Description

Varaico (Variation Research Advancing Insight in Complex Organisms) was created using literature mining, similar to AVADA. Varaico variants are generated by an automated process that extracts purely factual information about genes from scientific papers (by matching strings against gene names) and HGVS variant descriptions (using regular expressions). Varaico aims to reduce false-positive gene and variant mentions and link them together appropriately, but nonetheless, many variants displayed are not mapped to the genomic position intended by the authors.

For data questions, Varaico can be contacted at jbirgmei@gmail.com

Display Conventions and Configuration

Genomic locations of variants are labeled with the HGNC gene symbol and the variant change. Mouse over the variants to show the gene, variant, latest author/year/title, number of publications mentioning the variant, and variant effect.

Clicking on an item will provide a link directly to Varaico to view all publications mentioning this variant.

The items are colored based on the amount of literature support and are a gradient from the colors described on the table below:

Data access

The raw data can be explored interactively with the Table Browser or the Data Integrator. The data can be accessed from scripts through our API, the track name is "varaico".

For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from our download server. The file for this track is called varaico.bb. Individual regions or the whole genome annotation can be obtained using our tool bigBedToBed which can be compiled from the source code or downloaded as a precompiled binary for your system.

Instructions for downloading source code and binaries can be found here. The tool can also be used to obtain only features within a given range, e.g.

bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/varaico.bb -chrom=chr21 -start=0 -end=10000000 stdout