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Database Commons - The Ruby UCSC API

The Ruby UCSC API

Citations: 0

z-index 0.00

Short name The Ruby UCSC API
Full name
Description Accessing the UCSC genome database using Ruby.
URL http://rubyucscapi.userecho.com/
Year founded 2011
Last update & version 2012-09-01    0.5.2
Availability Not Available
University/Institution hosted Nagasaki University
Address Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan
City Nagasaki
Province/State
Country/Region Japan
Contact name Hiroyuki Mishima
Contact email hmishima@nagasaki-u.ac.jp
Data type(s)
Major organism(s)
Keyword(s)
  • application programming interface
  • UCSC Genome Database
Publication(s)
  • The Ruby UCSC API: accessing the UCSC genome database using Ruby. [PMID: 22994508]

    Hiroyuki Mishima, Jan Aerts, Toshiaki Katayama, Raoul J P Bonnal, Koh-ichiro Yoshiura
    BMC bioinformatics 2012:13
    0 Citations (Google Scholar as of 2016-06-09)

    Abstract: The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

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Tags

Literature
Homo sapiens
application programming interface UCSC Genome Database

Record metadata

  • Created on: 2015-06-30
  • Curated by:
    • Mengwei Li [2016-02-16]
    • Lin Liu [2016-01-27]
    • Guangyu Wang [2015-12-06]
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