refine evidence_direction #123
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harvester/civic.py
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| association['response_type'] = '{} {} {}'.format( | ||
| evidence_item['evidence_direction'], | ||
| evidence_item['evidence_type'], | ||
| description) |
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add check if description == 'n/a'. If so, do not add description to response_type string.
otherwise, CIViC looks good!
harvester/molecularmatch.py
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| @@ -238,7 +238,7 @@ def convert(evidence): | |||
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| # association['evidence_label'] = direction | |||
| association = el.evidence_label(tier, association, na=False) | |||
| association = ed.evidence_direction(tier, association, na=False) | |||
| association = ed.evidence_direction(evidence['direction'], association, na=False) | |||
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this is not returning the correct value to response_type. There are multiple different values from the source with different contexts which should be preserved (for now):
{
'conflicting': 35,
'decreased response': 394,
'no benefit': 265,
'not applicable': 69,
'predicted – resistant': 45,
'predicted – sensitive': 507,
'resistant': 976,
'sensitive': 3449,
'unknown': 6
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@ahwagner : where did you find these responses in molecularmatch data?
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cat /tmp/molecularmatch_raw.json | jq .direction | sort | uniq
"does_not_support"
"supports"
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I didn't save the code, and now I'm not sure. Looking at MM records, what we want for this field is clearly a combination of top level keys ['direction'] and ['clinicalSignificance']. I'm wondering if I was looking at a different source? Anyway, I'm trying to verify that molecularmatch was the source with the entries that needed adjusting, but search.cancervariants.org is not loading for me right now (timeout errors). I'll try again tonight and hopefully can get you some more info.
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@ahwagner Re. molecularmatch
association['response_type'] = '{} {}'.format(evidence['direction'], evidence['clinicalSignificance'])
before
after
| @@ -215,7 +215,7 @@ def _enrich_feature(gene, feature): | |||
| association = el.evidence_label(clinical['level'], | |||
| association, na=True) | |||
| association = ed.evidence_direction(clinical['level_label'], | |||
| association, na=True) | |||
| association, na=False) | |||
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That was a surprisingly easy fix. Live data look good.
Corrects evidence_direction see #122
@ahwagner latest data pushed onto search.cancervariants.org