G-Links: a gene-centric link acquisition service
Identifieur interne : 000109 ( Main/Exploration ); précédent : 000108; suivant : 000110G-Links: a gene-centric link acquisition service
Auteurs : Kazuki Oshita [Japon] ; Masaru Tomita [Japon] ; Kazuharu Arakawa [Japon]Source :
- F1000Research [ 2046-1402 ] ; 2015.
Abstract
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
Url:
DOI: 10.12688/f1000research.5754.2
PubMed: 26673001
PubMed Central: 4670005
Affiliations:
Links toward previous steps (curation, corpus...)
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- to stream Pmc, to step Curation: 000054
- to stream Pmc, to step Checkpoint: 000101
- to stream Ncbi, to step Merge: 000696
- to stream Ncbi, to step Curation: 000696
- to stream Ncbi, to step Checkpoint: 000696
- to stream Main, to step Merge: 000109
- to stream Main, to step Curation: 000109
Le document en format XML
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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
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sortKey="Bairoch, A" uniqKey="Bairoch A">A Bairoch</name></author><author><name sortKey="Boeckmann, B" uniqKey="Boeckmann B">B Boeckmann</name></author><author><name sortKey="Ferro, S" uniqKey="Ferro S">S Ferro</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bhagat, J" uniqKey="Bhagat J">J Bhagat</name></author><author><name sortKey="Tanoh, F" uniqKey="Tanoh F">F Tanoh</name></author><author><name sortKey="Nzuobontane, E" uniqKey="Nzuobontane E">E Nzuobontane</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Brazas, Md" uniqKey="Brazas M">MD Brazas</name></author><author><name sortKey="Yim, D" uniqKey="Yim D">D Yim</name></author><author><name sortKey="Yeung, W" uniqKey="Yeung W">W Yeung</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chatr Aryamontri, A" uniqKey="Chatr Aryamontri A">A Chatr-Aryamontri</name></author><author><name sortKey="Breitkreutz, Bj" uniqKey="Breitkreutz B">BJ Breitkreutz</name></author><author><name sortKey="Oughtred, R" uniqKey="Oughtred R">R Oughtred</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Cote, Rg" uniqKey="Cote R">RG Cote</name></author><author><name sortKey="Jones, P" uniqKey="Jones P">P Jones</name></author><author><name sortKey="Martens, L" uniqKey="Martens L">L Martens</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Demchak, B" uniqKey="Demchak B">B Demchak</name></author><author><name sortKey="Hull, T" uniqKey="Hull T">T Hull</name></author><author><name sortKey="Reich, M" uniqKey="Reich M">M Reich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Diehn, M" uniqKey="Diehn M">M Diehn</name></author><author><name sortKey="Sherlock, G" uniqKey="Sherlock G">G Sherlock</name></author><author><name sortKey="Binkley, G" uniqKey="Binkley G">G Binkley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Harris, Ma" uniqKey="Harris M">MA Harris</name></author><author><name sortKey="Clark, J" uniqKey="Clark J">J Clark</name></author><author><name sortKey="Ireland, A" uniqKey="Ireland A">A Ireland</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, H" uniqKey="Huang H">H Huang</name></author><author><name sortKey="Mcgarvey, Pb" uniqKey="Mcgarvey P">PB McGarvey</name></author><author><name sortKey="Suzek, Be" uniqKey="Suzek B">BE Suzek</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kanehisa, M" uniqKey="Kanehisa M">M Kanehisa</name></author><author><name sortKey="Goto, S" uniqKey="Goto S">S Goto</name></author><author><name sortKey="Sato, Y" uniqKey="Sato Y">Y Sato</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katayama, T" uniqKey="Katayama T">T Katayama</name></author><author><name sortKey="Arakawa, K" uniqKey="Arakawa K">K Arakawa</name></author><author><name sortKey="Nakao, M" uniqKey="Nakao M">M Nakao</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katayama, T" uniqKey="Katayama T">T Katayama</name></author><author><name sortKey="Wilkinson, Md" uniqKey="Wilkinson M">MD Wilkinson</name></author><author><name sortKey="Aoki Kinoshita, Kf" uniqKey="Aoki Kinoshita K">KF Aoki-Kinoshita</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katayama, T" uniqKey="Katayama T">T Katayama</name></author><author><name sortKey="Wilkinson, Md" uniqKey="Wilkinson M">MD Wilkinson</name></author><author><name sortKey="Micklem, G" uniqKey="Micklem G">G Micklem</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Katayama, T" uniqKey="Katayama T">T Katayama</name></author><author><name sortKey="Wilkinson, Md" uniqKey="Wilkinson M">MD Wilkinson</name></author><author><name sortKey="Vos, R" uniqKey="Vos R">R Vos</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kent, Wj" uniqKey="Kent W">WJ Kent</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Nilsen, Tw" uniqKey="Nilsen T">TW Nilsen</name></author><author><name sortKey="Graveley, Br" uniqKey="Graveley B">BR Graveley</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Obayashi, T" uniqKey="Obayashi T">T Obayashi</name></author><author><name sortKey="Okamura, Y" uniqKey="Okamura Y">Y Okamura</name></author><author><name sortKey="Ito, S" uniqKey="Ito S">S Ito</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oshita, K" uniqKey="Oshita K">K Oshita</name></author><author><name sortKey="Arakawa, K" uniqKey="Arakawa K">K Arakawa</name></author><author><name sortKey="Tomita, M" uniqKey="Tomita M">M Tomita</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Ballester</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Smith, Rn" uniqKey="Smith R">RN Smith</name></author><author><name sortKey="Aleksic, J" uniqKey="Aleksic J">J Aleksic</name></author><author><name sortKey="Butano, D" uniqKey="Butano D">D Butano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stein, L" uniqKey="Stein L">L Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Stein, Ld" uniqKey="Stein L">LD Stein</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wu, C" uniqKey="Wu C">C Wu</name></author><author><name sortKey="Macleod, I" uniqKey="Macleod I">I Macleod</name></author><author><name sortKey="Su, Ai" uniqKey="Su A">AI Su</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Oshita, Kazuki" sort="Oshita, Kazuki" uniqKey="Oshita K" first="Kazuki" last="Oshita">Kazuki Oshita</name></noRegion><name sortKey="Arakawa, Kazuharu" sort="Arakawa, Kazuharu" uniqKey="Arakawa K" first="Kazuharu" last="Arakawa">Kazuharu Arakawa</name><name sortKey="Tomita, Masaru" sort="Tomita, Masaru" uniqKey="Tomita M" first="Masaru" last="Tomita">Masaru Tomita</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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