EFO ontology differences between downloads and platform/OnToma

Data Access Data downloads
1

Hey all, thanks for creating such a great platform.

I was having trouble reconciling the disease names from the JSONs on the downloads page (e.g., Associations - indrect (by data type) and Human Phenotype Ontology) with the data that’s displayed on the platform.

For example, “Alopecia areata” from the platform isn’t listed in the data download files, but “patchy alopecia” is listed instead and with a different topology (e.g., differing ancestors). I was able to recreate the ontology seen on the platform using OnToma then mapping the IDs to names from the EFO download (The Experimental Factor Ontology < EMBL-EBI), but I can’t tie the new names to disease evidence because these still don’t match Associations - indrect (by data type).

I was wondering if maybe the downloads are older versions of the data that have an older EFO version? Or very likely I’m doing something wrong. Any help would be greatly appreciated!

2

The diseases dataset will give you the set of EFO terms that were used for the same Platform release. You should be able to use it to join the associations datasets with the disease properties without mismatches