observations of variant provided by clinvar and lovd -- can have multiple observations of same variant within single data source -- when same variant is observed by different independent parties it strengthens evidence on variant -- when conflicting interpretations on a variant are found it prompts communication and more research into its pathogenicity which leads to better data down the line.
variant interpretations come from enigma, clinvar, lovd, bic. each has different names for fields, maybe unify them? clinical significance, submitter, internal accession.
enigma: no unique identifier
clinvar: scv#
lovd: has unique identifier
bic: not sure if they have a unique identifier
maintain references to original source data -- point interpretation back to where it came from
Focus on separating variant interpretations into own objects.
Ideas: Interpretation table in DB with a source column foreign keyed to variants in variant table
Notes from initial conversation:
observations of variant provided by clinvar and lovd -- can have multiple observations of same variant within single data source -- when same variant is observed by different independent parties it strengthens evidence on variant -- when conflicting interpretations on a variant are found it prompts communication and more research into its pathogenicity which leads to better data down the line.
variant interpretations come from enigma, clinvar, lovd, bic. each has different names for fields, maybe unify them? clinical significance, submitter, internal accession.
enigma: no unique identifier clinvar: scv# lovd: has unique identifier bic: not sure if they have a unique identifier
maintain references to original source data -- point interpretation back to where it came from
Focus on separating variant interpretations into own objects.
Ideas: Interpretation table in DB with a source column foreign keyed to variants in variant table