Regarding Disease ID in Open Targets

Does Open Targets disease have a useful ID to link to other databases?
(For example, ICD codes, etc.)

Hi @bg7860, and welcome to the Open Targets Community! :tada:

We use the Experimental Factor Ontology from EMBL-EBI as a scaffold for our disease/phenotype entities, and we also include other IDs when they are available — see below for an example of liver disease, which is linked to the ICD codes K75 and K76.

Liver disease profile page in the Open Targets Platform

Does this answer your question?

Thank you @hcornu!
Will the information you gave me be included in the batch downloaded files?

Hi @bg7860!

The information is included in the data downloads, but not systematically — we capture all the cross references given by EFO in the dbXRefs field of the disease index, so we only have what they have.

See the table on the right, “database cross reference”, for an example of alternative IDs captured by EFO for Crohn’s disease.

An example how this information can be extracted from Google Bigquery:

A similar solution can of course be implemented when downloading the diseases dataset

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