1. Which variants are included in the Bibliome Variant Database?
All variants in the Bibliome Variant Database have been identified in open access publications. Currently, the database contains variants identified in over 140,000 publications among a total of over 3,500,000 publications examined.
2. How are variants assigned to genes?
Variants are assigned to genes using a combination of rule-based and machine-learning based methods.
3. Are variants mapped to only to HGNC-approved gene symbols?
No, variants are mapped to HGNC-approved gene symbols, as well as unique previous, alternate, and synonymous gene symbols. A unique gene symbol is a symbol that appears only once in the HGNC Total Approved Symbols datafile.
4. How often is the Bibliome Variant Database updated?
The Bibliome Variant Database will be updated at regular intervals of a currently undecided timespan.
5. How can I keep up-to-date with Bibliome Variant Database news and database content updates?
Follow @sam_w_baker on Twitter to keep up to date with database news and content update announcements.
6. Why is my variant-of-interest missing from the database?
The automated variant extraction methods can identify most HGVS-compliant and common non-HGVS-compliant variant representations within text. It is possible that missing variants were not identified during variant extraction or that the variant was assigned to the incorrect gene.
7. How can I cite the Bibliome Variant Database?
The manuscript describing the database is in preparation. Details to follow.
8. What are ideal use cases of the Bibliome Variant Database?
Ideal use cases of the BVdb include any context where gathering primary literature evidence describing a given variant is a time-consuming or repetitive necessity. Please note, the BVdb does not provide any variant interpretations - it only provides links to references and resources with which users can generate their own variant interpretations.
9. I tried searching for a common rsID I know should be in the database - why can't I find it?
This version of the BVdb does not contain intergenic rsID annotations. This will be rectified in a future update.
10. What is publication information displayed for only the 100 most recent publications containing a given variant?
This change was made to improve overall website performance and reduce page load times. The BVdb VCF file contains the PubMed IDs for all publications that contain a given variant.