diff --git a/src/ontology/apollo_sv-edit.owl b/src/ontology/apollo_sv-edit.owl index 1a429af..970c738 100644 --- a/src/ontology/apollo_sv-edit.owl +++ b/src/ontology/apollo_sv-edit.owl @@ -6469,7 +6469,7 @@ can't recall whether we should use process or processual_entity for future An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host - host + host organism @@ -13437,6 +13437,33 @@ By "similar vaccines" we typically mean same pathogen, but could be si + + + + + guardian's intent to have a ward under their care vaccinated + An intentionality inhering in a person bearing a guardian role and that is directed at their future participation in an authorization for the vaccination or other immunization of a person under their care and who bears a ward role. + William R. Hogan + The intent of a guardian to have a ward under their care vaccinated in the near future. + Legally, this covers the situation of a parent intending to have their child vaccinated. That is because the parent(s) is(are) the natural gaurdian of the child. Other individuals appointed by a court as guardian are legal guardians. If the specific case of parent / child is required, we could create a subclass of this one where the guardian = parent of the ward, and ward = child. However, that could get into issues of adoption, etc. At the current time we do not have guardian role and ward role classes in OMRSE. + intent to have a ward vaccinated + + + + + + + + + An intent to have a ward vaccinated where the guardian is a parent (natural or adoptive) and the ward is a child (natural or adopted) of that parent, and the parent has not otherwise been legally barred from making healthcare decisions for the child. + William R. Hogan + Intent to have one's child vaccinated. + The case of adult children is eliminated through the use of guardian and ward roles in the definition. The parent no longer has a guardian role, and the child no longer has a ward role, once the child is of legal age to make their own decisions. That is, those roles cease to exist. + intent to have a child vaccinated + + + + diff --git a/src/ontology/imports/geo_import.owl b/src/ontology/imports/geo_import.owl index 138634e..23078de 100644 --- a/src/ontology/imports/geo_import.owl +++ b/src/ontology/imports/geo_import.owl @@ -599,8 +599,8 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor preferred label"@en) -AnnotationAssertion(rdfs:label "editor preferred term"@en) AnnotationAssertion(rdfs:label "editor preferred term") +AnnotationAssertion(rdfs:label "editor preferred term"@en) AnnotationAssertion(rdfs:label "editor preferred term~editor preferred label") # Annotation Property: (example of usage) @@ -657,8 +657,8 @@ We also have the outstanding issue of how to aim different definitions to differ AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "textual definition") # Annotation Property: (editor note) @@ -688,8 +688,8 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") AnnotationAssertion(rdfs:label "alternative label"@en) @@ -1013,8 +1013,8 @@ SubAnnotationPropertyOf( (Source) -AnnotationAssertion(rdfs:label "Source"@en-us) AnnotationAssertion(rdfs:label "Source") +AnnotationAssertion(rdfs:label "Source"@en-us) # Annotation Property: (has_alternative_id) @@ -1160,7 +1160,6 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -1203,8 +1202,8 @@ ObjectPropertyRange( "c-has-part_at") AnnotationAssertion( "hasContinuantPartAt") -AnnotationAssertion( "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])"@en) AnnotationAssertion( "[copied from inverse property 'part of continuant at all times that whole exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t)") +AnnotationAssertion( "b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001])"@en) AnnotationAssertion( "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'.") AnnotationAssertion( "[copied from inverse property 'part of continuant at all times that whole exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times'") AnnotationAssertion( "http://purl.obolibrary.org/obo/bfo.owl") @@ -1257,9 +1256,9 @@ AnnotationAssertion( "Mary’s arm continuant_part_of Mary in the time of her life prior to her operation"@en) AnnotationAssertion( "the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists."@en) AnnotationAssertion( "[copied from inverse property 'has continuant part at all times that part exists'] forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t)") +AnnotationAssertion( "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.") AnnotationAssertion( "BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001])"@en) AnnotationAssertion( "BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion."@en) -AnnotationAssertion( "Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'.") AnnotationAssertion( "BFO2 Reference: continuant") AnnotationAssertion( "BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region.") AnnotationAssertion( "[copied from inverse property 'has continuant part at all times that part exists'] This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times'") @@ -1585,8 +1584,8 @@ ObjectPropertyRange( ObjectIntersect # Object Property: (has_specified_input) -AnnotationAssertion( "has_specified_input"@en) AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "has_specified_input"@en) AnnotationAssertion( "see is_input_of example_of_usage"@en) AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_input_of"@en) @@ -1615,8 +1614,8 @@ SubObjectPropertyOf( (has_specified_output) -AnnotationAssertion( "has_specified_output"@en) AnnotationAssertion( "has_specified_output") +AnnotationAssertion( "has_specified_output"@en) AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_output_of"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) @@ -1632,8 +1631,8 @@ ObjectPropertyDomain( (is_specified_output_of) -AnnotationAssertion( "is_specified_output_of"@en) AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( "is_specified_output_of"@en) AnnotationAssertion( ) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion( "Alan Ruttenberg"@en) @@ -2361,9 +2360,9 @@ AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) AnnotationAssertion( "the restaurants in Palo Alto"@en) AnnotationAssertion( "your collection of Meissen ceramic plates."@en) -AnnotationAssertion( "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)."@en) AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion( "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)."@en) AnnotationAssertion(Annotation( ) "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.") AnnotationAssertion(Annotation( ) "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])"@en) AnnotationAssertion(Annotation( ) "(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] ") @@ -2690,7 +2689,7 @@ AnnotationAssertion(rdfs:comment AnnotationAssertion(rdfs:label "geopolitical dependency"@en) SubClassOf( ) -# Class: (aggregate of major administrative subdivisions) +# Class: (group of major administrative subdivisions) AnnotationAssertion( "An aggregate of governmental organizations that is not itself a major administrative subdivision and whose members are only major administrative subdivisions that have some feature in common."@en) AnnotationAssertion( "Amanda Hicks"@en) @@ -3089,8 +3088,8 @@ AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000261") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3152,8 +3151,8 @@ AnnotationAssertion( "digital_entity"@en) AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000244") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3192,6 +3191,7 @@ AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some @@ -3199,7 +3199,6 @@ process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief"@en) -AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Chris Stoeckert"@en) AnnotationAssertion( "PERSON: Jonathan Rees"@en) @@ -3302,12 +3301,12 @@ SubClassOf( "obsolete_study interpretation"@en) AnnotationAssertion( ) AnnotationAssertion( "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses"@en) -AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"") AnnotationAssertion( "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.") +AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "Lawrence Hunter"@en) -AnnotationAssertion( "PERSON: Jennifer Fostel"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg") +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) AnnotationAssertion( "PERSON: Melanie Courtot") AnnotationAssertion( "conclusion") AnnotationAssertion( "OBI_0000005") @@ -3393,8 +3392,8 @@ AnnotationAssertion( "Replaced by defined version of figure"@en) AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000027") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_report figure"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3482,12 +3481,12 @@ SubClassOf( "report element"@en) AnnotationAssertion( ) AnnotationAssertion( "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)."@en) -AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "2009-03-16: needs some more work (clarify relations).") AnnotationAssertion( "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.") AnnotationAssertion( "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.") AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "Replaced by textual entity and figure") +AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Allyson Lister"@en) AnnotationAssertion( "PERSON: Melanie Courtot") @@ -3505,8 +3504,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000222") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary executable"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3533,8 +3532,8 @@ AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000265") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete_report table"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -3626,8 +3625,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000195") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital document"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -5217,8 +5216,8 @@ SubClassOf( "database extract, transform, and load process"@en) AnnotationAssertion( "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second."@en) -AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") +AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) AnnotationAssertion( "PERSON:Alan Ruttenberg") AnnotationAssertion( "ETL"@en) AnnotationAssertion( "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load") @@ -5893,7 +5892,7 @@ SubClassOf( (obsolete_class) AnnotationAssertion( "http://www.geneontology.org/formats/oboInOwl") -AnnotationAssertion( _:genid2147484124) +AnnotationAssertion( _:genid2147483648) AnnotationAssertion(rdfs:label "obsolete_class"@en) @@ -6093,8 +6092,8 @@ DifferentIndividuals( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ido_import.owl b/src/ontology/imports/ido_import.owl index af40396..9e73feb 100644 --- a/src/ontology/imports/ido_import.owl +++ b/src/ontology/imports/ido_import.owl @@ -262,8 +262,8 @@ We also have the outstanding issue of how to aim different definitions to differ AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "textual definition") # Annotation Property: (editor note) @@ -276,7 +276,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (term editor) +# Annotation Property: (definition editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -287,7 +287,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "term editor"@en) -# Annotation Property: (alternative term) +# Annotation Property: (alternative label) AnnotationAssertion( "alternative term"@en) AnnotationAssertion( ) @@ -303,8 +303,8 @@ AnnotationAssertion( ) AnnotationAssertion( "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"@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) -AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w") +AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition source"@en) @@ -513,7 +513,6 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -528,7 +527,7 @@ AnnotationAssertion(rdfs:label "con AnnotationAssertion(rdfs:label "results_in"@en) -# Object Property: (inheres in) +# Object Property: (characteristic of) AnnotationAssertion( "inheres in"@en) AnnotationAssertion( "this fragility inheres in this vase"@en) @@ -540,7 +539,7 @@ AnnotationAssertion( "inheres in"@en) InverseObjectProperties( ) -# Object Property: (bearer of) +# Object Property: (has characteristic) AnnotationAssertion( "bearer of"@en) AnnotationAssertion( "this apple is bearer of this red color"@en) @@ -692,8 +691,8 @@ SubObjectPropertyOf( (results in formation of) -AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) AnnotationAssertion( "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.") +AnnotationAssertion( "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)"@en) AnnotationAssertion( ) AnnotationAssertion( "Chris Mungall") AnnotationAssertion( "GOC:mtg_berkeley_2013") @@ -979,7 +978,7 @@ AnnotationAssertion(rdfs:isDefinedBy "role"@en) SubClassOf( ) -# Class: (fiat object) +# Class: (fiat object part) AnnotationAssertion( "fiat-object") AnnotationAssertion( "FiatObjectPart") @@ -1014,9 +1013,9 @@ AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) AnnotationAssertion( "the restaurants in Palo Alto"@en) AnnotationAssertion( "your collection of Meissen ceramic plates."@en) -AnnotationAssertion( "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)."@en) AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion( "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)."@en) AnnotationAssertion(Annotation( ) "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.") AnnotationAssertion(Annotation( ) "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])"@en) AnnotationAssertion(Annotation( ) "(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] ") @@ -1322,8 +1321,8 @@ AnnotationAssertion( "Alexander Diehl") AnnotationAssertion( "Lindsay Cowell") AnnotationAssertion( "opportunitistic pathogenic disposition"@en) -AnnotationAssertion(rdfs:comment "This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin)."@en) AnnotationAssertion(rdfs:comment "The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.") +AnnotationAssertion(rdfs:comment "This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin)."@en) AnnotationAssertion(rdfs:label "opportunistic infectious disposition"@en) SubClassOf( ) SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))))))) @@ -1679,7 +1678,7 @@ AnnotationAssertion( "Lindsay Cowell") AnnotationAssertion(rdfs:comment "An organism begins bearing a particular host role as soon as the extended organism contains the relevant material entity, regardless of that entity's location in the extended organism. An establishment process is any process by which the entity reaches a location in the extended organism in which it can persist and continue its lifecycle. For example, an organism is host to a virus as soon as any part of the extended organism is occupied by virus particles. During an establishment process, virus particles enter host cells of the relevant type, and viral DNA is integrated into host DNA."@en) AnnotationAssertion(rdfs:label "establishment of localization in host"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) SubClassOf( ) # Class: (appearance of disorder) @@ -1804,7 +1803,7 @@ AnnotationAssertion( "life-death temporal boundary") SubClassOf( ) -# Class: (Obsolete Class) +# Class: (obsolete_class) AnnotationAssertion(rdfs:label "Obsolete Class") @@ -1858,7 +1857,7 @@ AnnotationAssertion(rdfs:label "unc AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) AnnotationAssertion(rdfs:label "pending final vetting"@en) -# Individual: (core) +# Individual: (obsolete_core) AnnotationAssertion( "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) diff --git a/src/ontology/imports/pno_import.owl b/src/ontology/imports/pno_import.owl index f2f8229..be834d2 100644 --- a/src/ontology/imports/pno_import.owl +++ b/src/ontology/imports/pno_import.owl @@ -476,8 +476,8 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor preferred label"@en) -AnnotationAssertion(rdfs:label "editor preferred term"@en) AnnotationAssertion(rdfs:label "editor preferred term") +AnnotationAssertion(rdfs:label "editor preferred term"@en) # Annotation Property: (example of usage) @@ -545,7 +545,7 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (term editor) +# Annotation Property: (definition editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -561,8 +561,8 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") AnnotationAssertion(rdfs:label "alternative label"@en) @@ -990,7 +990,6 @@ AnnotationAssertion(rdfs:comment "P AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "occurs in"@en) InverseObjectProperties( ) -ObjectPropertyDomain( ) ObjectPropertyRange( ) # Object Property: (contains process) @@ -1279,8 +1278,8 @@ IrreflexiveObjectProperty() # Object Property: (has_specified_input) -AnnotationAssertion( "has_specified_input"@en) AnnotationAssertion( "has_specified_input") +AnnotationAssertion( "has_specified_input"@en) AnnotationAssertion( "see is_input_of example_of_usage"@en) AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_input_of"@en) @@ -1301,8 +1300,8 @@ AnnotationAssertion(rdfs:label "is_ # Object Property: (has_specified_output) -AnnotationAssertion( "has_specified_output"@en) AnnotationAssertion( "has_specified_output") +AnnotationAssertion( "has_specified_output"@en) AnnotationAssertion( ) AnnotationAssertion( "The inverse property of is_specified_output_of"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) @@ -1318,15 +1317,15 @@ ObjectPropertyDomain( (is_specified_output_of) -AnnotationAssertion( "is_specified_output_of"@en) AnnotationAssertion( "is_specified_output_of") +AnnotationAssertion( "is_specified_output_of"@en) AnnotationAssertion( ) AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion( "PERSON:Bjoern Peters") AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is_specified_output_of"@en) AnnotationAssertion(rdfs:label "is_specified_output_of") +AnnotationAssertion(rdfs:label "is_specified_output_of"@en) EquivalentObjectProperties( ObjectInverseOf()) SubObjectPropertyOf( ) ObjectPropertyRange( ) @@ -1344,7 +1343,7 @@ AnnotationAssertion(rdfs:label "char InverseObjectProperties( ) FunctionalObjectProperty() -# Object Property: (bearer_of) +# Object Property: (has characteristic) AnnotationAssertion( "bearer of"@en) AnnotationAssertion( "this apple is bearer of this red color"@en) @@ -1372,7 +1371,7 @@ InverseObjectProperties( ) ObjectPropertyRange( ) -# Object Property: (has_participant) +# Object Property: (has participant) AnnotationAssertion( "has participant"@en) AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) @@ -2032,9 +2031,9 @@ AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) AnnotationAssertion( "the restaurants in Palo Alto"@en) AnnotationAssertion( "your collection of Meissen ceramic plates."@en) -AnnotationAssertion( "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)."@en) AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion( "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)."@en) AnnotationAssertion(Annotation( ) "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.") AnnotationAssertion(Annotation( ) "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])"@en) AnnotationAssertion(Annotation( ) "(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] ") @@ -2448,8 +2447,8 @@ AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000261") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2511,8 +2510,8 @@ AnnotationAssertion( "digital_entity"@en) AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000244") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary digital entity"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2551,6 +2550,7 @@ AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some @@ -2558,7 +2558,6 @@ process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief"@en) -AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Chris Stoeckert"@en) AnnotationAssertion( "PERSON: Jonathan Rees"@en) @@ -2658,12 +2657,12 @@ SubClassOf( "obsolete_study interpretation"@en) AnnotationAssertion( ) AnnotationAssertion( "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses"@en) -AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"") AnnotationAssertion( "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.") +AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) AnnotationAssertion( "Lawrence Hunter"@en) -AnnotationAssertion( "PERSON: Jennifer Fostel"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg") +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) AnnotationAssertion( "PERSON: Melanie Courtot") AnnotationAssertion( "conclusion") AnnotationAssertion( "OBI_0000005") @@ -2749,8 +2748,8 @@ AnnotationAssertion( "Replaced by defined version of figure"@en) AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000027") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_report figure"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2838,12 +2837,12 @@ SubClassOf( "report element"@en) AnnotationAssertion( ) AnnotationAssertion( "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)."@en) -AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "2009-03-16: needs some more work (clarify relations).") AnnotationAssertion( "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.") AnnotationAssertion( "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.") AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "Replaced by textual entity and figure") +AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) AnnotationAssertion( "PERSON: Allyson Lister"@en) AnnotationAssertion( "PERSON: Melanie Courtot") @@ -2861,8 +2860,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digital entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000222") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_binary executable"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2889,8 +2888,8 @@ AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion") AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000265") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete_report table"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -2982,8 +2981,8 @@ AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 superclass was 'digial entity'"@en) AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( "OBI_0000195") +AnnotationAssertion( "group:OBI"@en) AnnotationAssertion( ) AnnotationAssertion(rdfs:label "obsolete2_digital document"@en) AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) @@ -4572,8 +4571,8 @@ SubClassOf( "database extract, transform, and load process"@en) AnnotationAssertion( "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second."@en) -AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") +AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) AnnotationAssertion( "PERSON:Alan Ruttenberg") AnnotationAssertion( "ETL"@en) AnnotationAssertion( "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load") @@ -4703,8 +4702,8 @@ AnnotationAssertion( "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) AnnotationAssertion( "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "proper name"@en) AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) AnnotationAssertion( "Mathias Brochhausen") @@ -4794,8 +4793,8 @@ SubClassOf( "A dubbing process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) AnnotationAssertion( "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "dubbing process"@en) AnnotationAssertion( "naming"@en) AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) @@ -4820,8 +4819,8 @@ SubClassOf( "A personal name is a proper name identifying an individual person."@en) AnnotationAssertion( "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "http://en.wikipedia.org/wiki/Personal_name") AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) AnnotationAssertion(rdfs:comment "Personal names \"today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names.\" (http://en.wikipedia.org/wiki/Personal_name)"@en) @@ -4836,8 +4835,8 @@ SubClassOf( "A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name"@en) AnnotationAssertion( "A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name"@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "first name"@en) AnnotationAssertion( "http://en.wikipedia.org/wiki/Given_name") AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) @@ -4850,8 +4849,8 @@ SubClassOf( ObjectSomeValuesFrom( "A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children."@en) AnnotationAssertion( "An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children."@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "last name"@en) AnnotationAssertion( "surname"@en) AnnotationAssertion( "http://en.wikipedia.org/wiki/Family_name") @@ -4867,8 +4866,8 @@ AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things."@en) AnnotationAssertion( "Alan Ruttenberg"@en) AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "Mathias Brochhausen") +AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion( "code map"@en) AnnotationAssertion( "code system"@en) AnnotationAssertion( "codeset"@en) @@ -5182,7 +5181,7 @@ SubClassOf( (pressure) -AnnotationAssertion( _:genid2147484058) +AnnotationAssertion( _:genid2147483649) AnnotationAssertion( "quality") AnnotationAssertion( ) AnnotationAssertion(rdfs:label "pressure"@en) @@ -5383,8 +5382,8 @@ DifferentIndividuals( ) SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/ro_import.owl b/src/ontology/imports/ro_import.owl index f512b09..39a491f 100644 --- a/src/ontology/imports/ro_import.owl +++ b/src/ontology/imports/ro_import.owl @@ -262,8 +262,8 @@ AnnotationAssertion( "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."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "example of usage"@en) AnnotationAssertion(rdfs:label "example of usage") +AnnotationAssertion(rdfs:label "example of usage"@en) # Annotation Property: (has curation status) @@ -300,8 +300,8 @@ Personally, I am more comfortable weakening definition to documentation, with in 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. "@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") +AnnotationAssertion(rdfs:label "definition"@en) # Annotation Property: (editor note) @@ -312,7 +312,7 @@ AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:label "editor note"@en) -# Annotation Property: (term editor) +# Annotation Property: (definition editor) AnnotationAssertion( "term editor"@en) AnnotationAssertion( ) @@ -327,8 +327,8 @@ AnnotationAssertion(rdfs:label "ter AnnotationAssertion( "alternative label"@en) AnnotationAssertion( ) AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) -AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") AnnotationAssertion(rdfs:label "alternative label"@en) @@ -453,7 +453,7 @@ SubAnnotationPropertyOf( ) -# Annotation Property: (has_broad_synonym) +# Annotation Property: (has broad synonym) AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") AnnotationAssertion( ) @@ -484,7 +484,7 @@ AnnotationAssertion(rdfs:label "has_narrow_synonym") AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") -# Annotation Property: (has_related_synonym) +# Annotation Property: (has related synonym) AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") AnnotationAssertion( ) @@ -527,12 +527,12 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "part of"@en) AnnotationAssertion(rdfs:label "part of") +AnnotationAssertion(rdfs:label "part of"@en) AnnotationAssertion(rdfs:seeAlso ) AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Part_of"^^xsd:anyURI) SubObjectPropertyOf( ) InverseObjectProperties( ) TransitiveObjectProperty() @@ -554,8 +554,8 @@ AnnotationAssertion( ) AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part"@en) AnnotationAssertion(rdfs:label "has part") +AnnotationAssertion(rdfs:label "has part"@en) SubObjectPropertyOf( ) TransitiveObjectProperty() @@ -627,11 +627,10 @@ AnnotationAssertion( ) AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:label "occurs in") +AnnotationAssertion(rdfs:label "occurs in"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Occurs_in"^^xsd:anyURI) InverseObjectProperties( ) -ObjectPropertyDomain( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -667,8 +666,8 @@ AnnotationAssertion( "bearer_of"@en) AnnotationAssertion( "is bearer of"@en) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has characteristic"@en) AnnotationAssertion(rdfs:label "has characteristic") +AnnotationAssertion(rdfs:label "has characteristic"@en) AnnotationAssertion(rdfs:seeAlso "https://github.com/oborel/obo-relations/pull/284") InverseFunctionalObjectProperty() ObjectPropertyRange( ) @@ -696,8 +695,8 @@ AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) AnnotationAssertion( "has_participant"@en) AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) AnnotationAssertion(rdfs:label "has participant") +AnnotationAssertion(rdfs:label "has participant"@en) ObjectPropertyDomain( ) ObjectPropertyDomain( ) ObjectPropertyRange( ) @@ -942,7 +941,7 @@ AnnotationAssertion(rdfs:label "ends SubObjectPropertyOf( ) TransitiveObjectProperty() -# Object Property: (immediately preceded by) +# Object Property: (immediately_preceded_by) AnnotationAssertion( "David Osumi-Sutherland") AnnotationAssertion( "starts_at_end_of") @@ -951,7 +950,7 @@ AnnotationAssertion(rdfs:label "imme SubObjectPropertyOf( ) InverseObjectProperties( ) -# Object Property: (immediately precedes) +# Object Property: (immediately_precedes) AnnotationAssertion( ) AnnotationAssertion( "David Osumi-Sutherland") @@ -1091,7 +1090,7 @@ AnnotationAssertion(rdfs:seeAlso ) SubObjectPropertyOf( ) -# Object Property: (obsolete has active participant) +# Object Property: (has active participant) AnnotationAssertion( "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y") AnnotationAssertion( ) @@ -1119,7 +1118,7 @@ SubObjectPropertyOf( ) ObjectPropertyRange( ) -# Object Property: (temporally related to) +# Object Property: (temporal relation) AnnotationAssertion( ) AnnotationAssertion( ) @@ -1348,8 +1347,8 @@ SubObjectPropertyOf( "inverse of enables") AnnotationAssertion( ) AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "enabled by"@en) AnnotationAssertion(rdfs:label "enabled by") +AnnotationAssertion(rdfs:label "enabled by"@en) AnnotationAssertion(rdfs:seeAlso "https://wiki.geneontology.org/Enabled_by"^^xsd:anyURI) SubObjectPropertyOf( ) SubObjectPropertyOf( ) @@ -1580,8 +1579,8 @@ SubObjectPropertyOf( (interacts with) AnnotationAssertion( "A relationship that holds between two entities in which the processes executed by the two entities are causally connected.") -AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion( "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.") +AnnotationAssertion( "Considering relabeling as 'pairwise interacts with'"^^xsd:anyURI) AnnotationAssertion( ) AnnotationAssertion( "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.") AnnotationAssertion( "in pairwise interaction with") @@ -2086,7 +2085,7 @@ AnnotationAssertion(rdfs:label "qua SubClassOf( ) SubClassOf( ObjectAllValuesFrom( )) -# Class: (characteristic) +# Class: (specifically dependent continuant) AnnotationAssertion( "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])"@en) AnnotationAssertion(rdfs:comment "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."@en) @@ -2493,10 +2492,10 @@ SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation( "true"^^xsd:boolean) Annotation(rdfs:comment "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z") Annotation(rdfs:label "infer input from direct reg") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ClassAtom( Variable()) ClassAtom( Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:comment "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'") Annotation(rdfs:label "enabling an MF enables its parts") Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) @@ -2505,19 +2504,19 @@ DLSafeRule(Body(ObjectPropertyAtom( V DLSafeRule(Annotation(rdfs:comment "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this.") Annotation(rdfs:label "inferring direct reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct neg reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Annotation(rdfs:label "inferring direct positive reg edge from input to regulatory subfunction") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "effector input is compound function input") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "Input of effector is input of its parent MF") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly regulates X, its parent MF directly regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:comment "if effector directly positively regulates X, its parent MF directly positively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "if effector directly negatively regulates X, its parent MF directly negatively regulates X") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Annotation(rdfs:label "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties).") Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ClassAtom(owl:Nothing Variable()) ClassAtom(owl:Nothing Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ObjectPropertyAtom( Variable() Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) AnnotationAssertion( "## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally'