griffithlab / griffithlab/civic-docs

Functional Evidence curation guidance is poor

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Description

Our Functional Curation Practices section has a subsection entitled "Functional Evidence from Clinical Trials". This sub-section needs to be moved or entirely reworked, as it seems to be describing the curation of Predictive evidence, instead of Functional. As this section is being reviewed, some additional attention should be paid to resolve the typos throughout.

In addition, we should provide guidance on how this type of functional classification differs from the common "Variant X is gain-of-function / loss-of-function for gene Y" type of functional statement. CIViC functional evidence (and later, functional assertions?) includes the notion of a disease type and variant origin, which is atypical for this type of statement in other resources. I believe the argument was that this is because the notion of functional variation is with respect to phenotypic function, where cells gain or lose clinically relevant (disease-linked) characteristics due to the variant. If so, we should state as much in our curation guidelines; and if not, we should consider revisiting the data model for Functional evidence types to omit variant origin and disease attributes.

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Research direction

Start with the Functional Curation Practices section at the linked documentation page, especially “Functional Evidence from Clinical Trials,” and compare its guidance with the intended distinction from Predictive evidence. Review the surrounding text for typos and determine whether the guidance should explain phenotypic function and disease or variant-origin attributes; done means an agreed, coherent revision of the section and its terminology.

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Assessment

Domain
documentation
Issue type
Documentation
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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