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The Ruby UCSC API: accessing the UCSC genome database using Ruby
http://hdl.handle.net/10069/30227
http://hdl.handle.net/10069/302274bf4c653-3fb4-43b7-9f7f-7384cf50982e
| 名前 / ファイル | ライセンス | アクション |
|---|---|---|
BMC13_240.pdf (847.9 kB)
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| Item type | 学術雑誌論文 / Journal Article(1) | |||||
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| 公開日 | 2013-01-15 | |||||
| タイトル | ||||||
| タイトル | The Ruby UCSC API: accessing the UCSC genome database using Ruby | |||||
| 言語 | ||||||
| 言語 | eng | |||||
| 資源タイプ | ||||||
| 資源タイプ識別子 | http://purl.org/coar/resource_type/c_6501 | |||||
| 資源タイプ | journal article | |||||
| 著者 |
Mishima, Hiroyuki
× Mishima, Hiroyuki× Aerts, Jan× Katayama, Toshiaki× Bonnal, Raoul J P× Yoshiura, Koh-ichiro |
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| 抄録 | ||||||
| 内容記述タイプ | Abstract | |||||
| 内容記述 | Background: 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. Results: 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). Conclusions: 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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| 書誌情報 |
BMC Bioinformatics 巻 13, p. 240, 発行日 2012-09-21 |
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| 出版者 | ||||||
| 出版者 | BioMed Central Ltd | |||||
| ISSN | ||||||
| 収録物識別子タイプ | ISSN | |||||
| 収録物識別子 | 14712105 | |||||
| DOI | ||||||
| 関連タイプ | isIdenticalTo | |||||
| 識別子タイプ | DOI | |||||
| 関連識別子 | 10.1186/1471-2105-13-240 | |||||
| 権利 | ||||||
| 権利情報 | © 2012 Mishima et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. | |||||
| 著者版フラグ | ||||||
| 出版タイプ | VoR | |||||
| 出版タイプResource | http://purl.org/coar/version/c_970fb48d4fbd8a85 | |||||
| 引用 | ||||||
| 内容記述タイプ | Other | |||||
| 内容記述 | BMC Bioinformatics, 13, 240; 2012 | |||||
