CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

By Malachi Griffith, N. Spies, K. Krysiak, Joshua F. McMichael, Adam C. Coffman, Arpad M. Danos, Benjamin J. Ainscough, Cody A. Ramirez, D. Rieke, Lynzey Kujan and 35 more. Nature Genetics, 2017

582 citations recorded by the source corpus.

CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants of all types. CIViC is committed to open-source code, open-access content, public application programming interfaces (APIs) and provenance of supporting evidence to allow for the transparent creation of current and accurate variant interpretations for use in cancer precision medicine.

Subfields: Cancer Research, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bc7bee4042d50127719cb17a9b30b0a86f51f23b

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Citations in the corpus

DGIdb 3.0: a redesign and expansion of the drug–gene interaction database (2017, unknown): “With these more frequent, incremental updates to the DGIdb, there has been a substantial increase in drug–gene interaction content from IUPHAR’s Guide to Pharmacology and CIViC, a 23 and 200% increase, respectively (5,11).”
Human Disease Ontology 2018 update: classification, content and workflow expansion (2018, background): “• rare cancers from Clinical Interpretation of Variants in Cancer (CIViC) (33), this work has enhanced DO’s content, for clinically actionable cancer variants, as represented in literature, and defined in the CIViC database.”
Precision Oncology: The Road Ahead (2017, background): “Multiple tools now include “interpretations” or summaries of the driver mutations written by clinicians – including the Precision Medicine Knowledgebase (at Weill Cornell) and the Personalized Cancer Therapy knowledge base (at MD Anderson) – or by the “crowd” [111, 112] (see list of references in Ta”
Analysis and Visualization of Longitudinal Genomic and Clinical Data from the AACR Project GENIE Biopharma Collaborative in cBioPortal (2023, methodology): “The cBioPortal is integrated with various other databases to help with interpretability of the genomic data, including OncoKB (5), CIVIC (6), MyCancerGenome (7), Cancer Hotspots (8), and gnomAD (9).”
JBrowse 2: a modular genome browser with views of synteny and structural variation (2022, background): “11), and plugins that provide data adapters for fetching data from the mygene. info [37] and the CIVIC API [38].”
Molecular profiling for precision cancer therapies (2020, methodology): “The details of the CIViC variant evidence score [78, 149] and The OncoKB level of evidence system [77, 150] are available in the literature and on the relevant websites.”
Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations (2017, background): “…and pre-clinical experiments, and currently several resources are dedicated to gather and curate these data, such as ClinVar [7], DoCM [8], OncoKB [9], My Cancer Genome (https://www.mycancergenome.org), PMKB [10], PCT (https://pct.mdanderson.org), CIViC [11], and JAX-CKB (https://ckb.jax.org).”
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts (2020, background): “For example, some claims from CIViC(22) can be imported with the additional category of drug resistance.”