MedDRA to EFO cross-references

[ireneisdoomed]

Hi,

from an analysis of FAERS data, we have obtained a list of approximately 10,000 MedDRA to EFO mappings that we believe have a very high level of confidence: meddra-mappings-0995-1.json.zip

This is part of an emerging pipeline we are working on to integrate the different methods of automatic disease mapping into a single tool.

The algorithm performs very well as long as there is a proper EFO. However, we are aware of a systemic error when the MedDRA label refers to a less common/more severe disorder in a set of diseases, e.g:

{"traitId":"10032168","traitName":"Other insomnia","score":1,"efoId":"EFO_0004698","efoName":"insomnia"}
{"traitId":"10031712","traitName":"Other cardiovascular syphilis","score":0.999,"efoId":"EFO_1001206","efoName":"syphilitic aortitis"}
{"traitId":"10032033","traitName":"Other endocarditis","score":1,"efoId":"EFO_0000465","efoName":"endocarditis"}

Could you please examine the mappings and consider how best to include this annotation in the ontology? Any feedback or comments is much appreciated.

Thanks!

[zoependlington]

I have added over 2000 MedDRA x-refs into EFO (https://github.com/EBISPOT/efo/pull/1121) where the MedDRA label and the EFO/Orphanet label are the same and we have high confidence in the mapping. I will continue to curate the remaining terms to make sure the x-refs are broad, exact, narrow or related.

For any mappings to Mondo, DOID, or HP terms, we will have to request these in Mondo, DOID, or HP which will then be imported into EFO after these domain ontologies have been released with the x-ref additions.

[ireneisdoomed]

Thank you very much. These are some great news!

As indicated, I have opened the independent tickets to MONDO, DOID and HP to take these MedDRA mappings into consideration:

• Request to MONDO
• Request to DOID
• Request to HP

[zoependlington]

Added further x-refs for 167 EFO terms that underwent manual curation.

A further 380 mappings require curation.