1. Which variants are included in the Bibliome Variant Database?
All variants in the Bibliome Variant Database have been identified in open access publications. The database is composed primarily of variants located within or adjacent to annotated genes, primarily protein coding. Intergenic SNPs are typically not included in the database.
2. How are variants assigned to genes?
Variants are assigned to genes based on the relative spatial positioning of the gene symbol and cDNA and/or protein annotation of interest with publication text. Variants are mapped to the genome using the MANE Select transcript for each gene; for genes without a MANE Select transcript, variants are mapped to the transcript ID that appears most commonly within the corpus of open access literature.
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?
Beginning summer 2022, the BVdb will be updated approximately monthly moving forward.
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. It is possible that the missing variant was not identified during variant extraction, 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.