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EBIvariation / trait-curation

A web application for manual curation of trait-to-ontology mappings, including provenance and integration with EBI SPOT stack.
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Prioritise traits which are linked to “NT expansion” variants #48

Open tskir opened 4 years ago

tskir commented 4 years ago

Traits have a field which tracks the number of how many source records contain that trait. This is used for prioritising which traits should be curated before others (the more records, the higher the priority).

However, there are certain cases when it's very important to curate a trait, even though the number of records linked to it is low. One such example is traits which are linked to NT expansion (or nucleotide repeat expansion) variants.

When importing data from ClinVar (#14), all traits linked to NT expansion repeats should be marked in some special way to prioritise them over others in terms of the number of source records.

The trait is defined to be linked to NT expansion variant if it appears at least once in a row where the column Type is equal to "NT expansion".

tskir commented 4 years ago

Before we start the implementation on this issue, we should first discuss the exact way this will be done. Perhaps it will be best to develop a general capability of marking the traits as "important" or "featured", kind of like emails in email clients can be marked by "star" symbols. In this case, on ClinVar import all traits which are linked to "NT expansion" variants will be automatically starred as important, but users will also be able to toggle this status manually from the individual trait page.

Alternatively, a system of tags for traits can be implemented, in which case such traits will receive a "NT expansion" tag on ClinVar import.

tskir commented 4 years ago

This PR in the main Open Targets repository might be helpful: https://github.com/EBIvariation/eva-cttv-pipeline/pull/103. It introduced roughly the same changes which I'm talking about in this issue.