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The Ruby UCSC API: accessing the UCSC genome database using Ruby.

Hiroyuki Mishima1, Jan Aerts, Toshiaki Katayama

  • 1Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan. hmishima@nagasaki-u.ac.jp

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Summary
This summary is machine-generated.

A new Ruby API allows biologists to programmatically access the University of California, Santa Cruz (UCSC) genome database. This tool simplifies genomic data retrieval for various organisms, enhancing research capabilities.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • The University of California, Santa Cruz (UCSC) genome database is a widely used resource for genomic annotation.
  • Existing access methods include a web browser and programmatic queries, but a biologist-friendly scripting language API was lacking.

Purpose of the Study:

  • To develop a Ruby-based Application Programming Interface (API) for accessing the UCSC genome database.
  • To provide biologists with a simplified, object-oriented method for programmatic genomic data retrieval.

Main Methods:

  • The API is implemented as a BioRuby plug-in using the ActiveRecord 3 framework for object-relational mapping.
  • It supports all organisms within the UCSC database and utilizes bin indexing for efficient querying of genomic intervals.
  • Genomic sequence queries are supported using local *.2bit files, independent of the main MySQL database.

Main Results:

  • The Ruby UCSC API facilitates direct programmatic access to the UCSC genome database.
  • It eliminates the need for manual SQL statement construction.
  • The API is compatible with various Ruby environments, including JRuby.

Conclusions:

  • The Ruby UCSC API simplifies programmatic querying of the UCSC genome database for biologists.
  • The tool is available via the RubyGem system, with source code and documentation accessible on GitHub.
  • User feedback and support are available through a dedicated website.