[DO NOT CLOSE] 📝 Guide to add new ontology

[sunnyosun]

Steps:

1. Add new ontology source metadata to the sources.yaml file:
2. Make sure you restart your notebook before proceeding. (If you installed lamindb, please run lamin close before restarting your notebook.)
3. Run the corresponding API; for instance, if you add a new cell type, run:

   bionty.base.CellType(source=<source_name>, version=<new version>).df()
   

   • this will create the corresponding two files df_xxxxx.parquet and ontology_xxxx in your local bionty/base/_dynamic/ folder (inside your bionty repo).
   • Note: Certain ontologies need manual curation to create the parquet file, please check this list: https://bionty-assets-gczz.netlify.app/ingest/
   • If your ontology is on the list, please make a new notebook copy to document the curation process. This notebook should be added with a new PR in bionty-assets.
   • For ExperimentalFactor, you need to run bionty.base.entities._experimentalfactor.efo_to_df to create the DataFrame and save it to a parquet file named df_all__efo__<new version>__ExperimentalFactor.parquet.
     Run it as bt.base.entities._experimentalfactor.efo_to_df(efo.to_pronto(), "efo", include_id_prefixes={'efo': ['EFO', 'http://www.ebi.ac.uk/efo/']}), where efo is an ExperimentalFactor object with the new version.
4. Ensure that the Source is registered:
   Load laminlabs/bionty-assets and run bionty.core.sync_all_sources_to_latest()
   Reload the instance via lamin load laminlabs/bionty-assets
5. Register these two files in laminlabs/bionty-assets lamindb instance following this example.
   • Please also track your ingestion notebook following the above example.
   • Please DO NOT directly upload to s3://bionty-assets!!!
6. Make a PR to bionty.
   • Please only update a single ontology in a PR:
     • Title: 🍱 New <entity_name> version: <source_name>-<version_name>
     • tag: new ontology