AVADA (Automatic Variant evidence DAtabase)

The AVADA database includes unvalidated (see disclaimer) variant evidence data, automatically retrieved from 61,116 full text papers deposited in PubMed until 07-2016.

Source code download

Git repository

Automatically retrieved variants download

Copyright disclaimer

Non-US users should consider copyright laws in their home countries before retrieving AVADA data.

Variant accuracy disclaimer

AVADA is an important step forward in automated variant evidence retrieval. Looking up AVADA evidence is very easy. But AVADA is far from perfect: 1. It is not comprehensive. Some key papers will be missing. 2. Automated mapping of author mentioned variants to the correct genomic coordinates is hard. AVADA gets many of these wrong. 3. AVADA attempts to curate only papers that seem relevant for Mendelian diseases, but makes mistakes there too. USE AVADA AT YOUR OWN RISK. VERIFY GENOMIC COORDINATE MAPPINGS, ASSESS VARIANT AND GENE PATHOGENICITY FROM ALL EVDIENCE YOU COLLECT. WE TAKE NO RESPONSIBILITY FOR MISUSE OF AVADA DATA.

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AVADA v1.00

Manuscript / How to cite

Johannes Birgmeier, Cole A. Deisseroth, Laura E. Hayward, Luisa M. T. Galhardo, Andrew P. Tierno, Karthik A. Jagadeesh, Peter D. Stenson, David N. Cooper, Jonathan A. Bernstein, Maximilian Haeussler, and Gill Bejerano:
AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature.
Genetics in Medicine, 2019. DOI: 10.1038/s41436-019-0643-6
PMID: 31467448