G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved]

• Main Authors: Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2015-11-01
• Series: F1000Research
• Subjects: Bioinformatics; Data Sharing
• Online Access: http://f1000research.com/articles/3-285/v2

With the availability of numerous curated databases, researchers are now able to efficiently use the multitude of biological data by integrating these resources via hyperlinks and cross-references. A large proportion of bioinformatics research tasks, however, may include labor-intensive tasks such as fetching, parsing, and merging datasets and functional annotations from distributed multi-domain databases. This data integration issue is one of the key challenges in bioinformatics. We aim to provide an identifier conversion and data aggregation system as a part of solution to solve this problem with a service named G-Links, 1) by gathering resource URI information from 130 databases and 30 web services in a gene-centric manner so that users can retrieve all available links about a given gene, 2) by providing RESTful API for easy retrieval of links including facet searching based on keywords and/or predicate types, and 3) by producing a variety of outputs as visual HTML page, tab-delimited text, and in Semantic Web formats such as Notation3 and RDF. G-Links as well as other relevant documentation are available at http://link.g-language.org/