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monarch-initiative / omim

Data ingest pipeline for OMIM.
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Bug: Matching on abbreviations #70

Closed joeflack4 closed 1 year ago

joeflack4 commented 1 year ago

Overview

Nicole V mentioned today that this is the only thing she knows thats wrong w/ the OMIM ingest currently. We have matchings that are sometimes done on abbreviations.

I'm not sure where in the ingest it is doing this at the moment.

Example of the problem (row within the following Google Sheet: unmapped_omim_lex):

subject_id  subject_label   predicate_id    object_id   mapping_justification   object_label    comment mapping_tool    confidence  subject_match_field object_match_field  match_string    Y/N Comment
MONDO:0019105   renal nutcracker syndrome   MONDO:equivalentTo  OMIM:259775 semapv:LexicalMatching  raine syndrome  LEXMATCH    oaklib  0.8 oio:hasExactSynonym oio:hasExactSynonym rns N   matching on abbreviation
nicolevasilevsky commented 1 year ago

I think we should just keep doing the mapping this way (matching on abbreviations) and have me and @sabrinatoro review them. Because if we don't match on them, we may lose some potential mappings.

joeflack4 commented 1 year ago

@nicolevasilevsky Alright, that sounds fine to me!