This document describes how to update the ontology versions used for searching and validation in the igvf application, ontology.json .
- Uber anatomy ontology (Uberon) and Cell Ontology (CL): composite-metazoan.owl
- Experimental Factor Ontology (EFO): EFO_inferred.owl
- Ontology for Biomedical Investigations (OBI): obi.owl
- Cell Line Ontology (CLO): clo.owl
- Human Disease Ontology (DOID): doid.owl
- The Human Phenotype Ontology (HPO): hp.owl
- Mondo Disease Ontology (MONDO): mondo.owl
- Ontology of Biological Attributes covering all kingdoms of life (OBA): oba.owl
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Install ontology script:
pip install . -
Run generate_ontology:
generate_ontology -
The ontology file generated has a file name format like this: ontology-YYYY-MM-DD.json
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Load new ontology file into the encoded-build/ontology directory on S3
aws s3 cp ontology-YYYY-MM-DD.json s3://...Locate the file on S3 and change the permissions so that "Read" permission is granted to "Everybody (public access)."
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Update the ontology version in the [Makefile]:
curl -o ontology.json https://.../ontology/ontology-YYYY-MM-DD.json -
Update the following information
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Site release version: N/A
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ontology.json file: N/A
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UBERON release date: 2023-07-25
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OBI release date: 2023-07-25
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EFO release date: 2023-07-17
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CLO release date: 2022-03-20
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DOID release date: 2023-07-24
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HP release date: 2023-07-21
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MONDO release date: 2023-07-03
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OBA release date: 2023-06-27
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