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added new object property has roost for issue #453 #672

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merged 16 commits into from
Jun 23, 2023
Merged

added new object property has roost for issue #453 #672

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566eb46
added new object property has roost for issue #453
diatomsRcool Jan 18, 2023
a722436
add habitat to other_import to be used as domain/range in relations
wdduncan Mar 29, 2023
952cbbc
change range of to
wdduncan Mar 29, 2023
ad439b1
change dc:creator to dcterms:contributor
wdduncan Mar 29, 2023
15e1380
remove habitat from other_imports
wdduncan Mar 30, 2023
ecc9176
update branch with master
wdduncan Mar 30, 2023
b629fe0
add "habitat" it envo_terms
wdduncan Mar 30, 2023
f00d557
fix dc/dce confusions
wdduncan Mar 30, 2023
a2e82f8
add habitat class using ODK
wdduncan Mar 30, 2023
33bed46
Update ro-edit.owl
matentzn Mar 30, 2023
6ef9d13
Delete other_import.owl
matentzn Mar 30, 2023
ad6d846
merge in updates from master
wdduncan Jun 20, 2023
c34e8bf
add domain of organism
wdduncan Jun 20, 2023
a3eac0e
add range habitat
wdduncan Jun 20, 2023
875a457
adding example of usage for has roost
diatomsRcool Jun 23, 2023
3f63c09
Merge branch 'master' into thessen-1
anitacaron Jun 23, 2023
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27 changes: 19 additions & 8 deletions src/ontology/ro-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -499,6 +499,7 @@ Declaration(ObjectProperty(obo:RO_0008505))
Declaration(ObjectProperty(obo:RO_0008506))
Declaration(ObjectProperty(obo:RO_0008507))
Declaration(ObjectProperty(obo:RO_0008508))
Declaration(ObjectProperty(obo:RO_0008509))
Declaration(ObjectProperty(obo:RO_0009001))
Declaration(ObjectProperty(obo:RO_0009002))
Declaration(ObjectProperty(obo:RO_0009003))
Expand Down Expand Up @@ -1726,8 +1727,8 @@ ObjectPropertyRange(obo:RO_0002103 ObjectUnionOf(obo:CL_0000540 ObjectSomeValues
AnnotationAssertion(obo:IAO_0000112 obo:RO_0002104 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]"@en)
AnnotationAssertion(obo:IAO_0000114 obo:RO_0002104 obo:IAO_0000125)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002104 "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part.")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 <https://orcid.org/0000-0001-9990-8331>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002104 <https://orcid.org/0000-0003-1617-8244>)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002104 <http://www.ncbi.nlm.nih.gov/pubmed/19243617>)
AnnotationAssertion(obo:IAO_0000424 obo:RO_0002104 "<http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)")
Expand Down Expand Up @@ -2082,8 +2083,8 @@ SubObjectPropertyOf(obo:RO_0002160 obo:RO_0002162)

AnnotationAssertion(obo:IAO_0000114 obo:RO_0002162 obo:IAO_0000125)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002162 "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 <https://orcid.org/0000-0001-9227-417X>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002162 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002162 <http://www.ncbi.nlm.nih.gov/pubmed/17921072>)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002162 <http://www.ncbi.nlm.nih.gov/pubmed/20973947>)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002162 subsets:ro-eco)
Expand Down Expand Up @@ -2197,9 +2198,9 @@ FunctionalObjectProperty(obo:RO_0002201)

AnnotationAssertion(obo:IAO_0000114 obo:RO_0002202 obo:IAO_0000125)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002202 "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 <https://orcid.org/0000-0001-9114-8737>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 <https://orcid.org/0000-0002-7073-9172>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 <https://orcid.org/0000-0001-9114-8737>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002202 <https://orcid.org/0000-0003-1980-3228>)
AnnotationAssertion(rdfs:comment obo:RO_0002202 "This is the transitive form of the develops from relation")
AnnotationAssertion(rdfs:label obo:RO_0002202 "develops from"@en)
Expand Down Expand Up @@ -2304,9 +2305,9 @@ SubObjectPropertyOf(obo:RO_0002210 obo:RO_0002203)
# Object Property: obo:RO_0002211 (regulates)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002211 "p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q.")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 <https://orcid.org/0000-0001-7476-6306>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 <https://orcid.org/0000-0002-3837-8864>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002211 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002211 <http://purl.obolibrary.org/obo/ro/docs/causal-relations>)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002211 "GO")
AnnotationAssertion(obo:IAO_0000232 obo:RO_0002211 "Regulation precludes parthood; the regulatory process may not be within the regulated process.")
Expand Down Expand Up @@ -2705,9 +2706,9 @@ SubObjectPropertyOf(obo:RO_0002255 obo:RO_0002385)

AnnotationAssertion(obo:IAO_0000114 obo:RO_0002256 obo:IAO_0000125)
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002256 "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 <https://orcid.org/0000-0001-9114-8737>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 <https://orcid.org/0000-0002-7073-9172>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002256 <https://orcid.org/0000-0001-9114-8737>)
AnnotationAssertion(obo:IAO_0000118 obo:RO_0002256 "induced by")
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002256 <http://www.ncbi.nlm.nih.gov/pubmed/20064205>)
AnnotationAssertion(obo:IAO_0000119 obo:RO_0002256 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)")
Expand Down Expand Up @@ -2954,9 +2955,9 @@ SubObjectPropertyOf(obo:RO_0002305 obo:RO_0004046)
# Object Property: obo:RO_0002309 (has exposure stimulus)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0002309 "A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.")
AnnotationAssertion(dc:contributor obo:RO_0002309 <https://orcid.org/0000-0001-6996-0040>)
AnnotationAssertion(dc:contributor obo:RO_0002309 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(dc:contributor obo:RO_0002309 <https://orcid.org/0000-0002-8461-9745>)
AnnotationAssertion(dc:contributor obo:RO_0002309 <https://orcid.org/0000-0001-6996-0040>)
AnnotationAssertion(oboInOwl:created_by obo:RO_0002309 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(oboInOwl:creation_date obo:RO_0002309 "2017-06-05T17:35:04Z"^^xsd:dateTime)
AnnotationAssertion(rdfs:label obo:RO_0002309 "has exposure stimulus")
Expand Down Expand Up @@ -3869,9 +3870,9 @@ SubObjectPropertyOf(obo:RO_0002438 obo:RO_0002574)
AnnotationAssertion(obo:IAO_0000112 obo:RO_0002439 "A wasp killing a Monarch larva in order to feed to offspring [http://www.inaturalist.org/observations/2942824]")
AnnotationAssertion(obo:IAO_0000112 obo:RO_0002439 "Baleen whale preys on krill")
AnnotationAssertion(obo:IAO_0000115 obo:RO_0002439 "An interaction relationship involving a predation process, where the subject kills the target in order to eat it or to feed to siblings, offspring or group members")
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 <https://orcid.org/0000-0001-7134-3324>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 <https://orcid.org/0000-0003-3138-4118>)
AnnotationAssertion(obo:IAO_0000117 obo:RO_0002439 <https://orcid.org/0000-0001-7134-3324>)
AnnotationAssertion(obo:IAO_0000118 obo:RO_0002439 "is subject of predation interaction with")
AnnotationAssertion(obo:IAO_0000118 obo:RO_0002439 "preys upon")
AnnotationAssertion(oboInOwl:inSubset obo:RO_0002439 subsets:ro-eco)
Expand Down Expand Up @@ -5828,6 +5829,16 @@ AnnotationAssertion(obo:IAO_0000115 obo:RO_0008508 "inverse of lays eggs on")
AnnotationAssertion(rdfs:label obo:RO_0008508 "has eggs laid on by")
SubObjectPropertyOf(obo:RO_0008508 obo:RO_0002619)

# Object Property: obo:RO_0008509 (has roost)

AnnotationAssertion(obo:IAO_0000115 obo:RO_0008509 "x 'has roost' y if and only if: x is an organism, y is a habitat, and y can support rest behaviors x.")
AnnotationAssertion(dce:creator obo:RO_0008509 <http://orcid.org/0000-0002-2908-3327>)
AnnotationAssertion(dce:date obo:RO_0008509 "2023-01-18T14:28:21Z"^^xsd:dateTime)
AnnotationAssertion(oboInOwl:inSubset obo:RO_0008509 subsets:ro-eco)
AnnotationAssertion(rdfs:comment obo:RO_0008509 "A population of xs will possess adaptations (either evolved naturally or via artifical selection) which permit it to rest in y.")
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can you please give a concrete example with terms in existing OBO ontologies as subject/predicate annotated with IAO:0000112 (example of usage)

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@cthoyt Do you mean just an example of how the term is used? E.g., "bird has roost some nest"

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yeah, that would be great, as long as it gives explicit references to Bird and Nest using OBO PURLs

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I don't think examples of usage have to use obo purls. Free text is fine. The purpose of "example of usage" is to provide extra context to disambiguate the term.

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I am just hoping there is a realistic, demonstrable scenario in which this relation will get used... like if there are no IRIs corresponding to entities that would actually use this, then how can we be sure this will be a useful relation? This is for the benefit of future users, who without a concrete example might not be able to figure out how to use the relationship

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This is for the benefit of future users, who without a concrete example might not be able to figure out how to use the relationship

I agree. That is the purpose of the annotation. We haven't required that OBO PURLs be used. See examples for example of usage in adjacent to, capable of, characteristic of, and many more ...

But @diatomsRcool if you can provide an example OBO PURLs, that would be nice.

AnnotationAssertion(rdfs:label obo:RO_0008509 "has roost"@en)
SubObjectPropertyOf(obo:RO_0008509 obo:RO_0002303)

# Object Property: obo:RO_0009001 (has substance added)

AnnotationAssertion(obo:IAO_0000112 obo:RO_0009001 "muffin 'has substance added' some 'baking soda'"@en)
Expand Down Expand Up @@ -5888,10 +5899,10 @@ AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "A drought sensitivity trait
AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)")
AnnotationAssertion(obo:IAO_0000112 obo:RO_0009501 "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.")
AnnotationAssertion(obo:IAO_0000115 obo:RO_0009501 "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.")
AnnotationAssertion(dc:contributor obo:RO_0009501 <https://orcid.org/0000-0001-6996-0040>)
AnnotationAssertion(dc:contributor obo:RO_0009501 <https://orcid.org/0000-0002-6601-2165>)
AnnotationAssertion(dc:contributor obo:RO_0009501 <https://orcid.org/0000-0002-7073-9172>)
AnnotationAssertion(dc:contributor obo:RO_0009501 <https://orcid.org/0000-0002-8461-9745>)
AnnotationAssertion(dc:contributor obo:RO_0009501 <https://orcid.org/0000-0001-6996-0040>)
AnnotationAssertion(Annotation(oboInOwl:hasDbXref "RO:cjm") oboInOwl:hasExactSynonym obo:RO_0009501 "triggered by process")
AnnotationAssertion(rdfs:label obo:RO_0009501 "realized in response to"@en)
AnnotationAssertion(rdfs:seeAlso obo:RO_0009501 "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit"^^xsd:anyURI)
Expand Down