High-performance web services for querying gene and variant annotation

Jiwen Xin; Adam Mark; Cyrus Afrasiabi; Ginger Tsueng; Moritz Juchler; Nikhil Gopal; Gregory S Stupp; Timothy E Putman; Benjamin J Ainscough; Obi L Griffith; Ali Torkamani; Patricia L Whetzel; Christopher J Mungall; Sean D Mooney; Andrew I Su; Chunlei Wu

doi:10.1186/s13059-016-0953-9

High-performance web services for querying gene and variant annotation

Genome Biol. 2016 May 6;17(1):91. doi: 10.1186/s13059-016-0953-9.

Authors

Jiwen Xin¹, Adam Mark^{1

2}, Cyrus Afrasiabi¹, Ginger Tsueng¹, Moritz Juchler³, Nikhil Gopal³, Gregory S Stupp¹, Timothy E Putman¹, Benjamin J Ainscough⁴, Obi L Griffith⁴, Ali Torkamani^{5

6}, Patricia L Whetzel⁷, Christopher J Mungall⁸, Sean D Mooney³, Andrew I Su^{9

10}, Chunlei Wu¹¹

Affiliations

¹ Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
² Current address: Avera Cancer Institute, 11099 North Torrey Pines Road, La Jolla, CA, 92037, USA.
³ Department of Biomedical Informatics and Medical Education, The University of Washington, Box SLU-BIME 358047, Seattle, WA, 98195, USA.
⁴ McDonnell Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St. Louis, MO, 63108, USA.
⁵ Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
⁶ The Scripps Translational Science Institute, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
⁷ Center for Research in Biological Systems, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
⁸ Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.
⁹ Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA. asu@scripps.edu.
¹⁰ The Scripps Translational Science Institute, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA. asu@scripps.edu.
¹¹ Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA. cwu@scripps.edu.

Abstract

Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community.

Keywords: API; Annotation; Cloud; Database; Gene; Repository; Variant.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Database Management Systems
Databases, Genetic
Genetic Variation*
Humans
Internet
Molecular Sequence Annotation*
Sequence Analysis, DNA*
Software*
User-Computer Interface

Abstract

Publication types

MeSH terms

Grants and funding