High-performance web services for querying gene and variant annotation

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

doi:10.1186/s13059-016-0953-9

High-performance web services for querying gene and variant annotation

Journal Article · Fri May 06 00:00:00 EDT 2016 · Genome Biology (Online)

DOI:https://doi.org/10.1186/s13059-016-0953-9· OSTI ID:1626935

Xin, Jiwen ^[1]; Mark, Adam ^[2]; Afrasiabi, Cyrus ^[3]; Tsueng, Ginger ^[3]; Juchler, Moritz ^[4]; Gopal, Nikhil ^[4]; Stupp, Gregory S. ^[3]; Putman, Timothy E. ^[3]; Ainscough, Benjamin J. ^[5]; Griffith, Obi L. ^[5]; Torkamani, Ali ^[6]; Whetzel, Patricia L. ^[7]; Mungall, Christopher J. ^[8]; Mooney, Sean D. ^[4]; Su, Andrew I. ^[9]; Wu, Chunlei ^[3]

The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular and Experimental Medicine; DOE/OSTI
The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular and Experimental Medicine; Avera Cancer Inst., La Jolla, CA (United States)
The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular and Experimental Medicine
Univ. of Washington, Seattle, WA (United States). Dept. of Biomedical Informatics and Medical Education
Washington Univ., St. Louis, MO (United States). School of Medicine, McDonnell Genome Inst.
The Scripps Research Inst., La Jolla, CA (United States). Dept. of Integrative Structural and Computational Biology and The Scripps Translational Science Inst.
Univ. of California, San Diego, CA (United States). Center for Research in Biological Systems
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
The Scripps Research Inst., La Jolla, CA (United States). Dept. of Molecular and Experimental Medicine and The Scripps Translational Science Inst.

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Univ. of California, San Diego, CA (United States)

Sponsoring Organization:: National Center for Advancing Translational Sciences (NCATS); National Institutes of Health (NIH); USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626935

Journal Information:: Genome Biology (Online), Journal Name: Genome Biology (Online) Journal Issue: 1 Vol. 17; ISSN 1474-760X

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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Variant

Additional file 10 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524764.v1 The current record is supplemented by this text	text	January 2021
Additional file 11 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524767 The current record is supplemented by this dataset	dataset	January 2021
Additional file 1 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524770.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 2 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524773 The current record is supplemented by this dataset	dataset	January 2021
Additional file 3 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524776 The current record is supplemented by this dataset	dataset	January 2021
Additional file 4 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524779 The current record is supplemented by this dataset	dataset	January 2021
Additional file 4 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524779.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 5 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524782 The current record is supplemented by this dataset	dataset	January 2021
Additional file 5 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524782.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 6 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524785 The current record is supplemented by this dataset	dataset	January 2021
Additional file 6 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524785.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 7 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524788 The current record is supplemented by this dataset	dataset	January 2021
Additional file 7 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524788.v1 The current record is supplemented by this dataset	dataset	January 2021
Additional file 8 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524791 The current record is supplemented by this text	text	January 2021
Additional file 8 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524791.v1 The current record is supplemented by this text	text	January 2021
Additional file 9 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524794 The current record is supplemented by this text	text	January 2021
Additional file 9 of Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.14524794.v1 The current record is supplemented by this text	text	January 2021
High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399 The current record is supplemented by this collection	collection	January 2016
High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399.v1 The current record is supplemented by this collection	collection	January 2016
Additional file 1: Table S1. of High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399_d1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 1: Table S1. of High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399_d1.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 3: Table S2. of High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399_d2 The current record is supplemented by this dataset	dataset	January 2016
Additional file 3: Table S2. of High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399_d2.v1 The current record is supplemented by this dataset	dataset	January 2016
Additional file 2: of High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399_d3 The current record is supplemented by this text	text	January 2016
Additional file 2: of High-performance web services for querying gene and variant annotation Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus https://doi.org/10.6084/m9.figshare.c.3605399_d3.v1 The current record is supplemented by this text	text	January 2016
Comparative genomics of the coconut crab and other decapod crustaceans: exploring the molecular basis of terrestrial adaptation Veldsman, Werner Pieter; Ma, Ka Yan; Hui, Jerome Ho Lam https://doi.org/10.6084/m9.figshare.c.5409696 The current record is supplemented by this collection	collection	January 2021

High-performance web services for querying gene and variant annotation

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