MyGene.info and MyVariant.info: Gene and Variant Annotation Query Services

MyGene.info and MyVariant.info provide high-performance data APIs for querying gene and variant annotation information. They demonstrate a new model for organizing biological annotation information by utilizing a cloud-based scalable infrastructure. MyGene.info and MyVariant.info can be accessed at http://mygene.info and http://myvariant.info. Content: The accumulation of biomedical knowledge is growing exponentially. There have been tremendous efforts seeking to structure research findings as annotations on various biological entities (e.g., genes, genetic variants, pathways). However, these annotations are fragmented among many resources that range greatly in terms of size, funding, and visibility (e.g., Ensembl, Uniprot, PROSITE and Reactome). Tools for knowledge integration enable more efficient analysis of genome-scale data sets and discovery of relationships between biological entities. Bioinformaticians facing data integration problems generally pursue one of two strategies: data warehousing and data federation. Data warehousing involves downloading flat-files from various sources, writing parsers to process the files, and then loading the parsed data in a local database. This strategy has the advantage of very high performance, but also requires significant initial effort to write the parsers and ongoing effort to keep the resource peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/035667 doi: bioRxiv preprint first posted online Dec. 30, 2015;