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Updated EFO/MONDO mapping using OT custom EFO ontology #420

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ewafula opened this issue Oct 5, 2022 · 1 comment
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Updated EFO/MONDO mapping using OT custom EFO ontology #420

ewafula opened this issue Oct 5, 2022 · 1 comment
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@ewafula
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ewafula commented Oct 5, 2022

What analysis module should be updated and why?

efo-modo-mapping module

What changes need to be made? Please provide enough detail for another participant to make the update.

Update the module to replace automated OLS ontology search to retrieve EFO, MONDO, and NCIT codes for OpenPedCan cancer groups with a custom EFO ontology file curated specifically for OpenTargets and released by EFO efo_otar_slim.owl

What input data should be used? Which data were used in the version being updated?

The MTP uses EFO v3.40.0 according to @zdorman as discussed on ticket #418, but we might need to discuss the EFO release version to use for v12 during the OT catchup meeting next week

When do you expect the revised analysis will be completed?

Next sprint

Who will complete the updated analysis?

@sangeetashukla

@ewafula ewafula changed the title Updated analysis: Updated EFO/MONDO mapping using OT custom EFO ontology Oct 5, 2022
@chinwallaa chinwallaa added the v12 label Oct 6, 2022
@ewafula
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ewafula commented Oct 13, 2022

NOTE: @sangeetashukla, module to be updated using efo_otar_slim.owl EFO v3.45.0 (or a version that matches MTP portal) for v12 data release as discussed in during the 10/12/2012 EFO annotation impromptu meeting with @taylordm and @chinwallaa.

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