Add Source: CIViC

[mbrush]

Source Name:
CIViC (Clinical Interpretation of Variants in Cancer)

Source Data Description:
CIVIC data is a crowd-sourced, variant-centric database that holds four types of assertions curated from the literature about the clinical relevance of genetic variants to cancer:

1. Diagnostic claims that a variant is associated with a particular type (or subtype) of cancer (but not necessarily causal? - i.e. could this be a marker or non-driver mutation?)
2. Predictive claims that a variant confers sensitivity or resistance to a treatment (in the context of a particular cancer)
3. Prognostic claims that a variant impacts disease progression, severity, or patient survival
4. Predisposition claims that a variant increases likelihood of developing a particular cancer)

Scope of Ingest:
Take 'predictive' associations first, specific elements to be ingested on first pass is TBD.

Source Data Location:
Data releases (tsv): https://civic.genome.wustl.edu/#/releases
API: https://genome.github.io/civic-api-docs/

Source Documentation:
FAQ links to all relevant documentation are here: https://civic.genome.wustl.edu/#/faq

Additional Notes:

[mbrush]

Note that Wikidata ingests this resource already - and may be a possible route of ingest into SciGraph. We should explore if their ingest includes all data/metadata we would want, e.g. regarding evidence and provenance.

One potential issue is that in cases where a variant effect is assessed for two drugs used in combination, WD seems to make separate 'claims' that the variant confers sensitivity or resistance to each drug individually. This doesn't seem right - but more complex modeling would be needed to handle cases of combination therapies.

See tickets here and here.

[kshefchek]

replaced by #813