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partial implementation of annotation properties for NMDC environmental context value sets #1593

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Jan 13, 2025
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partial implementation of annotation properties for NMDC environmental context value sets #1593

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71c8fc9
partial implementation of annotation properties for NMDC environmenta…
turbomam Jan 13, 2025
e47dbb2
Merge branch 'master' into 1590-create-nmdc-environmental-context-sub…
pbuttigieg Jan 13, 2025
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80 changes: 79 additions & 1 deletion src/envo/envo-edit.owl
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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 @@ -11159,9 +11237,9 @@ SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000424> <http://purl.obolibrar
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <https://en.wikipedia.org/wiki/Ocean_floor>) Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "MA:ma") <http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/ENVO_00000426> "A marine bed which lies below an ocean.")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> <http://purl.obolibrary.org/obo/ENVO_00000426> "FTT:1020")
AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean bed")
AnnotationAssertion(Annotation(rdfs:comment "When \"ocean basin\" is used in a hydrological sense, then \"ocean basin floor\" is any floor under seawater. In ENVO, the class \"ocean basin\" is used in a geological sense, which does not include all areas of ocean floor.") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean basin floor")
AnnotationAssertion(Annotation(<http://www.geneontology.org/formats/oboInOwl#hasDbXref> "ADL:FTT") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean floor feature")
AnnotationAssertion(Annotation(rdfs:comment "Seas are smaller than oceans and are usually located where the land and ocean meet. However, these two terms are often used interchangeably."@en) <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "seafloor"@en)
AnnotationAssertion(Annotation(rdfs:comment "When \"ocean basin\" is used in a hydrological sense, then \"ocean basin floor\" is any floor under seawater. In ENVO, the class \"ocean basin\" is used in a geological sense, which does not include all areas of ocean floor.") <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym> <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean basin floor")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00000426> "ocean floor")
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000426> <http://purl.obolibrary.org/obo/ENVO_01001378>)
SubClassOf(<http://purl.obolibrary.org/obo/ENVO_00000426> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000050> <http://purl.obolibrary.org/obo/ENVO_00002450>))
Expand Down
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