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griffithlab / civic-client

Web client for CIViC: Clinical Interpretations of Variants in Cancer
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Need to add synonymous variant in the SO preferred terms table #1522

Closed kkrysiak closed 3 years ago

kkrysiak commented 3 years ago

https://civic.readthedocs.io/en/latest/model/variants/types.html#curation-guidelines-for-specific-sequence-ontology-types

We have synonymous, synonymous variant and silent sequence ontology terms in CIViC. We need to unify this and add instructions to the docs.

kkrysiak commented 3 years ago

I would add this above the N/A (last row of the table)

Sequence Ontology Term | Sequence Ontology Definition | Comments synonymous_variant | A sequence variant where there is no resulting change to the encoded amino acid. | --

http://www.sequenceontology.org/browser/current_svn/term/SO:0001819

susannasiebert commented 3 years ago

What about synonymous and silent? Do these terms needs to be fixed on the database side of things (combined with synonymous_variant)?

kkrysiak commented 3 years ago

I was imagining that we'd do this as curators in the interface. There is only 1 instance of Synonymous and actually when I used the Variant Search Silent doesn't bring anything up. That seems weird unless someone fixed that since yesterday (my guess would be Lana).

kkrysiak commented 3 years ago

Confirmed. Lana fixed these.

@susannasiebert is there an easy way to limit those SO IDs so they can't be picked? I'm not saying we should do so but it might be worth considering if it would be simple.

susannasiebert commented 3 years ago

we could remove them from the database but they would probably just be added back in next time the SO scraper runs. We would need to update the logic to skip them, which shouldn't me too difficult.

kkrysiak commented 3 years ago

Maybe we should add that to the next CIViC agenda as a consideration or create an issue for a v2 thing. I think we'd want to do this for more than just these 2 SO terms. Since that may also be confusing to users who go directly to SO, I don't want to take this too lightly.

susannasiebert commented 3 years ago

ok, for now I can just add the synonymous_variant term to the documentation with the details you provided above.

susannasiebert commented 3 years ago

During yesterday's meeting it was decided that we would not be skipping terms like synonymous and silent for import. Instead a better typeahead sorting was proposed in https://github.com/griffithlab/civic-client/issues/1536