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

1. Install ontology script:

   pip install .

2. Run generate_ontology:

   generate_ontology

3. The ontology file generated has a file name format like this: ontology-YYYY-MM-DD.json

4. 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)."

5. Update the ontology version in the [Makefile]:

   curl -o ontology.json https://.../ontology/ontology-YYYY-MM-DD.json

6. Update the following information

   • Site release version: N/A

   • ontology.json file: N/A

   • UBERON release date: 2022-04-18

   • OBI release date: 2022-01-03

   • EFO release date: 2022-04-19

   • CLO release date: 2022-03-20

   • DOID release date: 2022-04-28

   • HP release date: 2022-04-14

   • MONDO release date: 2022-05-02

   • OBA release date: 2022-05-06

7. Resources

   • Uber anatomy ontology (Uberon)

   • Cell Ontology (CL)

   • Experimental Factor Ontology (EFO)

   • Ontology for Biomedical Investigations (OBI)

   • Cell Line Ontology (CLO)

   • Human Disease Ontology (DOID)

   • Uberon download

   • EFO src tree

   • OBI download

   • CLO download

   • DOID download

   • UBERON release date

   • OBI release date

   • EFO release date

   • CLO release date

   • DOID release date