Curating and Suggesting Sources¶
All curated CIViC Evidence, Assertions, Variant Summaries, and Gene Summaries are based on peer-reviewed sources from the biomedical literature, currently limited to those publications indexed in PubMed or the ASCO Meeting Library. As soon as any publication is cited in CIViC, a separate Source Record is created and can be browsed or searched within the CIViC knowledgebase. Each Source Record includes details about the publication such as title, authors, abstract, and journal, as well as a table linking to all CIViC evidence curated for that source. Comments can be added to any Source Record at any time. Source comments are a useful place to document general or specific notes to aid current and future curation. For example, if a source has an overlapping patient population with another study already curated within CIViC, this can be documented in the comments. In other cases, the reference sequence used for determining variant coordinates might be recorded.
The direct submission of a “Source Suggestion” for future consideration and curation is an essential, yet simple, curation task. Once a manuscript containing clinically relevant cancer variant data is identified, a curator simply accesses the Add -> Source Suggestion form, selects a Source Type (PubMed or ASCO) and then enters a PubMed ID or ASCO Web ID. A comment must be included describing the relevance of this source to CIViC. The objective of the comment is to aid curators in selecting the suggested source for review and curation. Ideally, the comment will offer a brief summary of general study details and results. Optionally, a curator may also “pre-curate” the Gene Name, Variant Name, and Disease described by the source. More than one Source Suggestion can be made for a single source. For example, multiple lines of evidence might be proposed for curation for multiple genes, variants, or diseases from the same publication. After submission, a Source Suggestion can be accessed from the Source Suggestion Queue or through the source’s individual Source Record Page. Each Source Suggestion can be curated using the ‘Add Evidence Item’ action, which activates the Add Evidence form and pre-populates with any gene, variant, or disease details pre-curated for the source. After each Source Suggestion has been curated, curators can use the “Mark Suggestion as Curated” action. Once all Source Suggestions for a Source have been marked as curated, the Source itself attains a status of “Fully Curated”. Lastly, if upon review a Source Suggestion is determined to be unsuitable for curation in CIViC, the Source Suggestion is rejected using the “Reject Suggestion” action.