Open jjgao opened 4 years ago
I like the design, but I am by no means an expert. One issue of concern is that for passenger/driver filtering by count and enrichment endpoints the JSON field for custom driver annotations (_DRIVERFILTER) in the _alterationannotation table would have to be queried. This could be done with a generated column that maps out and indexes a JSON field as a column. However, this approach does not play well with the dynamic way you envision the ANNOTATION_JSON field to be used in. Perhaps we have to move queried fields out of the JSON and add as fixed fields in the _alterationannotation table?
@pvannierop Good question. I think we should be able to query inside json but I am not familiar with that. One option is below, in which, we only deal with string/varchar.
@jjgao It is not clear to me what solution to the problem you are proposing. You mean that certain fields in the JSON can be extracted into a meta table? I do not see how that is different from the _generatedcolumn mechanism conceptually.
@pvannierop I mean we don't store any json but limit the annotation to strings.
I think we may have got into too deep into details. It would be good to have a discussion with others before discussing it too deep.
@jjgao Ah I get it now. Yes, feedback from others here is essential to work towards a final plan.
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This is copied from here. Given the multiple recent developments (FACETS, OncoKB, custom-JSON) around enhancement to variant annotation, it would be good to step back and see whether we can implement a generalized solution. The design below is meant for discussion towards a database schema which the community is agreed upon.
It contains two main changes:
Annotation integration (
alteration_annotation
&annotation_source
)annotation_source
, including versionParent
alteration
table that includes mutations, CNAs, and SVsCombined Alteration
tab in the Comparison page (and in the future Study View)genetic_entity
makes it flexible for future extension for other alteration types, e.g. arm-level CNA.To summarize, a few existing and future projects can be benefit from this design:
Combined Alterations
tab in Comparison page RFC58@pvannierop @Sjoerd-van-Hagen @n1zea144 @sheridancbio @inodb @zhx828 @kalletlak