Hi.
I wanted to understand a particular case where the earlier versions of the OpenTargets platform did provide information about a disease named Dermatitis, atopic (MONDO:0011292). After the latest update, I’m unable to locate the particular disease and any other related information previously available for the same.
Can you help me with understanding this issue? Why the particular disease is not being shown and how do I access the related information about the same?
Hi Divya,
First of all, we can only capture evidence between targets and only those diseases that are found in EFO, that we use as a disease index. Unfortunately this disease (MONDO:0011292) is no longer in our disease index from 24.09 to 25.03 update.
Looking into this issue, what has happened is that MONDO deprecated this term in favour of atopic eczema, which is in EFO (EFO_0000274). Usually, when a term is deprecated in EFO, we automatically link to the term it was replaced with. It doesn’t work this case, as the deprecation happened in MONDO, which is imported into EFO.
What is the impact on our association data? As the disease is missing, and there’s no other disease to fall back, evidence annotated with this MONDO term, are deemed as invalid. Looking at the ETL output, we are losing 100 evidence exclusively from ChEMBL.
We have contacted EFO team to explore if we can capture such obsoletion in the future. Let us know if you have further question.