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Human CFTR does not show up when searching for cystic fibrosis #319

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kshefchek opened this issue Apr 2, 2020 · 3 comments
Open

Human CFTR does not show up when searching for cystic fibrosis #319

kshefchek opened this issue Apr 2, 2020 · 3 comments
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blocked Something needs to be done before work can proceed decision needed dipper dependency

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@kshefchek
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I thought at first it was related to #214, but it turns out this is because gene definitions are fetched on the client/browser by querying mygene, so these do not make it into solr. Cystic fibrosis does not appear in the solr document at any other point (ie synonym), https://solr-dev.monarchinitiative.org/solr/search/select/?q=*:*&fq=id:%22HGNC:1884%22&wt=json

possible solutions:

  1. ingest gene definitions in dipper
  2. ingest gene definitions when loading solr search
@kshefchek kshefchek added blocked Something needs to be done before work can proceed decision needed dipper dependency labels Apr 2, 2020
@kshefchek
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Looking at this closer, it looks like we only index synonyms on the clique leader id, but not those on equivalent Ids, which have additional synonyms, see
https://api-dev.monarchinitiative.org/api/graph/edges/from/HGNC:1884?relationship_type=equivalentClass

If we were to index the synonyms from equivalent ids then we would get CFTR when searching for cystic fibrosis.

Relocating this to the solr loader

@kshefchek
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Reopening on the UI side since this is still an issue, another example is BRCA1 and breast cancer

@kshefchek kshefchek reopened this Dec 21, 2020
@kshefchek
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I added synonyms of equivalent terms to our search index with SciGraph/golr-loader@ef14285

This adds labels that should help with this issue, for example:
CFTR: cystic fibrosis transmembrane conductance regulator

BRCA1: breast cancer type 1 susceptibility protein

However, this hasn't entirely helped

cystic
brca1

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