KBWS: an EMBOSS associated package for accessing bioinformatics web services
Identifieur interne : 000659 ( Pmc/Curation ); précédent : 000658; suivant : 000660KBWS: an EMBOSS associated package for accessing bioinformatics web services
Auteurs : Kazuki Oshita [Japon] ; Kazuharu Arakawa [Japon] ; Masaru Tomita [Japon]Source :
- Source Code for Biology and Medicine [ 1751-0473 ] ; 2011.
Abstract
The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from
Url:
DOI: 10.1186/1751-0473-6-8
PubMed: 21529350
PubMed Central: 3101651
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">KBWS: an EMBOSS associated package for accessing bioinformatics web services</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="I1">1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520</wicri:regionArea></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="I1">1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520</wicri:regionArea></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="I1">1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21529350</idno><idno type="pmc">3101651</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101651</idno><idno type="RBID">PMC:3101651</idno><idno type="doi">10.1186/1751-0473-6-8</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000659</idno><idno type="wicri:Area/Pmc/Curation">000659</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">KBWS: an EMBOSS associated package for accessing bioinformatics web services</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="I1">1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520</wicri:regionArea></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="I1">1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520</wicri:regionArea></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="I1">1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520</wicri:regionArea></affiliation></author></analytic><series><title level="j">Source Code for Biology and Medicine</title><idno type="eISSN">1751-0473</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from <ext-link ext-link-type="uri" xlink:href="http://www.g-language.org/kbws/">http://www.g-language.org/kbws/</ext-link> and GitHub repository <ext-link ext-link-type="uri" xlink:href="http://github.com/cory-ko/KBWS">http://github.com/cory-ko/KBWS</ext-link>. Users can utilize the SOAP services implemented in Perl directly via WSDL file at <ext-link ext-link-type="uri" xlink:href="http://soap.g-language.org/kbws.wsdl">http://soap.g-language.org/kbws.wsdl</ext-link> (RPC Encoded) and <ext-link ext-link-type="uri" xlink:href="http://soap.g-language.org/kbws_dl.wsdl">http://soap.g-language.org/kbws_dl.wsdl</ext-link> (Document/literal).</p></div></front><back><div1 type="bibliography"><listBibl><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><author><name sortKey="Laurent, T" uniqKey="Laurent T">T Laurent</name></author><author><name sortKey="Orlowski, J" uniqKey="Orlowski J">J Orlowski</name></author><author><name sortKey="Roos, M" uniqKey="Roos M">M Roos</name></author><author><name sortKey="Wolstencroft, K" uniqKey="Wolstencroft K">K Wolstencroft</name></author><author><name sortKey="Aleksejevs, S" uniqKey="Aleksejevs S">S Aleksejevs</name></author><author><name sortKey="Stevens, R" uniqKey="Stevens R">R Stevens</name></author><author><name sortKey="Pettifer, S" uniqKey="Pettifer S">S Pettifer</name></author><author><name sortKey="Lopez, R" uniqKey="Lopez R">R Lopez</name></author><author><name sortKey="Goble, Ca" uniqKey="Goble C">CA Goble</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="Stockinger, H" uniqKey="Stockinger H">H Stockinger</name></author><author><name sortKey="Attwood, T" uniqKey="Attwood T">T Attwood</name></author><author><name sortKey="Chohan, Sn" uniqKey="Chohan S">SN Chohan</name></author><author><name sortKey="Cote, R" uniqKey="Cote R">R Côté</name></author><author><name sortKey="Cudre Mauroux, P" uniqKey="Cudre Mauroux P">P Cudré-Mauroux</name></author><author><name sortKey="Falquet, L" uniqKey="Falquet L">L Falquet</name></author><author><name sortKey="Fernandes, P" uniqKey="Fernandes P">P Fernandes</name></author><author><name sortKey="Finn, Rd" uniqKey="Finn R">RD Finn</name></author><author><name sortKey="Hupponen, T" uniqKey="Hupponen T">T Hupponen</name></author><author><name sortKey="Korpelainen, E" uniqKey="Korpelainen E">E Korpelainen</name></author><author><name sortKey="Labarga, A" uniqKey="Labarga A">A Labarga</name></author><author><name sortKey="Laugraud, A" uniqKey="Laugraud A">A Laugraud</name></author><author><name sortKey="Lima, T" uniqKey="Lima T">T Lima</name></author><author><name sortKey="Pafillis, E" uniqKey="Pafillis E">E Pafillis</name></author><author><name sortKey="Pagni, M" uniqKey="Pagni M">M Pagni</name></author><author><name sortKey="Pettifer, S" uniqKey="Pettifer S">S Pettifer</name></author><author><name sortKey="Phan, I" uniqKey="Phan I">I 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Source Code Biol Med</journal-id><journal-title-group><journal-title>Source Code for Biology and Medicine</journal-title></journal-title-group><issn pub-type="epub">1751-0473</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">21529350</article-id><article-id pub-id-type="pmc">3101651</article-id><article-id pub-id-type="publisher-id">1751-0473-6-8</article-id><article-id pub-id-type="doi">10.1186/1751-0473-6-8</article-id><article-categories><subj-group subj-group-type="heading"><subject>Brief Reports</subject></subj-group></article-categories><title-group><article-title>KBWS: an EMBOSS associated package for accessing bioinformatics web services</article-title></title-group><contrib-group><contrib contrib-type="author" id="A1"><name><surname>Oshita</surname><given-names>Kazuki</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>cory@g-language.org</email></contrib><contrib contrib-type="author" corresp="yes" id="A2"><name><surname>Arakawa</surname><given-names>Kazuharu</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>gaou@sfc.keio.ac.jp</email></contrib><contrib contrib-type="author" id="A3"><name><surname>Tomita</surname><given-names>Masaru</given-names></name><xref ref-type="aff" rid="I1">1</xref><email>mt@sfc.keio.ac.jp</email></contrib></contrib-group><aff id="I1"><label>1</label>1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan</aff><pub-date pub-type="collection"><year>2011</year></pub-date><pub-date pub-type="epub"><day>29</day><month>4</month><year>2011</year></pub-date><volume>6</volume><fpage>8</fpage><lpage>8</lpage><history><date date-type="received"><day>12</day><month>2</month><year>2011</year></date><date date-type="accepted"><day>29</day><month>4</month><year>2011</year></date></history><permissions><copyright-statement>Copyright ©2011 Oshita et al; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2011</copyright-year><copyright-holder>Oshita et al; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0">http://creativecommons.org/licenses/by/2.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><self-uri xlink:href="http://www.scfbm.org/content/6/1/8"></self-uri><abstract><p>The availability of bioinformatics web-based services is rapidly proliferating, for their interoperability and ease of use. The next challenge is in the integration of these services in the form of workflows, and several projects are already underway, standardizing the syntax, semantics, and user interfaces. In order to deploy the advantages of web services with locally installed tools, here we describe a collection of proxy client tools for 42 major bioinformatics web services in the form of European Molecular Biology Open Software Suite (EMBOSS) UNIX command-line tools. EMBOSS provides sophisticated means for discoverability and interoperability for hundreds of tools, and our package, named the Keio Bioinformatics Web Service (KBWS), adds functionalities of local and multiple alignment of sequences, phylogenetic analyses, and prediction of cellular localization of proteins and RNA secondary structures. This software implemented in C is available under GPL from <ext-link ext-link-type="uri" xlink:href="http://www.g-language.org/kbws/">http://www.g-language.org/kbws/</ext-link> and GitHub repository <ext-link ext-link-type="uri" xlink:href="http://github.com/cory-ko/KBWS">http://github.com/cory-ko/KBWS</ext-link>. Users can utilize the SOAP services implemented in Perl directly via WSDL file at <ext-link ext-link-type="uri" xlink:href="http://soap.g-language.org/kbws.wsdl">http://soap.g-language.org/kbws.wsdl</ext-link> (RPC Encoded) and <ext-link ext-link-type="uri" xlink:href="http://soap.g-language.org/kbws_dl.wsdl">http://soap.g-language.org/kbws_dl.wsdl</ext-link> (Document/literal).</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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