Update genetic matching to use correct solved/candidate genes

phenotips / patient-network

Patient matching extension for PhenoTips

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Update genetic matching to use correct solved/candidate genes #86

Closed buske closed 9 years ago

buske commented 9 years ago

Gene sections will be unified by PR https://github.com/phenotips/phenotips/pull/1742, but this uses the same field for candidate, solved, and excluded genes, so matching will then incorrectly be done on all of them.

For matching:

if any genes with "solved" status are present, they should be used exclusively
elif any genes with "candidate" status are present, they should be used exclusively
else: no genes should be used for boosting the matching.

buske commented 9 years ago

Changes will have to be made to: https://github.com/phenotips/patient-network/blob/master/similarity-data-impl/src/main/java/org/phenotips/data/similarity/internal/DefaultPatientGenotype.java#L98-L122

buske commented 9 years ago

Should also include gene names from candidate variants that have been entered, with pathogenic status 3-5 (VUS or higher).

buske commented 9 years ago

Replaced by: https://phenotips.atlassian.net/browse/PN-87