mygene

The software tool "MyGene" addresses the challenge of fragmented biomedical knowledge across various data repositories by providing a centralized platform for accessing gene annotations. The tool, accessible through high-performance web services at http://mygene.info, enables bioinformatics developers to retrieve gene annotation data programmatically. Since its previous release in 2013, MyGene has undergone complete refactoring, expanding its support from nine to over 14,000 species and covering more than 17 million genes with over 50 gene-specific annotation types.
The updated infrastructure of MyGene.info ensures scalability, offering high performance and concurrency. With two simple web service endpoints, the tool provides efficient query access to aggregated gene annotations, streamlining the integration of comprehensive knowledge from diverse resources.

Topic

Molecular genetics

Detail

  • Operation: Data retrieval;ID mapping

  • Software interface: Command-line user interface,Library

  • Language: R

  • License: Artistic License 2.0

  • Cost: Free

  • Version name: 1.38.0

  • Credit: -

  • Input: Gene symbol [Matrix format]

  • Output: Gene ID (NCBI) [Matrix format], Ensembl gene ID [Matrix format]

  • Contact: Adam Mark, Cyrus Afrasiabi, Chunlei Wu cwu@scripps.edu

  • Collection: -

  • Maturity: Stable

Publications

  • MyGene.info: gene annotation query as a service
  • Xin J, Mark A, Afrasiabi C, Tsueng G, Juchler M, Gopal N, Stupp GS, Putman TE, Ainscough BJ, Griffith OL, Torkamani A, Whetzel PL, Mungall CJ, Mooney SD, Su AI, Wu C. 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. PMID: 27154141; PMCID: PMC4858870.
  • https://doi.org/10.1186/s13059-016-0953-9
  • PMID: 27154141
  • PMC: PMC4858870

Download and documentation

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