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NMDC environmental context bindings #1599

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merged 15 commits into from
Feb 4, 2025
Merged

NMDC environmental context bindings #1599

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8888065
one intended and only one spurious edit
turbomam Jan 15, 2025
713d562
template compiles but now with DOSDP errors
turbomam Jan 16, 2025
0e77a99
use ROBOT AI directive for IRI annotations
turbomam Jan 17, 2025
7b49411
still not importing NMDC annotations
turbomam Jan 17, 2025
bcc1ec9
more enum docs see alsoo
turbomam Jan 17, 2025
183ecfe
NMDC PlantAssociated subsets
turbomam Jan 22, 2025
15182b8
building $(SRC) without explicit modules/nmdc_env_context_subset_memb…
turbomam Jan 22, 2025
e3f6e5e
larger NMDC env context subsets
turbomam Jan 22, 2025
da3921f
replaced some rdfs:comments with rdfs:seeAlsos
turbomam Jan 22, 2025
a8a7c47
Merge branch 'master' into 1598-try-creating-the-new-see_also-from-pr…
turbomam Feb 4, 2025
51c6ec3
refresh modules/nmdc_env_context_subset_membership.*
turbomam Feb 4, 2025
aeb28f5
robot_templates not modules
turbomam Feb 4, 2025
887b5a8
submission-schema tie-in
turbomam Feb 4, 2025
cd6d71f
always say robot_templates
turbomam Feb 4, 2025
f95e3ab
really always say robot_templates
turbomam Feb 4, 2025
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15 changes: 14 additions & 1 deletion src/envo/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ $(ONT).json: $(ONT)-full.owl
# by default we use ELK to perform a reason-relax-reduce chain
# after that we annotate the ontology with the release versionInfo

OTHER_SRC =
OTHER_SRC = robot_templates/nmdc_env_context_subset_membership.owl


$(ONTOLOGYTERMS): $(SRC) $(OTHER_SRC)
Expand Down Expand Up @@ -567,6 +567,19 @@ modules/%.obo: modules/%.owl
modules/ebi_biomes.owl: modules/ebi_biomes.csv
$(ROBOT) template --template $< -i imports/ro_import.owl -o [email protected] && mv [email protected] $@

.PHONY: nmdc-robot-clean nmdc-robot-all

nmdc-robot-clean:
rm -rf robot_templates/nmdc_env_context_subset_membership.owl

nmdc-robot-all: nmdc-robot-clean robot_templates/nmdc_env_context_subset_membership.owl

robot_templates/nmdc_env_context_subset_membership.owl: robot_templates/nmdc_env_context_subset_membership.tsv
# this TSV will be built with `make env-triad-robot-all` in https://github.com/microbiomedata/submission-schema
# which currently requires the latest envo.owl even if it is pre-release
$(ROBOT) template --template $< -o [email protected] && mv [email protected] $@ # why not just output to $@ ?


envo-edit.csv: envo-edit.owl
$(OWLTOOLS) $(USECAT) $< --merge-support-ontologies --export-table [email protected] && cut -f1 [email protected] | grep ENVO_ | perl -npe 's@https@http@' > $@

Expand Down
1 change: 1 addition & 0 deletions src/envo/catalog-v001.xml
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Expand Up @@ -26,5 +26,6 @@
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl" uri="modules/entity_attribute.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl" uri="modules/entity_attribute_location.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl" uri="modules/entity_quality_location.owl"/>
<uri id="User Entered Import Resolution" name="http://purl.obolibrary.org/obo/envo/robot_templates/nmdc_env_context_subset_membership.owl" uri="robot_templates/nmdc_env_context_subset_membership.owl"/>
<group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base=""/>
</catalog>
45 changes: 44 additions & 1 deletion src/envo/envo-edit.owl
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Expand Up @@ -26,6 +26,7 @@ Import(<http://purl.obolibrary.org/obo/envo/modules/chemical_concentration.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_attribute_location.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/entity_quality_location.owl>)
Import(<http://purl.obolibrary.org/obo/envo/robot_templates/nmdc_env_context_subset_membership.owl>)
Import(<http://purl.obolibrary.org/obo/envo/modules/process_attribute.owl>)
Annotation(<http://purl.org/dc/elements/1.1/contributor> <https://orcid.org/0000-0002-2996-719X>)
Annotation(<http://purl.org/dc/elements/1.1/creator> <https://orcid.org/0000-0002-4366-3088>)
Expand Down Expand Up @@ -4474,9 +4475,13 @@ 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_03605016>))
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/ENVO_03605022>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605023>))
Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/ENVO_03605024>))
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 @@ -4577,6 +4582,7 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605013>
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/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605013> <https://microbiomedata.github.io/submission-schema/EnvBroadScaleSoilEnum/>)
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)
Expand All @@ -4585,6 +4591,7 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605014>
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/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605014> <https://microbiomedata.github.io/submission-schema/EnvLocalScaleSoilEnum/>)
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)
Expand All @@ -4593,14 +4600,21 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605015>
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/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605015> <https://microbiomedata.github.io/submission-schema/EnvMediumSoilEnum/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605015> <http://purl.obolibrary.org/obo/ENVO_03605011>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605016> (NMDC PlantAssociated value sets)

AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605016> "NMDC PlantAssociated value sets"@en)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605016> <http://purl.obolibrary.org/obo/ENVO_03605010>)

# 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/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605017> <https://microbiomedata.github.io/submission-schema/EnvBroadScaleWaterEnum/>)
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)
Expand All @@ -4609,6 +4623,7 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605018>
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/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605018> <https://microbiomedata.github.io/submission-schema/EnvLocalScaleWaterEnum/>)
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)
Expand All @@ -4617,8 +4632,36 @@ AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605019>
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/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605019> <https://microbiomedata.github.io/submission-schema/EnvMediumWaterEnum/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605019> <http://purl.obolibrary.org/obo/ENVO_03605012>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605022> (NMDC PlantAssociated broad scale value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605022> "Used to annotate EnvO classes appropriate for the MIxS env_broad_scale field in plant associated sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605022> "NMDC PlantAssociated broad scale value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605022> <https://genomicsstandardsconsortium.github.io/mixs/0000012/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605022> <https://genomicsstandardsconsortium.github.io/mixs/0016010/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605022> <https://microbiomedata.github.io/submission-schema/EnvBroadScalePlantAssociatedEnum/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605022> <http://purl.obolibrary.org/obo/ENVO_03605016>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605023> (NMDC PlantAssociated local scale value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605023> "Used to annotate EnvO classes appropriate for the MIxS env_local_scale field in plant associated sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605023> "NMDC PlantAssociated local scale value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605023> <https://genomicsstandardsconsortium.github.io/mixs/0000013/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605023> <https://genomicsstandardsconsortium.github.io/mixs/0016010/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605023> <https://microbiomedata.github.io/submission-schema/EnvLocalScalePlantAssociatedEnum/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605023> <http://purl.obolibrary.org/obo/ENVO_03605016>)

# Annotation Property: <http://purl.obolibrary.org/obo/ENVO_03605024> (NMDC PlantAssociated environmental medium value set)

AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/ENVO_03605024> "Used to annotate EnvO classes appropriate for the MIxS env_medium field in plant associated sample records. Supports consistent metadata annotation for systems like NCBI BioSample.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_03605024> "NMDC PlantAssociated environmental medium value set"@en)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605024> <https://genomicsstandardsconsortium.github.io/mixs/0000014/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605024> <https://genomicsstandardsconsortium.github.io/mixs/0016010/>)
AnnotationAssertion(rdfs:seeAlso <http://purl.obolibrary.org/obo/ENVO_03605024> <https://microbiomedata.github.io/submission-schema/EnvMediumPlantAssociatedEnum/>)
SubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/ENVO_03605024> <http://purl.obolibrary.org/obo/ENVO_03605016>)

# 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 @@ -14259,9 +14302,9 @@ 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 seawater")
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.")
AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/ENVO_00002150> "coastal sea water")
Expand Down
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