Comments (6)
kaiiam
commented on June 1, 2024
1
Splitting it up into the two sheets one for the hierarchical NCF with is a relationships and one for the derivative terms. The rational is that following Chris Mungalls advice any terms with an equivalence axiom should follow a design pattern analogous to a DOSDP. Here it's a python script generating the formulaic input for a Robot template, but the result is very similar to using a DOSDP where it's programmatic based on a compositional combination of inputs.
NCF terms:
robot template --template nutritional_components_framework.tsv -i ../cdno-edit.owl --prefix "CDNO:http://purl.obolibrary.org/obo/CDNO_" --prefix "CHEBI:http://purl.obolibrary.org/obo/CHEBI_" --prefix "ENVO:http://purl.obolibrary.org/obo/ENVO_" -o nutritional_components_framework.owl
Sugar derivative terms:
robot template --template sugar_derivatives.tsv -i ../cdno-edit.owl --prefix "CDNO:http://purl.obolibrary.org/obo/CDNO_" --prefix "CHEBI:http://purl.obolibrary.org/obo/CHEBI_" --prefix "ENVO:http://purl.obolibrary.org/obo/ENVO_" -o sugar_derivatives.owl
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kaiiam
commented on June 1, 2024
This will be very similar to the work done in UA-SRC-data/srpdio#7 and FoodOntology/foodon#116.
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kaiiam
commented on June 1, 2024
Testing this in branch 9, see this sheet as robot template input.
run in modules/
robot template --template test_nut_comp.tsv -i ../cdno-edit.owl --prefix "TEST:http://purl.obolibrary.org/obo/TEST_" -o test_nut_comp.owl
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kaiiam
commented on June 1, 2024
Trying it with the test output of a python script converting unreleased version of CDNO_nutritional_components_framework_v7.9 from @LilyAndres.
robot template --template CDNO_nutritional_components_framework_v7.9_test.tsv -i ../cdno-edit.owl --prefix "CDNO:http://purl.obolibrary.org/obo/CDNO_" --prefix "CHEBI:http://purl.obolibrary.org/obo/CHEBI_" --prefix "ENVO:http://purl.obolibrary.org/obo/ENVO_" -o CDNO_nutritional_components_framework_v7.9_test.owl
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kaiiam
commented on June 1, 2024
Doing it hopefully one last time with the full version of the output CDNO_nutritional_components_framework_v7.9
robot template --template CDNO_NCF_v7.9_output_for_ROBOT.tsv -i ../cdno-edit.owl --prefix "CDNO:http://purl.obolibrary.org/obo/CDNO_" --prefix "CHEBI:http://purl.obolibrary.org/obo/CHEBI_" --prefix "ENVO:http://purl.obolibrary.org/obo/ENVO_" -o CDNO_NCF_v7.9_output_for_ROBOT.owl
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kaiiam
commented on June 1, 2024
Addressed in #12 instead of here, can close this issue and #10.
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Related Issues (20)
- Error in the design pattern during the release HOT 12
- version IRI in OLS does not resolve HOT 14
- duplicate terms under different ids now under 'concentration of' HOT 18
- xrefs are malformed - CURIEs should not have space after the colon HOT 1
- Multiple labels for ChEBI chemicals HOT 13
- Update CDNO/tooling to lastest owl API HOT 7
- Add term deprication/obsolete template HOT 2
- Create CDNO annotation documentation HOT 2
- Lignin should be a subclass of insoluble fibre? HOT 3
- Addition of dietary energy and related terms to CDNO HOT 1
- protein class suggested updates HOT 1
- floating term at top level PR_000000001 HOT 1
- Update USDA compoent prefix in mappings HOT 3
- CDNO Ontology Description missing from OLS HOT 1
- Suggestion to update template for consistency HOT 1
- Suggestion to import vitamin (role) from ChEBI
- Change parent terms for amino acid HOT 1
- Synonyms in nutritional_components_framework.csv template overriding imported synonyms HOT 1
- CDNO has some CHEBI terms with right bracket hidden in URI HOT 9
- Dietary Fiber Ontology Working Group: Fiber term updates HOT 2
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