DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Identifieur interne : 000575 ( Pmc/Curation ); précédent : 000574; suivant : 000576DASMIweb: online integration, analysis and assessment of distributed protein interaction data
Auteurs : Hagen Blankenburg ; Fidel Ramírez ; Joachim Büch ; Mario AlbrechtSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2009.
Abstract
In recent years, we have witnessed a substantial increase of the amount of available protein interaction data. However, most data are currently not readily accessible to the biologist at a single site, but scattered over multiple online repositories. Therefore, we have developed the DASMIweb server that affords the integration, analysis and qualitative assessment of distributed sources of interaction data in a dynamic fashion. Since DASMIweb allows for querying many different resources of protein and domain interactions simultaneously, it serves as an important starting point for interactome studies and assists the user in finding publicly accessible interaction data with minimal effort. The pool of queried resources is fully configurable and supports the inclusion of own interaction data or confidence scores. In particular, DASMIweb integrates confidence measures like functional similarity scores to assess individual interactions. The retrieved results can be exported in different file formats like MITAB or SIF. DASMIweb is freely available at
Url:
DOI: 10.1093/nar/gkp438
PubMed: 19502495
PubMed Central: 2703953
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">DASMIweb: online integration, analysis and assessment of distributed protein interaction data</title><author><name sortKey="Blankenburg, Hagen" sort="Blankenburg, Hagen" uniqKey="Blankenburg H" first="Hagen" last="Blankenburg">Hagen Blankenburg</name></author><author><name sortKey="Ramirez, Fidel" sort="Ramirez, Fidel" uniqKey="Ramirez F" first="Fidel" last="Ramírez">Fidel Ramírez</name></author><author><name sortKey="Buch, Joachim" sort="Buch, Joachim" uniqKey="Buch J" first="Joachim" last="Büch">Joachim Büch</name></author><author><name sortKey="Albrecht, Mario" sort="Albrecht, Mario" uniqKey="Albrecht M" first="Mario" last="Albrecht">Mario Albrecht</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19502495</idno><idno type="pmc">2703953</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703953</idno><idno type="RBID">PMC:2703953</idno><idno type="doi">10.1093/nar/gkp438</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000575</idno><idno type="wicri:Area/Pmc/Curation">000575</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">DASMIweb: online integration, analysis and assessment of distributed protein interaction data</title><author><name sortKey="Blankenburg, Hagen" sort="Blankenburg, Hagen" uniqKey="Blankenburg H" first="Hagen" last="Blankenburg">Hagen Blankenburg</name></author><author><name sortKey="Ramirez, Fidel" sort="Ramirez, Fidel" uniqKey="Ramirez F" first="Fidel" last="Ramírez">Fidel Ramírez</name></author><author><name sortKey="Buch, Joachim" sort="Buch, Joachim" uniqKey="Buch J" first="Joachim" last="Büch">Joachim Büch</name></author><author><name sortKey="Albrecht, Mario" sort="Albrecht, Mario" uniqKey="Albrecht M" first="Mario" last="Albrecht">Mario Albrecht</name></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>In recent years, we have witnessed a substantial increase of the amount of available protein interaction data. However, most data are currently not readily accessible to the biologist at a single site, but scattered over multiple online repositories. Therefore, we have developed the DASMIweb server that affords the integration, analysis and qualitative assessment of distributed sources of interaction data in a dynamic fashion. Since DASMIweb allows for querying many different resources of protein and domain interactions simultaneously, it serves as an important starting point for interactome studies and assists the user in finding publicly accessible interaction data with minimal effort. The pool of queried resources is fully configurable and supports the inclusion of own interaction data or confidence scores. In particular, DASMIweb integrates confidence measures like functional similarity scores to assess individual interactions. The retrieved results can be exported in different file formats like MITAB or SIF. DASMIweb is freely available at <ext-link ext-link-type="uri" xlink:href="http://www.dasmiweb.de">http://www.dasmiweb.de</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Frishman, D" uniqKey="Frishman D">D Frishman</name></author><author><name sortKey="Albrecht, M" uniqKey="Albrecht M">M Albrecht</name></author><author><name sortKey="Blankenburg, H" uniqKey="Blankenburg H">H Blankenburg</name></author><author><name sortKey="Bork, P" uniqKey="Bork P">P Bork</name></author><author><name sortKey="Harrington, Ed" uniqKey="Harrington E">ED Harrington</name></author><author><name sortKey="Hermjakob, H" uniqKey="Hermjakob H">H Hermjakob</name></author><author><name sortKey="Jensen, Lj" uniqKey="Jensen L">LJ Jensen</name></author><author><name sortKey="Juan, Da" uniqKey="Juan D">DA Juan</name></author><author><name sortKey="Lengauer, T" uniqKey="Lengauer T">T Lengauer</name></author><author><name sortKey="Pagel, P" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19502495</article-id><article-id pub-id-type="pmc">2703953</article-id><article-id pub-id-type="doi">10.1093/nar/gkp438</article-id><article-id pub-id-type="publisher-id">gkp438</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>DASMIweb: online integration, analysis and assessment of distributed protein interaction data</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Blankenburg</surname><given-names>Hagen</given-names></name><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Ramírez</surname><given-names>Fidel</given-names></name></contrib><contrib contrib-type="author"><name><surname>Büch</surname><given-names>Joachim</given-names></name></contrib><contrib contrib-type="author"><name><surname>Albrecht</surname><given-names>Mario</given-names></name></contrib></contrib-group><aff>Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbrücken, Germany</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>+49 681 9325 328</phone>; Fax: <fax>+49 681 9325 399</fax>; Email: <email>hagen.blankenburg@mpi-inf.mpg.de</email></corresp></author-notes><pub-date pub-type="ppub"><day>1</day><month>7</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>5</day><month>6</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>5</day><month>6</month><year>2009</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>37</volume><issue>Web Server issue</issue><fpage>W122</fpage><lpage>W128</lpage><history><date date-type="received"><day>28</day><month>2</month><year>2009</year></date><date date-type="rev-recd"><day>25</day><month>4</month><year>2009</year></date><date date-type="accepted"><day>11</day><month>5</month><year>2009</year></date></history><permissions><copyright-statement>© 2009 The Author(s)</copyright-statement><copyright-year>2009</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/">http://creativecommons.org/licenses/by-nc/2.0/uk/</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>In recent years, we have witnessed a substantial increase of the amount of available protein interaction data. However, most data are currently not readily accessible to the biologist at a single site, but scattered over multiple online repositories. Therefore, we have developed the DASMIweb server that affords the integration, analysis and qualitative assessment of distributed sources of interaction data in a dynamic fashion. Since DASMIweb allows for querying many different resources of protein and domain interactions simultaneously, it serves as an important starting point for interactome studies and assists the user in finding publicly accessible interaction data with minimal effort. The pool of queried resources is fully configurable and supports the inclusion of own interaction data or confidence scores. In particular, DASMIweb integrates confidence measures like functional similarity scores to assess individual interactions. The retrieved results can be exported in different file formats like MITAB or SIF. DASMIweb is freely available at <ext-link ext-link-type="uri" xlink:href="http://www.dasmiweb.de">http://www.dasmiweb.de</ext-link>.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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