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NMDC environmental context bindings (#1599)
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* one intended and only one spurious edit

* template compiles but now with DOSDP errors

* use ROBOT AI directive for IRI annotations

* still not importing NMDC annotations

* more enum docs see alsoo

* NMDC PlantAssociated subsets

* building $(SRC) without explicit modules/nmdc_env_context_subset_membership.owl

* larger NMDC env context subsets

* replaced some rdfs:comments with rdfs:seeAlsos

* refresh modules/nmdc_env_context_subset_membership.*

* robot_templates not modules

* submission-schema tie-in

* always say robot_templates

* really always say robot_templates
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@turbomam
turbomam authored Feb 4, 2025
1 parent 6c51446 commit 46b10ea
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15 changes: 14 additions & 1 deletion src/envo/Makefile
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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 $@.tmp.owl && mv $@.tmp.owl $@

.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 $@.tmp.owl && mv $@.tmp.owl $@ # why not just output to $@ ?


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

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1 change: 1 addition & 0 deletions src/envo/catalog-v001.xml
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Original file line number Diff line number Diff line change
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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Original file line number Diff line number Diff line change
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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