NOTE:
+Some rights reserved. This work permits non-commercial use, distribution and reproduction in any
+medium, provided the original author and source are credited. The data and code underlying this
+project are copyright Johannes Birgmeier.
+
+We take no responsibility for diagnoses or medical decisions based on information obtained from this
+website.
+Varaico +stands for "Variation Research Advancing Insight in Complex Organisms". Varaico 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 + +
+ ++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 as described on the table below: +
+ ++
| Color | +Level of literature support | +
|---|---|
| + | More than 20 papers mention the variant | +
| + | Some papers mention the variant | +
| + | Few papers mention the variant | +
+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 "varChat".
+ ++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
+De Paoli F, Berardelli S, Limongelli I, Rizzo E, Zucca S. VarChat: the generative AI +assistant for the interpretation of human genomic variations. Bioinformatics. +2024Mar29;40(4). PMID: 38579245; PMC: PMC11055464