Mapping obsolete ontology terms

[bschilder]

Hi there,

Thanks for the awesome package! I've decided to make it the primary object type for my new knowledge graph R package KGExplorer.

One thing I was wondering is whether there is a way to access mappings between obsolete ontology terms their corresponding updated IDs. Is this already baked into the DAG_ontology object somewhere? Are there flags I can provide when using import_ontology to include obsolete terms (or at least mappings to them)?

An example would be CL:0000003 ("native cell") --> CL:0000000 ("cell") in the Cell Ontology:
https://www.ebi.ac.uk/ols4/ontologies/cl/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FCL_0000003?lang=en

This came up when I tried mapping CL IDs in a scRNA-seq dataset (which used an older version of CL) using the latest version of CL.

All the best,
Brian

[jokergoo]

Emm... Currently, the obsolete terms are not considered. But I think it should be an important feature for people working on older versions of ontologies.

Currently, the paper for this package is under review. I will add support for obsolete terms during paper revision (if luckily it goes to the second round :)).

[bschilder]

Emm... Currently, the obsolete terms are not considered. But I think it should be an important feature for people working on older versions of ontologies.

Currently, the paper for this package is under review. I will add support for obsolete terms during paper revision (if luckily it goes to the second round :)).

Thanks @jokergoo ! It does seem a bit backwards but it comes up quite often as some ontologies get updated rather frequently. My current solution is to manually map obsolete terms onto their updated equivalents by searching OLS
https://www.ebi.ac.uk/ols4

[jokergoo]

just my notes

I will support the following tags in .obo file:

• alt_id
• replaced_by
• consider

which provide mappings from alternative/removed terms to DAG terms.

Also the there tags (or similar) should be supported in the .owl file.