G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved]
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 a...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
F1000 Research Ltd
2015-11-01
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| Series: | F1000Research |
| Subjects: | |
| Online Access: | http://f1000research.com/articles/3-285/v2 |
| _version_ | 1818438617085771776 |
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| author | Kazuki Oshita Masaru Tomita Kazuharu Arakawa |
| author_facet | Kazuki Oshita Masaru Tomita Kazuharu Arakawa |
| author_sort | Kazuki Oshita |
| collection | DOAJ |
| description | 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/ |
| first_indexed | 2024-12-14T17:43:25Z |
| format | Article |
| id | doaj.art-6e06f198f9854b7d80beef475ca84fbe |
| institution | Directory Open Access Journal |
| issn | 2046-1402 |
| language | English |
| last_indexed | 2024-12-14T17:43:25Z |
| publishDate | 2015-11-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | F1000Research |
| spelling | doaj.art-6e06f198f9854b7d80beef475ca84fbe2022-12-21T22:52:47ZengF1000 Research LtdF1000Research2046-14022015-11-01310.12688/f1000research.5754.26534G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved]Kazuki Oshita0Masaru Tomita1Kazuharu Arakawa2Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, JapanInstitute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, JapanInstitute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, JapanWith 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/http://f1000research.com/articles/3-285/v2BioinformaticsData Sharing |
| spellingShingle | Kazuki Oshita Masaru Tomita Kazuharu Arakawa G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved] F1000Research Bioinformatics Data Sharing |
| title | G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved] |
| title_full | G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved] |
| title_fullStr | G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved] |
| title_full_unstemmed | G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved] |
| title_short | G-Links: a gene-centric link acquisition service [version 2; referees: 2 approved] |
| title_sort | g links a gene centric link acquisition service version 2 referees 2 approved |
| topic | Bioinformatics Data Sharing |
| url | http://f1000research.com/articles/3-285/v2 |
| work_keys_str_mv | AT kazukioshita glinksagenecentriclinkacquisitionserviceversion2referees2approved AT masarutomita glinksagenecentriclinkacquisitionserviceversion2referees2approved AT kazuharuarakawa glinksagenecentriclinkacquisitionserviceversion2referees2approved |