Skip to content

Commit

Permalink
Merge branch 'master' into issue-1574
Browse files Browse the repository at this point in the history
  • Loading branch information
@pbuttigieg
pbuttigieg authored Jan 14, 2025
2 parents 5195346 + 4fd549c commit 984a8db
Show file tree
Hide file tree
Showing 3 changed files with 126 additions and 364 deletions.
87 changes: 82 additions & 5 deletions src/envo/envo-edit.owl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4465,6 +4465,15 @@ Declaration(NamedIndividual(<https://www.wikidata.org/wiki/Q2>))
Declaration(NamedIndividual(<https://www.wikidata.org/wiki/Q2306597>))
Declaration(NamedIndividual(<https://www.wikidata.org/wiki/Q525>))
Declaration(NamedIndividual(<https://www.wikidata.org/wiki/Q715269>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605010>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605011>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605012>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605013>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605014>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605015>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605017>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605018>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605019>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000116>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000232>))
Expand Down Expand Up @@ -4538,6 +4547,75 @@ Declaration(AnnotationProperty(<http://xmlns.com/foaf/0.1/homepage>))
# Annotation Properties
############################

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605010> (NMDC environmental context value sets)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605010> "Root of the NMDC environmental context value set hierarchy. This property organizes subset properties used to annotate EnvO classes relevant for MIxS environmental context fields (e.g., env_broad_scale, env_local_scale, env_medium_scale). This structure guides data annotation in systems like NCBI BioSample, refining recommendations from the ENVO-MIxS integration guide, addressing questions such as 'Which EnvO classes are reasonable for populating the env_broad_scale field in a soil sample versus a water sample.\"")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605010> "NMDC environmental context value sets"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605010> <https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605010> <http://www.geneontology.org/formats/oboInOwl#SubsetProperty>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605011> (NMDC Soil value sets)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605011> "Subset of NMDC environmental context value sets for annotating EnvO classes suitable for MIxS environmental context fields related to soil samples. Recommended for use in metadata preparation for repositories like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605011> "NMDC Soil value sets"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605011> <https://genomicsstandardsconsortium.github.io/mixs/0016012/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605011> <http://purl.obolibrary.org/obo/ENVO_03605010>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605012> (NMDC Water value sets)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605012> "Subset of NMDC environmental context value sets for annotating EnvO classes applicable to MIxS environmental context fields in water-related samples. Intended for use in metadata annotation workflows, including submissions to NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605012> "NMDC Water value sets"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605012> <https://genomicsstandardsconsortium.github.io/mixs/0016014/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605012> <http://purl.obolibrary.org/obo/ENVO_03605010>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605013> (NMDC Soil broad scale value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605013> "Used to annotate EnvO classes appropriate for the MIxS env_broad_scale field in soil sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605013> "NMDC Soil broad scale value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605013> <https://genomicsstandardsconsortium.github.io/mixs/0000012/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605013> <https://genomicsstandardsconsortium.github.io/mixs/0016012/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605013> <http://purl.obolibrary.org/obo/ENVO_03605011>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605014> (NMDC Soil local scale value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605014> "Used to annotate EnvO classes relevant for the MIxS env_local_scale field in soil sample metadata. Recommended for standardizing annotations in systems such as NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605014> "NMDC Soil local scale value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605014> <https://genomicsstandardsconsortium.github.io/mixs/0000013/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605014> <https://genomicsstandardsconsortium.github.io/mixs/0016012/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605014> <http://purl.obolibrary.org/obo/ENVO_03605011>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605015> (NMDC Soil environmental medium value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605015> "Used to annotate EnvO classes appropriate for the MIxS env_medium field in soil sample records. Intended to guide consistent environmental medium annotations in systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605015> "NMDC Soil environmental medium value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605015> <https://genomicsstandardsconsortium.github.io/mixs/0000014/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605015> <https://genomicsstandardsconsortium.github.io/mixs/0016012/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605015> <http://purl.obolibrary.org/obo/ENVO_03605011>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605017> (NMDC Water broad scale value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605017> "Used to annotate EnvO classes appropriate for the MIxS env_broad_scale field in water sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605017> "NMDC Water broad scale value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605017> <https://genomicsstandardsconsortium.github.io/mixs/0000012/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605017> <https://genomicsstandardsconsortium.github.io/mixs/0016014/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605017> <http://purl.obolibrary.org/obo/ENVO_03605012>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605018> (NMDC Water local scale value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605018> "Used to annotate EnvO classes appropriate for the MIxS env_local_scale field in water sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605018> "NMDC Water local scale value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605018> <https://genomicsstandardsconsortium.github.io/mixs/0000013/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605018> <https://genomicsstandardsconsortium.github.io/mixs/0016014/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605018> <http://purl.obolibrary.org/obo/ENVO_03605012>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605019> (NMDC Water environmental medium value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605019> "Used to annotate EnvO classes appropriate for the MIxS env_medium field in water sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605019> "NMDC Water environmental medium value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605019> <https://genomicsstandardsconsortium.github.io/mixs/0000014/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605019> <https://genomicsstandardsconsortium.github.io/mixs/0016014/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605019> <http://purl.obolibrary.org/obo/ENVO_03605012>)

# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0000112> (example of usage)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/IAO_0000112> "example of usage")
Expand Down Expand Up @@ -14166,7 +14244,6 @@ AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <ht
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00002149> "LTER:701")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00002149> "SWEETRealm:SeaWater")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00002149> "https://en.wikipedia.org/wiki/Sea_water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00002149> "ocean water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00002149> "seawater")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym> <http://purl.obolibrary.org/obo/ENVO_00002149> "sea water")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00002149> "This definition is scoped to Earth's ocean, although it may also be applied to other telluric planets, moons, and similar astronomical bodies. As more evidence of other ocean types (and thus ocean water) emerge, this class may be made a subclass of a more general \"ocean\" class, and its label changed accordingly. This classes PURL / PID will remain stable. https://en.wikipedia.org/wiki/Planetary_oceanography")
Expand All @@ -14178,8 +14255,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00002149> <http://purl.obolibrar

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00002150> "Coastal sea water is sea water that is adjacent to a coast.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal ocean water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal oceanic water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal ocean water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal oceanic water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal seawater")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#inSubset> <http://purl.obolibrary.org/obo/ENVO_00002150> <http://purl.obolibrary.org/obo/envo#envoPolar>)
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_00002150> "The limits of what qualifies as \"adjacent to\" vary greatly. This should be defined on a data level and is left intentionally fuzzy here. The label is \"coastal sea water\" rather than \"coastal water\" as some large lakes are often said to have coasts.")
Expand Down Expand Up @@ -37678,13 +37755,13 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_01001964> <http://purl.obolibrar

# Class: <http://purl.obolibrary.org/obo/ENVO_01001966> (coastal ocean water)

AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001966> "Coastal sea water is sea water that is adjacent to a coast.")
AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_01001966> "Coastal ocean water is sea water that is adjacent to a coast.")
AnnotationAssertion(<http://purl.org/dc/elements/1.1/creator> <http://purl.obolibrary.org/obo/ENVO_01001966> <https://orcid.org/0000-0002-4366-3088>)
AnnotationAssertion(<http://purl.org/dc/elements/1.1/date> <http://purl.obolibrary.org/obo/ENVO_01001966> "2024-12-09T18:39:16Z"^^xsd:dateTime)
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym> <http://purl.obolibrary.org/obo/ENVO_01001966> "coastal water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01001966> "coastal ocean water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01001966> "coastal oceanic water")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_01001966> "coastal seawater")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_01001966> "coastal seawater")
AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_01001966> "The limits of what qualifies as \"adjacent to\" vary greatly. This should be defined on a data level and is left intentionally fuzzy here. The label is \"coastal sea water\" rather than \"coastal water\" as some large lakes are often said to have coasts.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_01001966> "coastal ocean water"@en)
EquivalentClasses(<http://purl.obolibrary.org/obo/ENVO_01001966> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/ENVO_00002149> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0002220> <http://purl.obolibrary.org/obo/ENVO_00000303>)))
Expand Down
Loading

0 comments on commit 984a8db

Please sign in to comment.