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...)
- to stream Pmc, to step Corpus: 000054
- 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
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">G-Links: a gene-centric link acquisition service</title>
<author><name sortKey="Oshita, Kazuki" sort="Oshita, Kazuki" uniqKey="Oshita K" first="Kazuki" last="Oshita">Kazuki Oshita</name>
<affiliation wicri:level="1"><nlm:aff id="a1">Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882</wicri:regionArea>
<wicri:noRegion>252-0882</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Tomita, Masaru" sort="Tomita, Masaru" uniqKey="Tomita M" first="Masaru" last="Tomita">Masaru Tomita</name>
<affiliation wicri:level="1"><nlm:aff id="a1">Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882</wicri:regionArea>
<wicri:noRegion>252-0882</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Arakawa, Kazuharu" sort="Arakawa, Kazuharu" uniqKey="Arakawa K" first="Kazuharu" last="Arakawa">Kazuharu Arakawa</name>
<affiliation wicri:level="1"><nlm:aff id="a1">Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882</wicri:regionArea>
<wicri:noRegion>252-0882</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">26673001</idno>
<idno type="pmc">4670005</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4670005</idno>
<idno type="RBID">PMC:4670005</idno>
<idno type="doi">10.12688/f1000research.5754.2</idno>
<date when="2015">2015</date>
<idno type="wicri:Area/Pmc/Corpus">000054</idno>
<idno type="wicri:Area/Pmc/Curation">000054</idno>
<idno type="wicri:Area/Pmc/Checkpoint">000101</idno>
<idno type="wicri:Area/Ncbi/Merge">000696</idno>
<idno type="wicri:Area/Ncbi/Curation">000696</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">000696</idno>
<idno type="wicri:Area/Main/Merge">000109</idno>
<idno type="wicri:Area/Main/Curation">000109</idno>
<idno type="wicri:Area/Main/Exploration">000109</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">G-Links: a gene-centric link acquisition service</title>
<author><name sortKey="Oshita, Kazuki" sort="Oshita, Kazuki" uniqKey="Oshita K" first="Kazuki" last="Oshita">Kazuki Oshita</name>
<affiliation wicri:level="1"><nlm:aff id="a1">Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882</wicri:regionArea>
<wicri:noRegion>252-0882</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Tomita, Masaru" sort="Tomita, Masaru" uniqKey="Tomita M" first="Masaru" last="Tomita">Masaru Tomita</name>
<affiliation wicri:level="1"><nlm:aff id="a1">Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882</wicri:regionArea>
<wicri:noRegion>252-0882</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Arakawa, Kazuharu" sort="Arakawa, Kazuharu" uniqKey="Arakawa K" first="Kazuharu" last="Arakawa">Kazuharu Arakawa</name>
<affiliation wicri:level="1"><nlm:aff id="a1">Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan</nlm:aff>
<country xml:lang="fr">Japon</country>
<wicri:regionArea>Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882</wicri:regionArea>
<wicri:noRegion>252-0882</wicri:noRegion>
</affiliation>
</author>
</analytic>
<series><title level="j">F1000Research</title>
<idno type="eISSN">2046-1402</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>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
<ext-link ext-link-type="uri" xlink:href="http://link.g-language.org/">http://link.g-language.org/</ext-link>
</p>
</div>
</front>
<back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aoki Kinoshita, Kf" uniqKey="Aoki Kinoshita K">KF Aoki-Kinoshita</name>
</author>
<author><name sortKey="Kinjo, Ar" uniqKey="Kinjo A">AR Kinjo</name>
</author>
<author><name sortKey="Morita, M" uniqKey="Morita M">M Morita</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Arakawa, K" uniqKey="Arakawa K">K Arakawa</name>
</author>
<author><name sortKey="Kido, N" uniqKey="Kido N">N Kido</name>
</author>
<author><name sortKey="Oshita, K" uniqKey="Oshita K">K Oshita</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><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 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 sortKey="Oshita, K" uniqKey="Oshita K">K Oshita</name>
</author>
<author><name sortKey="Arakawa, K" uniqKey="Arakawa K">K Arakawa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rice, P" uniqKey="Rice P">P Rice</name>
</author>
<author><name sortKey="Longden, I" uniqKey="Longden I">I Longden</name>
</author>
<author><name sortKey="Bleasby, A" uniqKey="Bleasby A">A Bleasby</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rose, Pw" uniqKey="Rose P">PW Rose</name>
</author>
<author><name sortKey="Bi, C" uniqKey="Bi C">C Bi</name>
</author>
<author><name sortKey="Bluhm, Wf" uniqKey="Bluhm W">WF Bluhm</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Smedley, D" uniqKey="Smedley D">D Smedley</name>
</author>
<author><name sortKey="Haider, S" uniqKey="Haider S">S Haider</name>
</author>
<author><name sortKey="Ballester, B" uniqKey="Ballester B">B 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)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/CyberinfraV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000109 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000109 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= CyberinfraV1 |flux= Main |étape= Exploration |type= RBID |clé= PMC:4670005 |texte= G-Links: a gene-centric link acquisition service }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:26673001" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \ | NlmPubMed2Wicri -a CyberinfraV1
![]() | This area was generated with Dilib version V0.6.25. | ![]() |