Add GeneDiseaseValidityProposition#406
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| type: | ||
| extends: type | ||
| const: GeneValidityProposition | ||
| default: GeneValidityProposition |
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there's a fairly consistent convention to add a description parameter like so
description: MUST be "GeneValidityProposition".
it feels kind of redundant to me but it's employed elsewhere in the schema
larrybabb
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I think this is a fine starting draft PR. I made a couple of comments, but nothing that should slow things down. those items can be addressed anytime in the future.
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@korikuzma notes that we also need to run I think the note about intended proposition scope would be good context to add in docs, but that could be postponed if the goal is to get this merged in time for a new schema release |
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I think I remember having a bit of a discussion with @mbrush about including an example of the intended use case in the description (specifically citing the 2015 ACMG criteria, for instance), and that it was not preferred to do so, but I might be making that up. I don't disagree that making the scope clearer would be a good idea though, and it's a little hard to do without using those references. Can see about generating those artifacts. My machine isn't set up to run those, would someone have documentation available of requirements for running a build? (or submit a PR to my PR with the appropriate artifacts?) |
Most definitely -- tnavatar#1 |
Fix ref and generate artifacts
| required: | ||
| - predicate | ||
| - subjectGene | ||
| - objectCondition |
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@tnavatar just double checking because I believe the GenCC requires MOI on their GDV classifications. Does the GCI or the ClinGen GDV SOP require MOI to be declared on every classification? The fallback is that some folks do put in the moi term "unknown" which I agree is a cop out. Just wondering if you considered this.
larrybabb
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the
public review ready
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TODO: fix tests |
Don't quote me on this, but i believe this is an upstream test failure, and that Kori has a PR for fixing it |
Correct. #404 |
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Per the PR, a GeneDiseaseValidityProposition is used as a subject of a statement about the level of evidence supporting a gene disease association of the type curated by ClinGen, and reported by GenCC.
While the incorporation of all the evidence contributing to these types of statements is a major project likely requiring a new community profile, this proposition is a start, and will enable the production of standard gene disease validity statements leveraging the rest of VA-Spec.