The OT Platform describes associations to ‘non-alcoholic fatty liver disease’ (NAFLD). The disease has been gradually substituted with ‘metabolic dysfunction-associated steatotic liver disease’ (MASLD) (such as in the journal), but the Platform seems not to include the new term. Could anyone please explain whether or how the OT Platform will update the database (e.g., replacement or co-existence of the old and new terms)?
Hi @tzukuo
Thanks for bringing it to our attention.
Open Targets Platform uses the EMBL-EBI Experimental Factor Ontology (EFO) as a scaffold for the disease or phenotype entity. Hence, it would be best if you could kindly raise this issue with the EFO team and request them to add the new disease term to their repository. The disease terms in the Open Targets Platform will get updated once it has been added to the Experimental Factor Ontology (EFO).
Regards,
Prashant
Many thanks for your feedback, @Prashant_Uniyal . I will bring this to my team!
Thank you again for your feedback. @dsuveges has also mentioned in another thread that disease terms are about the same as the source descriptions while OT adds EFO ids accordingly. I wonder how updates of EFO will influence diseases shown in OT. Could you please explain more?
I wonder how updates of EFO will influence diseases shown in OT. Could you please explain more?
On OpenTargets Platform, the ETL processes disease annotation from all sources making sure labels are always grounded to the most recent version of EFO. Eg. all terms that are not found in the most up to date EFO are dropped as invalid, or if a term got obsoleted, the new term will replace the old one. This validation however not yet happening in the Genetics Portal.
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I didn’t know the difference. Thank you for clarifying that!