behavioral studies, sociology, and ecology. Population and Community Ontology http://creativecommons.org/publicdomain/zero/1.0/ The Population and Community Ontology (PCO) is licensed under a Creative Commons zero (CC0) license - http://creativecommons.org/publicdomain/zero/1.0/. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. We ask that anyone using this ontology follow the standards of the scientific ontology community by re-using ontology identifiers whenever possible and properly citing the ontology and its creators. 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 label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label 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 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 has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. 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.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note true editor_note 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 term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term 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 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 Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source definition_source curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note 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 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 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 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 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) has_MedDRA_id Mathias Brochhausen OOSTT user-centered description has_alternative_id database_cross_reference has_exact_synonym has_related_synonym in_subset label label GAZ:00001088 Congo Republic of the Congo GAZ:00006882 Afghanistan GAZ:00002953 Albania GAZ:00000563 Algeria GAZ:00003957 American Samoa GAZ:00002948 Andorra GAZ:00001095 Angola GAZ:00009159 Anguilla GAZ:00006883 Antigua and Barbuda GAZ:00002928 Argentina GAZ:00004094 Armenia GAZ:00004025 Aruba GAZ:00000463 Australia GAZ:00002942 Austria GAZ:00004941 Azerbaijan GAZ:00005281 Bahrain GAZ:00003750 Bangladesh GAZ:00001251 Barbados GAZ:00006886 Belarus GAZ:00002938 Belgium GAZ:00002934 Belize GAZ:00000904 Benin GAZ:00001264 Bermuda GAZ:00003920 Bhutan GAZ:00002511 Bolivia GAZ:00006887 Bosnia and Herzegovina GAZ:00001097 Botswana GAZ:00002828 Brazil GAZ:00003961 British Virgin Islands GAZ:00003901 Brunei Darussalam Brunei GAZ:00002950 Bulgaria GAZ:00000905 Burkina Faso GAZ:00001090 Burundi GAZ:00006888 Cambodia GAZ:00001093 Cameroon GAZ:00002560 Canada GAZ:00001227 Cape Verde GAZ:00003986 Cayman Islands GAZ:00001089 Central African Republic GAZ:00000586 Chad GAZ:00001539 Channel Islands GAZ:00002825 Chile GAZ:00002845 China GAZ:00005915 Christmas Island GAZ:00002929 Colombia GAZ:00005820 Comoros GAZ:00053798 Cook Islands GAZ:00002901 Costa Rica GAZ:00002719 Croatia GAZ:00003762 Cuba GAZ:00012582 Curacao GAZ:00453362 Cyprus GAZ:00002954 Czech Republic GAZ:00001086 Democratic Republic of the Congo GAZ:00002635 Denmark GAZ:00000582 Djibouti GAZ:00006890 Dominica GAZ:00003952 Dominican Republic GAZ:00006913 Timor-Leste East Timor GAZ:00002912 Ecuador GAZ:00003934 Egypt GAZ:00002935 El Salvador GAZ:00001091 Equatorial Guinea GAZ:00000581 Eritrea GAZ:00002959 Estonia GAZ:00000567 Ethiopia Faroe Islands GAZ:00059206 Faeroe Islands GAZ:00001412 Falkland Islands (Malvinas) Falkland Islands GAZ:00006897 Micronesia (Federated States of) GAZ:00006891 Fiji GAZ:00002937 Finland GAZ:00002940 France GAZ:00002516 French Guiana GAZ:00002918 French Polynesia GAZ:00001092 Gabon GAZ:00002646 Germany GAZ:00000908 Ghana GAZ:00003987 Gibraltar GAZ:00002945 Greece GAZ:00001507 Greenland GAZ:02000573 Grenada GAZ:00067135 Guadeloupe GAZ:00006933 Guam GAZ:00002936 Guatemala GAZ:00000909 Guinea GAZ:00000910 Guinea-Bissau GAZ:00002522 Guyana GAZ:00003953 Haiti GAZ:00003103 Holy See GAZ:00002894 Honduras GAZ:00003203 China, Hong Kong SAR Hong Kong GAZ:00002952 Hungary GAZ:00000843 Iceland GAZ:00002839 India GAZ:00003727 Indonesia GAZ:00004474 Iran (Islamic Republic of) Iran GAZ:00004483 Iraq GAZ:00052477 Isle of Man GAZ:00002476 Israel GAZ:00002650 Italy GAZ:00000906 Ivory Coast Côte d'Ivoire GAZ:00003781 Jamaica GAZ:00002747 Japan GAZ:00002473 Jordan GAZ:00004999 Kazakhstan GAZ:00001101 Kenya GAZ:00006894 Kiribati GAZ:00011337 Kosovo GAZ:00005285 Kuwait GAZ:00006893 Kyrgyzstan GAZ:00006889 Lao People's Democratic Republic Laos GAZ:00002958 Latvia GAZ:00002478 Lebanon GAZ:00001098 Lesotho GAZ:00000911 Liberia GAZ:00000566 Libyan Arab Jamahiriya Libya GAZ:00003858 Liechtenstein GAZ:00002960 Lithuania GAZ:00002947 Luxembourg GAZ:00003202 China, Macao SAR Macau GAZ:00001108 Madagascar GAZ:00001105 Malawi GAZ:00003902 Malaysia GAZ:00006896 Maldives GAZ:00000584 Mali GAZ:00004017 Malta GAZ:00007161 Marshall Islands GAZ:00003947 Martinique GAZ:00000583 Mauretania Mauritania GAZ:00003745 Mauritius GAZ:00003943 Mayotte GAZ:00002852 Mexico GAZ:00003897 Republic of Moldova Moldova GAZ:00003857 Monaco GAZ:00008744 Mongolia GAZ:00006898 Montenegro GAZ:00003988 Montserrat GAZ:00000565 Morocco GAZ:00001100 Mozambique GAZ:00006899 Burma Myanmar GAZ:00001096 Namibia GAZ:00006900 Nauru GAZ:00004399 Nepal GAZ:00001549 Netherlands GAZ:00004019 Netherlands Antilles GAZ:00005206 New Caledonia GAZ:00000469 New Zealand GAZ:00002978 Nicaragua GAZ:00000585 Niger GAZ:00000912 Nigeria Niue Fekai GAZ:00006902 Niue GAZ:00005913 Norfolk Island GAZ:00002801 Democratic People's Republic of Korea North Korea GAZ:00003958 Northern Mariana Islands Kingdom of Norway GAZ:00002699 Norway GAZ:00005283 Oman GAZ:00005246 Pakistan GAZ:00006905 Palau GAZ:00002475 Occupied Palestinian Territory Palestinian Territories GAZ:00002892 Panama GAZ:00003922 Papua New Guinea GAZ:00002933 Paraguay GAZ:00002932 Peru The Philippines GAZ:00004525 Philippines Pitcairn GAZ:00005867 Pitcairn, Henderson, Ducie and Oeno Islands Pitcairn Islands GAZ:00002939 Poland Portugese Republic GAZ:00002944 Portugal Commonwealth of Puerto Rico GAZ:00006935 Puerto Rico GAZ:00005286 Qatar GAZ:00002943 Ireland Republic of Ireland GAZ:00006895 The former Yugoslav Republic of Macedonia Republic of Macedonia GAZ:00002951 Romania GAZ:00002721 Russian Federation Russia GAZ:00001087 Rwanda GAZ:00053746 Réunion GAZ:00000849 St. Helena Saint Helena GAZ:00006906 Saint Kitts and Nevis GAZ:00006909 Saint Lucia GAZ:00005841 Saint Martin GAZ:00003942 Saint-Pierre-et-Miquelon Saint Pierre and Miquelon GAZ:02000565 Saint Vincent and the Grenadines GAZ:00006910 Samoa GAZ:00003102 San Marino GAZ:00005279 Saudi Arabia GAZ:00002639 Scotland GAZ:00000913 Senegal GAZ:00002957 Serbia GAZ:00005821 Seychelles GAZ:00000914 Sierra Leone GAZ:00003923 Singapore GAZ:00012579 Sint Maarten GAZ:00002956 Slovakia GAZ:00002955 Slovenia GAZ:00005275 Solomon Islands GAZ:00001104 Somalia GAZ:00000553 South Africa GAZ:00002802 Republic of Korea South Korea GAZ:00233439 South Sudan GAZ:00000591 Spain GAZ:00003924 Sri Lanka GAZ:00000560 Sudan GAZ:00002525 Suriname GAZ:00001099 Swaziland GAZ:00002729 Sweden GAZ:00002941 Switzerland GAZ:00002474 Syria GAZ:00006927 São Tomé and Príncipe GAZ:00005341 Taiwan GAZ:00006912 Tajikistan GAZ:00001103 United Republic of Tanzania Tanzania GAZ:00003744 Thailand GAZ:00002733 Bahamas The Bahamas GAZ:00000907 Gambia The Gambia GAZ:00000915 Togo GAZ:00006914 Tokelau GAZ:00006916 Tonga GAZ:00003767 Trinidad and Tobago GAZ:00000562 Tunisia GAZ:00000558 Turkey GAZ:00005018 Turkmenistan GAZ:00003955 Turks and Caicos Islands GAZ:00009715 Tuvalu GAZ:00001102 Uganda GAZ:00002724 Ukraine GAZ:00005282 United Arab Emirates GAZ:00002637 U.K. United Kingdom U.S. GAZ:00002459 United States of America United States GAZ:00003959 U.S. Virgin Islands United States Virgin Islands GAZ:00002930 Uruguay GAZ:00004979 Uzbekistan GAZ:00006918 Vanuatu GAZ:00002931 Venezuela GAZ:00003756 Vietnam GAZ:00007191 Wallis and Futuna Islands Wallis and Futuna GAZ:00000564 Western Sahara GAZ:00005284 Yemen GAZ:00001107 Zambia GAZ:00001106 Zimbabwe GAZ:00009721 Cocos (Keeling) Islands GAZ:00004942 Georgia 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 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]) 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 (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) 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] 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] 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 A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. 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] 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. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. 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] 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] 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] 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] sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) 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] 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] 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] 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. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. 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] 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] 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] 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] 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]) A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. See https://github.com/EnvironmentOntology/envo/issues/264 for discussion. This definition needs a lot of clean up and links to household and related classes must be made to form logical definitions for inference to work. Subclasses will be added by inference. human dwelling A self-contained constructed feature used by one or more households as a home, such as a house, apartment, mobile home, houseboat or other 'substantial' structure. A dwelling typically includes nearby outbuildings, sheds etc. within the curtilage of the property, excluding any 'open fields beyond'. It has significance in relation to search and seizure, conveyancing of real property, burglary, trespass, and land use planning. https://en.wikipedia.org/wiki/Dwelling accessed 11/25/2015 One of the large, unbroken masses of land into which the Earth's surface is divided. GAZ:00190836 major area continent The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. jl 2012-09-20T14:06:08Z GO:0023032 GO:0044708 GO:0044709 Wikipedia:Behavior behavioral response to stimulus behaviour behavioural response to stimulus biological_process single-organism behavior GO:0007610 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). behavior The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. GOC:ems GOC:jl ISBN:0395448956 PMID:20160973 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. jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. 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. GOC:pdt Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour biological_process cooperative behavior GO:0035176 Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. GOC:jh2 PMID:12848939 Wikipedia:Social_behavior Any process in which an organism has an effect on an organism of the same species. https://github.com/geneontology/go-ontology/issues/20191 intraspecies interaction between organisms intraspecies interaction with other organisms biological_process GO:0051703 biological process involved in intraspecies interaction between organisms Any process in which an organism has an effect on an organism of the same species. GOC:ai Any geographic area greater than an individual country but smaller than a continent, used as a convenience reference. Please note that most geographic areas may not be formally defined and exact boundaries can be debatable. geographical area region A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. NCIT:C25464 country GAZ:00000457 Africa GAZ:00000465 Asia GAZ:00000464 Europe GAZ:00000468 Oceania GAZ:00000459 Latin America and the Caribbean GAZ:00000458 Northern America GAZ:00000556 Eastern Africa Middle Africa GAZ:00000555 Northern Africa GAZ:00000553 Southern Africa GAZ:00000554 Western Africa South-Central Asia GAZ:00000559 South-Eastern Asia Western Asia Eastern Europe Northern Europe Southern Europe Western Europe Caribbean GAZ:00000459 South America GAZ:00002891 Central America Australia/New Zealand GAZ:00005860 Melanesia GAZ:00005862 Micronesia GAZ:00005861 Polynesia GAZ:00002471 Eastern Asia Scandinavia GAZ:00002472 South Asia 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 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 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 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 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 publication about an investigation Most scientific journal articles A publication that is about an investigation PERSON: Lawrence Hunter scientific publication publication about an investigation patent US Patent 6,449,603 A document that has been accepted by a patent authority PERSON: Lawrence Hunter patent 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 A document that is in preparation for submission to be published. PERSON: Jie Zheng EFO_0001795 in preparation VEuPathDB document in preparation for publication A document that is a collection of identifiers that has been created to identify and annotate core ideas of a specified domain, and where the intention of its creators is that the identifiers have a one-to-one correspondence with entities in reality outside the aggregate. Mathias Brochhausen code system codeset coding system controlled vocabulary Clint Dowland Matt Diller Sarah Bost William R. Hogan Does not imply absence vs. presence of any taxonomy. Does not imply that identifiers denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities (e.g., SNOMED and even various OBO ontologies have identifiers that identify entities in all three categories). Each identifier 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 identifiers take the form of human language words. For example, a “sex” or “gender” code set could have identifiers “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 and annotating core ideas of a specified domain. The identifiers do not denote each other. code set A document that denotes some identity and is concretized by the bearer of some credential role. Amanda Hicks identity document A role that inheres in a concretization of an identity document and is realized by an authentication process. Amanda Hicks credential role 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 obligor role 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 obligee role 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 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 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 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 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 A social act that creates or revokes a deontic role. Mathias Brochhausen deontic declaration 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 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 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 A social act that postulates a socio-legal fact for a specified group of people or organizations. Mathias Brochhausen enactment standing declaration medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury. The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, "Acupuncture as a therapeutic intervention is widely practiced in the United States," Reference: http://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. YH WEB: http://wiki.answers.com/Q/What_is_medical_intervention medical intervention Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery. YH, SS surgical procedure WEB: http://en.wikipedia.org/wiki/Surgery WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm 10042609 surgery a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result. YH, SS WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm medical procedure planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process 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 entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. 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 A social role inhering in a human being. Mathias Brochhausen William R. Hogan human social role party to a legal entity party to a legal proceeding party to a legal agreement party to a marriage contract party to a power of attorney A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. Mathias Brochhausen http://en.wikipedia.org/wiki/Gender_role gender role A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the male sex in the context of the culture in question. Mathias Brochhausen male gender male gender role A gender role borne by a human being that is realized in behaviour which is considered socially appropriate for individuals of the female sex in the context of the culture in question. Mathias Brochhausen female gender female gender role 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, or undergoing diagnosis. William R. Hogan health care role Mathias Brochhausen human health care role 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. 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 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 William R. Hogan health care provider role 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 physician role 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 nurse role A role that inheres in an organization and that is realized by the providing of services in a health care encounter. Mathias Brochhausen Amanda Hicks health care provider organization role person health care provider role A health care provider organization role that inheres in an organization consisting of two or more physicians. Amanda Hicks physician practice A health care provider organization role that inheres in an organization that is comprised of other organizations. Amanda Hicks integrated delivery network A role in human social processes that inheres in an organization. William R. Hogan 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 A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen 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 An organization social role that, if realized, is realized by either a health care process or an ancillary health care process Previous definition: An organization social role played by an organization in health care processes. organization health care role A patient role that inheres in a human being. human patient role 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.owl It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations A role borne by a human individual or by a collection of humans regarded as possessing rights and duties enforeable at law. Mathias Brochhausen Malcolm N. Shaw: International Law. Cambridge University Press, Cambridge, 2008. We are aware of the fact that Wikipedia's definition differs from ours by saying that "Legal personality (...) is the characteristic of a non-living entity regarded by law to have the status of personhood" (http://en.wikipedia.org/wiki/Legal_personality) However, Shaw explicates: "In any legal system, certain entities, whether they be individuals or companies, will be regarded as possessing rights and duties enforceable at law. Thus an individual may prosecute or be prosecuted for assault and a company can sue for breach of contract. They are able to do this because the law recognises them as 'legal persons' possessing the capacity to have and to maintain certain rights, and being subject to perform specific duties. (...) In municipal law individuals, limited companies and public corporations are recognized as each possessing a distinct legal personality, the terms of which are circumscribed by the relevant legislation" (Shaw MN: International Law. Sixth Edition. Cambridge University Press, Cambridge, 2008). We hold that Shaw's position is ontological more prolific since it not only allows to explain how groups of individuals become recognized as unities at law, but also how different individuals can hold different legal personality roles (always against the context of one legal system). The latter will proof useful when dealing with the representing comatous patients or minorsat law in ontologies. legal person role A role that inheres in an organism and is realized by habitually smoking tobacco products. smoker role intravenous drug user material entity role organism role Homo sapiens role organization role A function inhering in a material entity that, if realized, is realized by the material entity being the site at which inpatient and outpatient healthcare is provided to a patient population. Mathias Brochhausen hospital function A function inhering in a material entity that, if realized, is realized by that material entity being the site at which formal education is provided to a student population. Mathias Brochhausen school function A healthcare provider role that inheres in an organization and is realized by providing inpatient care. Mathias Brochhausen hospital role An organization social role that inheres in an organization and is realized by providing formal education to students. Mathias Brochhausen school role An organization that is the bearer of a hospital role. Mathias Brochhausen hospital organization An organization that is the bearer of a school role. Mathias Brochhausen school organization Mathias Brochhausen nursery school role Mathias Brochhausen primary school role A material entity that is a human made strcuture with firm connection between its foundation and the ground. Mathias Brochhausen http://de.wikipedia.org/wiki/Bauwerk "Building" is a subclass of this. This type of entity is referred to as "Bauwerk" or "Bauliche Anlage". architectural structure An architectural structure that bears some function. Mathias Brochhausen facility A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function. Mathias Brochhausen William Hogan hospital facility A facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen school facility Mathias Brochhausen secondary school role A trauma patient role that inheres in a homo sapiens who is under the age of 15 years. Amanda Hicks pediatric trauma patient The following definition for 'pediatric trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. "A trauma patient who is under the age of 15 years." pediatric trauma patient role 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. injured patient role A patient role that inheres in an organism suffering a thermal, electrical, chemical or radiation burn. Amanda Hicks The following definition for 'burn patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient suffering a thermal, electrical, chemical or radiation burn. burn patient burn patient role A physician role that is created by training and certification in rehabilitation/physical medicine and that is realized by the provision of or supervising of the provision of rehabilitation or physical therapy to a patient. Amanda Hicks physiatrist The following definition for 'physiatrist' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A physician with training and certification in rehabilitation/physical medicine. Definition updated May 5, 2016. Original definitions was, a health care role borne by a human being and realized by training and certification in rehabilitation medicine. physiatrist role A patient role that inheres in an organism with some non-superficial traumatic injury. The role is realized by admision to a hospital, transfer from one hospital to another for the purpose of trauma care, or has death as a result of the traumatic injury. Amanda Hicks trauma patient The following definition for 'trauma patient' was approved by the CAFE team of domain experts (experts in trauma care) May 29, 2015. A patient sustaining an injury who has been admitted to the hospital, transferred from one hospital to another for the purpose of trauma care, or has died as a result of the traumatic injury. trauma patient role A function that inheres in a material entity and, if realized, is realized by protecting persons and their possessions from weather and by some person or group of persons habitually sleeping in at least one site that is contained by that material entity. Amanda Hicks residence function A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of that housing unit's residence function. Amanda Hicks Note in OMRSE it is the housing unit, not the people living there, that are the bearers of a "residence function". Note the distinction between being a residence and a resident. Note that it is not possible in OWL 2, at least that we have yet found, to say that the housing unit in which the process occurs is the same one that is the bearer of the residence function (that the process realizes). household A role in human social processes that, if realized, is realized when the bearer provides labor or services in exchange for a wage or salary as specified by some deontic declaration. Amanda hicks employee job role Amanda Hicks workplace facility a function inhering in a material entity that, if realized, is realized by that material entity being the site where the work of some organization is carried out Amanda Hicks workplace function A US Census householder role is a human social role that, if realized, is realized by that person being a member of a household and either owning or renting the housing unit in which that household resides and being designated as the householder. If there is only one member of the household who owns or rents the housing unit, that person is designated the householder by default. Amanda Hicks http://www.census.gov/cps/about/cpsdef.html last accessed on June 30, 2015 US census householder role A US cenus reference person role is a human social role that inheres in a Homo sapiens who is a member of a household and is realized by other persons in the household being recorded in the US census in relation to that person. Amanda Hicks http://www.census.gov/cps/about/cpsdef.html last accessed June 30, 2015 US Census reference person role A role that concretizes a socio-lega generically dependent continuant Amanda Hicks obsolete socio-legal human social role true a role in human social processes that is realized when the bearer provides a wage or salary in exchange for some labour or services as specified by some declaration employer role A document that records a legally binding agreement between two or more parties. A contract is a document that is the specified output of a legally binding document act and records a legally binding agreement between two or more parties. contract A role that inheres in an organism that is able to receive benefits from an insurance policy. The role, if realized, is realized by receiving benefits that are covered by the insurance policy. Amanda Hicks insured party role An organization that secures a group of people against pecuniary loss by payment of a sum of money if a a specified event occurs. Amanda Hicks insurance company payer role party to an insurance policy A facility bearing the function to provide healthcare and that is administered by a health care organization for the purpose of providing health care to a patient or patient population. William Hogan health care facility A human social role that inheres in a human who is legally eligible to work, is conferred by the U.S. Census Bureau, and is realized by the bearer not working and either making active efforts to find employment in the four weeks prior to the reference week or waiting to be recalled from temporary layoff. Amanda Hicks US Census unemployed role A health care facility that bears a function to provide healthcare to the sick or terminally ill Amanda Hicks Emma Norris William Hogan Human Behaviour Change Project hospice facility Amanda Hicks skilled nursing facility A facility to assist in physical or addiction recovery Amanda Hicks Emma Norris William Hogan Human Behaviour Change Project rehabilitation facility A facility that is run by a nursing home organization and is the bearer of a nursing home function. Amanda Hicks nursing home facility A community living health care facility that provides health care services in a home-like setting Amanda Hicks William Hogan residential health care facility Amanda Hicks overnight dialysis facility A health care facility that bears a function to provide low intensity healthcare services to patients on a short-term basis, with patients leaving on the same date as arriving (i.e., without them staying overnight) Amanda Hicks Emma Norris William Hogan Human Behaviour Change Project Broadened from treatment to healthcare services generally. "Low intensity" is not defined at the moment, but is needed to differentiate from same-day surgery centers or observation stays in hospitals that last <24 hours. The idea is that few invasive procedures are performed, and the ones that are invasive are not typically much worse than a blood draw. Maybe bone marrow biopsy is as aggressive as it gets. I wonder if hematologists do that on an outpatient basis. outpatient clinic facility Amanda Hicks physician office facility Amanda Hicks ambulatory surgery facility Amanda Hicks urgent care facility A health care facility that bears a function to provide emergency healthcare services and the acute care of patients who present without prior appointment, having arrived either by their own means or by ambulance Amanda Hicks Emma Norris William Hogan Adapted from Human Behaviour Change Project emergency department facility urgent care function Amanda Hicks ambulatory surgery function hospice function emergency department function physician office function outpatient clinic function overnight dialysis function rehabilitation function skilled nursing function residential function nursing home function A deontic document act that concludes an inpatient encounter. Amanda Hicks discharge process patient discharge 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. US physician assistant role A physician role that inheres a human being and, 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 by making decisions independently of a supervising physician regarding the adminstration of such medication. anesthesiologist role Amanda Hicks identification process surgeon role A surgeon role realized by its bearer using performing neurosurgery. neurosurgeon role An information content entity that is about human travel. https://github.com/ufbmi/OMRSE/issues/79 Jie Zheng Amanda Hicks human traveling information A surgeon role borne by a human being and that, if realized, is realized by its bearer using operative manual and instrumental techniques on preadult patients to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance or to repair unwanted ruptured areas. Amanda Hicks pediatric surgeon role a facility that is run by an adult foster home organization and is the bearer of an adult foster home organization Amanda Hicks adult foster home facility adult foster home function a health care facility that also bears a residence function and thus one in which the patients are also residents of the facility community living health care facility registered nurse role A facility that is run by an assisted living facility organization and is the bearer of an assisted living facility function. assisted living facility assisted living function obsolete medical advice true home health care organization home health care function palliative function hospice organization health care function A role that inheres in an organism and is realized by habitually smoking 10 or more tobacco cigerettes a day or the equivalent in other tobacco products. heavy smoker role A role that inheres in an organism and is realized by habitually smoking 1>10 tobacco cigerettes a day or the equivalent in other tobacco products. light smoker role residential facility A facility that has at least one housing unit as part in which a person or persons live Emma Norris William Hogan Modified version of definition provided by Human Behaviour Change Project residential facility A maximal aggregate of material entities such that each member bears a linguistic competence for the same language. Matthew Diller Mathias Brochhausen S. Clint Dowland William R. Hogan linguistic community a communication in which some participant requests of some other participant an information content entity about some portion of reality S. Clint Dowland As with the parent class, 'participant' in the definition need not refer to a human agent. The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be. information content entity-request process an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the ethnic identity of that other participant S. Clint Dowland information content entity request about ethnic identity an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the racial identity of that other participant S. Clint Dowland information content entity request about racial identity 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 admission process An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan We include (i)-(iii) to acknowledge that there are different senses of "identify" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way. social identity information content entity A social identity information content entity that is about whether some person identifies as some ethnicity. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian. ethnic identity information content entity An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity. OMB ethnic identity information content entity An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan It comprehends people of Portuguese culture or origin in Brazil. OMB Hispanic or Latino identity information content entity An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB not Hispanic or Latino identity information content entity A social identity information content entity that is about whether some person identifies as some gender. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan gender identity information content entity A gender identity information content entity that is about some person's identifying as female in gender. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan female gender identity information content entity A gender identity information content entity that is about some person's identifying as male in gender. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan male gender identity information content entity A gender identity information content entity that is about some person's identifying as non-binary in gender. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan non-binary identity information content entity A social identity information content entity that is about whether some person identifies as some race. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan racial identity information content entity A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB racial identity information content entity An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment. OMB American Indian or Alaska Native identity information content entity An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB Asian identity information content entity An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB black or African American identity information content entity An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB Native Hawaiian or other Pacific Islander identity information content entity An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa. S. Clint Dowland Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan OMB white identity information content entity A social identity information content entity that is about whether some person identifies as having some sexual orientation. Amanda Hicks Mathias Brochhausen Matthew Diller Sarah Bost William R. Hogan sexual orientation identity information content entity A social act that creates an information content entity that is about some geographical region in which a human being dwells. Matthew Diller Hansi Zhang Mathias Brochhausen S. Clint Dowland Sarah Bost William R. Hogan disclosure of residence awarding of an academic degree A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree. William R. Hogan Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam). awarding an academic degree A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone. Matthew Diller John Judkins S. Clint Dowland William R. Hogan caregiver role A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption. http://purl.obolibrary.org/obo/ERO_0002033 John Judkins S. Clint Dowland William R. Hogan We are also intending on including other family arrangements. This is something we are working on. family relationship A process in which some participant shares some generically dependent continuant with some other participant. The former utilizes some specifically dependent continuant that concretizes the generically dependent continuant intended to be shared, while the latter interprets that specifically dependent continuant to concretize some particular generically dependent continuant, aiming to accurately infer the other participant’s intent. S. Clint Dowland Mathias Brochhausen Matthew Diller William R. Hogan For example, if you tell someone, “It is raining,” you produce sounds that have patterns that concretize information about the weather. Your utilization of that concretization is part of the communication. When the other person hears you, they interpret those patterns to concretize something, which may or may not be the same as what you intended to convey. In other words, they interpret the sounds you produce to have meanings associated with them, and that interpretation process is another part of the communication. If a process does not have a part of each type, it is not a communication. The interpretation need not correspond exactly to what was intended by the other participant. The term 'participant' in the definition need not refer to a human agent. communication A communication in which some participant states a preference for some communicative process to be in a certain language, via some concretization of some preferred language information content entity. S. Clint Dowland Mathias Brochhausen Matthew Diller William R. Hogan disclosure of preferred language A role inhering in an entity realized by social interactions in human society. Matthew Diller Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes 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 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 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 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 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 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 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities quality (PATO) PATO:0000072 quality PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG quality PATO:0000068 TODO: define this or obsolete it and move children somewhere else. qualitative A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. quality PATO:0000069 deviation (from_normal) A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average. PATOC:GVG The number of entities of this type that are part of the whole organism. PATO:0000053 PATO:0000071 PATO:0001169 PATO:0001226 presence or absence in organism quantitative quality count in organism number presence PATO:0000070 This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10. amount The number of entities of this type that are part of the whole organism. PATOC:GVG A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. quality PATO:0000161 rate A quality of a single process inhering in a bearer by virtue of the bearer's occurrence per unit time. PATOC:melissa A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. quality average PATO:0000461 normal A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average. PATOC:GVG A quality inhering in a bearer by virtue of the bearer's existence. quality present in organism PATO:0000467 present A quality inhering in a bearer by virtue of the bearer's existence. PATOC:GVG An amount which is relatively high. PATO:0000420 PATO:0000650 increased number present in greater numbers in organism supernumerary quality accessory increased PATO:0000470 increased amount An amount which is relatively high. PATOC:GVG A rate which is relatively low. slow rate quality PATO:0000911 decreased rate A rate which is relatively low. PATO:GVG A rate which is relatively high. fast rate high rate quality PATO:0000912 increased rate A rate which is relatively high. PATO:GVG A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities. PATO:0002079 Wikipedia:Physical_property relational physical quality quality 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. PATOC:GVG A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. quality density PATO:0001019 mass density A physical quality which inheres in a bearer by virtue of some influence is exerted by the bearer's mass per unit size. WordNet:WordNet A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. quality PATO:0001164 dense A physical quality which inheres in a bearer by virtue of the bearer's exhibiting density. PATOC:GVG A quality which inheres in an process. PATO:0001239 PATO:0001240 quality of a process quality of occurrent quality of process relational quality of occurrent quality PATO:0001236 See comments of relational quality of a physical entity. process quality A quality which inheres in an process. PATOC:GVG A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles. physical object quality A quality which inheres in a continuant. PATOC:GVG A biological sex quality inhering in a population of multiple sexes. quality PATO:0001338 For example a mixture of females and male or males and hermaphrodites. mixed sex A biological sex quality inhering in a population of multiple sexes. MGED:MGED A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. quality PATO:0001415 morbidity A quality inhering in a population by virtue of the proportion of its members that are ill at a given time. PATOC:GVG The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. OBO_REL:has_part extra or missing physical or functional parts has or lacks parts of type mereological quality number of quality cardinality number PATO:0001555 has number of The number of parts of a particular type that the bearer entity has. This is a relational quality, and thus holds between two entities: the bearer of the quality, and the type of parts. PATOC:CJM A density which is higher relative to the normal or average. high density quality PATO:0001788 increased mass density A density which is higher relative to the normal or average. PATOC:GVG A density which is lower relative to the normal or average. low density quality PATO:0001790 decreased mass density A density which is lower relative to the normal or average. PATOC:GVG An amount which is relatively low. PATO:0000419 PATO:0000468 decreased number present in fewer numbers in organism quality decreased reduced subnumerary PATO:0001997 decreased amount An amount which is relatively low. PATOC:GVG A quality that inheres in an entire population or part of a population. quality PATO:0002003 population quality A quality that inheres in an entire population or part of a population. PATOC:GVG george 2009-06-05T09:16:46Z quality PATO:0002062 physical quality of a process A quality that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:39:43Z quality PATO:0002300 increased quality A quality that has a value that is increased compared to normal or average. PATOC:GVG A quality that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:40:15Z quality PATO:0002301 decreased quality A quality that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:50:59Z quality PATO:0002302 decreased process quality A quality of a process that has a value that is decreased compared to normal or average. PATOC:GVG A quality of an object that has a value that is decreased compared to normal or average. George Gkoutos 2011-06-16T06:51:54Z quality PATO:0002303 decreased object quality A quality of an object that has a value that is decreased compared to normal or average. PATOC:GVG A quality of a process that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:53:08Z quality PATO:0002304 increased process quality A quality of a process that has a value that is increased compared to normal or average. PATOC:GVG A quality of an object that has a value that is increased compared to normal or average. George Gkoutos 2011-06-16T06:54:01Z quality PATO:0002305 increased object quality A quality of an object that has a value that is increased compared to normal or average. PATOC:GVG Examples include: population, community, species (meaning the collection of organisms that makes up a species, not the taxonomic rank), and family. A material entity that consists of two or more organisms, viruses, or viroids. group of organism organism collection May be of the same or different species. collection of organisms A quality that inheres in a population of organisms. See Chris's comments on population qualities at: http://code.google.com/p/popcomm-ontology/issues/detail?id=4. These may not belong under BFO:quality. May be better to call them population characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. This class is used only for qualities of PCO:population of organsism, while PATO:population quality can inhere in either a population of organisms or an ecological community. Includes qualities like population size, population growth rate, carrying capacity, immigration rate, emigration rate, fecundity, and death rate. A population quality may depend on the qualities of individual organisms in the population, but cannot be measured or described for a single organism. This term may be replaced by a PATO term. quality of a population A quality that inheres in a community. These may not belong under BFO:quality. May be better to call them community characteristics, and classify as specifically dependent continuants. Need to look at process profiles in BFO2. Includes qualities like diversity, species richness, stability, resilience, community structure, number of trophic levels. A community quality may depend on the qualities of individual organism in the community, but cannot be measured or described for a single individual. quality of an ecological community A process that has as primary participant a population. Includes processes such as population growth, extinction, evolution, selection, and adaptation. Population processes may depend on the processes of individual organisms {e.g., population growth reflects the cumulative multicellular organism reproduction (GO:0032504) and death (GO:0016265) of all individuals in a population}, but cannot be described for an individual organism. Some of these processes (e.g., evolution, extinction) can also occur at the species level, so PCO distinguishes between, for example, population extinction and species extinction. The GO has the terms 'multi-organism process' (GO:0051704) and 'intraspecies interactions between organisms' (GO:0051703), but these categories are only defined for interactions between two individuals. It is unclear at this point if 'biological process' (GO:0008150) encompasses population processes. population process The rate of birth of a population of organisms. population birth rate The rate of death of a population of organsisms. population death rate The rate of growth of a population. population growth rate The number of different species represented in an ecological community. This is a quality of an ecological community (PCO_0000002). If your metric includes the abundances of species (evenness) as well as the number, you should use community species diversity (PCO_0000019). adapted from http://en.wikipedia.org/wiki/Species_richness community species richness A process that leads to a change in the number of individuals (positive or negative) in a population. population growth A population process that leads to an increase in the numbers of individuals in a population following a logistic (S-shaped) curve. Generally occurs when the population has a carrying capacity in a particular habitat. logistic population growth A population growth process that leads to an exponential increase in the number of individuals in a population. exponential population growth A material entity that has as parts two or more organisms, viruses, or viroids of the same species and no members of any other species. collection of organisms of the same species single-species collection of organisms The number of different species that are represented in a given community, weighted by their abundance. Community species diversity can be calculated in different ways, but consists of two components: species richness and species evenness. If your metric does not include the abundances of different species, but rather just the numer of species, you should use community species richness (PCO_0000010). More specific subclasses or instances of this class may be created to describe specific ways of measuring diversity. adapted from http://en.wikipedia.org/wiki/Species_diversity The Shannon Index and Simpson Index are examples of ways in which species diversity is quantified. community species diversity A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption. Needs axioms for family relationships. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173 Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. family A population process that ultimately leads to the death of all individuals in a population. population extinction If there are 40 foxes, and 1000 dogs, the community is not very even, but if there are 40 foxes and 42 dogs, the community is quite even. A quality of an ecological community that reflects how close in abundance all species in a community are. adapted from http://en.wikipedia.org/wiki/Species_evenness community species evenness An organismal entity that consists of one or more people who live in the same dwelling and also share at meals or living accommodation, and may consist of a single family or some other grouping of people. WEB: http://en.wikipedia.org/wiki/Household household A collection of organisms of the same species that has as members only humans. human community human population collection of humans A household in which the majority of the income of its members is derived from agricultural activities. This is a more narrow definition in which the majority of income of a house comes from agricultural activities, as opposed to the broad definition in which any income comes from agricultural activities. The narrow definition was chosen to be consistent with the SDGIO (UN Sustainable Development Goals) which requested this term. agricultural household A material entity that is one or more organisms, viruses or viroids. organismal entity A collection of organisms of the same species whose members are all either genealogically related to each other or have mated with each other. genealogical family Matthew Brush, as part of http://datamodel.clinicalgenome.org/interpretation/ biological family A type of social behavior in which a collection of humans intentionally gathers together on a temporary basis to engage socially. Intented to replace http://purl.obolibrary.org/obo/GENEPIO_0001029 GenEpiO curators human social gathering activity A human social event in which humans living in the same area or neighborhood gather to carry out activiites relevent to the people living in the area. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001034 GenEpio curators human community event A human social gathering in which the intention is to have a good time. Often the intention is to celebrate something like a birthday, anniversary, or holiday, but there is not always a purpose. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001030 GenEpiO curators party A human social gathering at which each participant is expected to bring food to share. A potluck also can be party, a social meal, or some other type of social gathering. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001033 GenEpio curators potluck A human social gathering at which two people are married. May include a legal or social ceremony. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001031 GenEpio curators wedding A human social gathering at which the key participant is an expectant parent and other guests bring presents for the soon to be born baby. Intended to replace http://purl.obolibrary.org/obo/GENEPIO_0001032 GenEpiO curators baby shower A physical object quality that is inhered in a material entity that is too small to be viewed by the unaided eye. should move to PATO invisible to unaided eye An increased mass density of a population of organisms such that the density of organisms in an area is increased beyond sustainable levels. increased density of population overcrowded population A quality of a human population such that the density humans in an area is increased beyond sustainable levels. overcrowded human population A community species diversity metric that accounts for both the abundance and evenness of the species present quantified via the following formula: the negative sum of, the product of the proportion of species i relative to the total number of species (pi) multiplied by the natural logarithm of this proportion (ln pi). Shannon entropy Shannon's diversity index Shannon-Wiener index Shannon diversity index A community species diversity metric that is quantified via the following formula: the reciprocal of the sum of squared proportion of species i relative to the total number of species (pi). Simpson index Simpson diversity index A community species diversity metric that is quantified via the following formula: the sum of squared proportion of species i relative to the total number of species (pi). inverse Simpson diversity index A community species diversity that is the mean species diversity at a site or within a specific habitat. α-diversity alpha diversity A community species diversity that is the ratio between regional and local species diversity. true beta diversity β-diversity beta diversity A community species diversity that is the total species diversity in a landscape. The area or landscape of interest may be of very different sizes in different situations, but it should encompass multiple sites or habitats as measured by alpha diversity. γ-diversity gamma diversity TBD: add logical definition The density of plants in an ecological community or population, often measured as the number of plants per area. plant density The density of seedlings in an ecological community or population, often measured as the number of seedlings per area. TBD: add logical definition seedling density The density of plants in a population or organisms (a single species), often measured as the number of plants per area. TBD: add logical definition plant density of a population The density of plants in an ecological community (multiple species), often measured as the number of plants per area. TBD: add logical definition plant density of an ecological community The density of seedlings in a population or organisms (a single species), often measured as the number of seedlings per area. TBD: add logical definition seedling density of a population The density of seedlings in an ecological community (multiple species), often measured as the number of plants per area. TBD: add logical definition seedling density of an ecological community A population process during which a population moves from one area to another. https://en.wikipedia.org/wiki/Migration The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. population migration A population migration during which a population of humans moves from one area to another with the intention of settling permanently in the new location. https://en.wikipedia.org/wiki/Human_migration The distance between the areas is not specified here, nor is the minimum distance required for such movements to be considered migrations. "Nomadic movements are normally not regarded as migrations as there is no intention to settle in the new place and because the movement is generally seasonal. Only a few nomadic people have retained this form of lifestyle in modern times. Also, the temporary movement of people for the purpose of travel, tourism, pilgrimages, or the commute is not regarded as migration, in the absence of an intention to live and settle in the visited places." - https://en.wikipedia.org/wiki/Human_migration human population migration A migratory population of humans, travelling with the intention of settling in a new area. https://en.wikipedia.org/wiki/Human_migration human migratory population A material entity consisting of multiple components that are causally integrated. May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43 Chris Mungall http://www.jbiomedsem.com/content/4/1/43 system