DASMI: exchanging, annotating and assessing molecular interaction data
Identifieur interne : 000645 ( Pmc/Checkpoint ); précédent : 000644; suivant : 000646DASMI: exchanging, annotating and assessing molecular interaction data
Auteurs : Hagen Blankenburg [Allemagne] ; Robert D. Finn ; Andreas Prli ; Andrew M. Jenkinson [Royaume-Uni] ; Fidel Ramírez [Allemagne] ; Dorothea Emig [Allemagne] ; Sven-Eric Schelhorn [Allemagne] ; Joachim Büch [Allemagne] ; Thomas Lengauer [Allemagne] ; Mario Albrecht [Allemagne]Source :
- Bioinformatics [ 1367-4803 ] ; 2009.
Abstract
Url:
DOI: 10.1093/bioinformatics/btp142
PubMed: 19420069
PubMed Central: 2677739
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">DASMI: exchanging, annotating and assessing molecular interaction data</title><author><name sortKey="Blankenburg, Hagen" sort="Blankenburg, Hagen" uniqKey="Blankenburg H" first="Hagen" last="Blankenburg">Hagen Blankenburg</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Finn, Robert D" sort="Finn, Robert D" uniqKey="Finn R" first="Robert D." last="Finn">Robert D. Finn</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA</nlm:aff><wicri:noCountry code="subfield">CB10 1SA</wicri:noCountry></affiliation></author><author><name sortKey="Prli, Andreas" sort="Prli, Andreas" uniqKey="Prli A" first="Andreas" last="Prli">Andreas Prli</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA</nlm:aff><wicri:noCountry code="subfield">CB10 1SA</wicri:noCountry></affiliation></author><author><name sortKey="Jenkinson, Andrew M" sort="Jenkinson, Andrew M" uniqKey="Jenkinson A" first="Andrew M." last="Jenkinson">Andrew M. Jenkinson</name><affiliation wicri:level="1"><nlm:aff id="AFF1">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD</wicri:regionArea><wicri:noRegion>CB10 1SD</wicri:noRegion></affiliation></author><author><name sortKey="Ramirez, Fidel" sort="Ramirez, Fidel" uniqKey="Ramirez F" first="Fidel" last="Ramírez">Fidel Ramírez</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Emig, Dorothea" sort="Emig, Dorothea" uniqKey="Emig D" first="Dorothea" last="Emig">Dorothea Emig</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Schelhorn, Sven Eric" sort="Schelhorn, Sven Eric" uniqKey="Schelhorn S" first="Sven-Eric" last="Schelhorn">Sven-Eric Schelhorn</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Buch, Joachim" sort="Buch, Joachim" uniqKey="Buch J" first="Joachim" last="Büch">Joachim Büch</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Lengauer, Thomas" sort="Lengauer, Thomas" uniqKey="Lengauer T" first="Thomas" last="Lengauer">Thomas Lengauer</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country 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type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677739</idno><idno type="RBID">PMC:2677739</idno><idno type="doi">10.1093/bioinformatics/btp142</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">000503</idno><idno type="wicri:Area/Pmc/Curation">000503</idno><idno type="wicri:Area/Pmc/Checkpoint">000645</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">DASMI: exchanging, annotating and assessing molecular interaction data</title><author><name sortKey="Blankenburg, Hagen" sort="Blankenburg, Hagen" uniqKey="Blankenburg H" first="Hagen" last="Blankenburg">Hagen Blankenburg</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Finn, Robert D" sort="Finn, Robert D" uniqKey="Finn R" first="Robert D." last="Finn">Robert D. Finn</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA</nlm:aff><wicri:noCountry code="subfield">CB10 1SA</wicri:noCountry></affiliation></author><author><name sortKey="Prli, Andreas" sort="Prli, Andreas" uniqKey="Prli A" first="Andreas" last="Prli">Andreas Prli</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA</nlm:aff><wicri:noCountry code="subfield">CB10 1SA</wicri:noCountry></affiliation></author><author><name sortKey="Jenkinson, Andrew M" sort="Jenkinson, Andrew M" uniqKey="Jenkinson A" first="Andrew M." last="Jenkinson">Andrew M. Jenkinson</name><affiliation wicri:level="1"><nlm:aff id="AFF1">European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD</wicri:regionArea><wicri:noRegion>CB10 1SD</wicri:noRegion></affiliation></author><author><name sortKey="Ramirez, Fidel" sort="Ramirez, Fidel" uniqKey="Ramirez F" first="Fidel" last="Ramírez">Fidel Ramírez</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Emig, Dorothea" sort="Emig, Dorothea" uniqKey="Emig D" first="Dorothea" last="Emig">Dorothea Emig</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Schelhorn, Sven Eric" sort="Schelhorn, Sven Eric" uniqKey="Schelhorn S" first="Sven-Eric" last="Schelhorn">Sven-Eric Schelhorn</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Buch, Joachim" sort="Buch, Joachim" uniqKey="Buch J" first="Joachim" last="Büch">Joachim Büch</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Lengauer, Thomas" sort="Lengauer, Thomas" uniqKey="Lengauer T" first="Thomas" last="Lengauer">Thomas Lengauer</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author><author><name sortKey="Albrecht, Mario" sort="Albrecht, Mario" uniqKey="Albrecht M" first="Mario" last="Albrecht">Mario Albrecht</name><affiliation wicri:level="3"><nlm:aff id="AFF1">Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken</wicri:regionArea><placeName><region type="land" nuts="2">Sarre (Land)</region><settlement type="city">Sarrebruck</settlement></placeName></affiliation></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</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><bold>Motivation:</bold> Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.</p><p><bold>Results:</bold> We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.</p><p><bold>Availability:</bold> The DASMI tools are available at <ext-link ext-link-type="uri" xlink:href="http://www.dasmi.de/">http://www.dasmi.de/</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://ipfam.sanger.ac.uk/graph">http://ipfam.sanger.ac.uk/graph</ext-link>. The DAS registry and the DAS 1.53E specification is found at <ext-link ext-link-type="uri" xlink:href="http://www.dasregistry.org/">http://www.dasregistry.org/</ext-link>.</p><p><bold>Contact:</bold> <email>mario.albrecht@mpi-inf.mpg.de</email></p><p><bold>Supplementary information:</bold> <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btp142/DC1">Supplementary data</ext-link> and all figures in color are available at <italic>Bioinformatics</italic> online.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aloy, P" uniqKey="Aloy P">P Aloy</name></author><author><name sortKey="Russell, Rb" uniqKey="Russell R">RB Russell</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Aragues, R" uniqKey="Aragues R">R Aragues</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Avila Campillo, I" uniqKey="Avila Campillo I">I 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">bioinformatics</journal-id><journal-id journal-id-type="hwp">bioinfo</journal-id><journal-title-group><journal-title>Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1367-4803</issn><issn pub-type="epub">1460-2059</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19420069</article-id><article-id pub-id-type="pmc">2677739</article-id><article-id pub-id-type="doi">10.1093/bioinformatics/btp142</article-id><article-id pub-id-type="publisher-id">btp142</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Papers</subject><subj-group><subject>Databases and Ontologies</subject></subj-group></subj-group></article-categories><title-group><article-title>DASMI: exchanging, annotating and assessing molecular 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="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Finn</surname><given-names>Robert D.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Prlić</surname><given-names>Andreas</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Jenkinson</surname><given-names>Andrew M.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ramírez</surname><given-names>Fidel</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Emig</surname><given-names>Dorothea</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Schelhorn</surname><given-names>Sven-Eric</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Büch</surname><given-names>Joachim</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lengauer</surname><given-names>Thomas</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Albrecht</surname><given-names>Mario</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Max Planck Institute for Informatics, Campus E 1.4, 66123 Saarbrücken, Germany,<sup>2</sup>Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA and<sup>3</sup>European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed.</corresp><fn><p>Associate Editor: Jonathan D. Wren</p></fn></author-notes><pub-date pub-type="ppub"><day>15</day><month>5</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>5</day><month>5</month><year>2009</year></pub-date><pub-date pub-type="pmc-release"><day>5</day><month>5</month><year>2009</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>25</volume><issue>10</issue><fpage>1321</fpage><lpage>1328</lpage><history><date date-type="received"><day>14</day><month>8</month><year>2008</year></date><date date-type="rev-recd"><day>27</day><month>1</month><year>2009</year></date><date date-type="accepted"><day>9</day><month>3</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><bold>Motivation:</bold> Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet.</p><p><bold>Results:</bold> We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions.</p><p><bold>Availability:</bold> The DASMI tools are available at <ext-link ext-link-type="uri" xlink:href="http://www.dasmi.de/">http://www.dasmi.de/</ext-link> and <ext-link ext-link-type="uri" xlink:href="http://ipfam.sanger.ac.uk/graph">http://ipfam.sanger.ac.uk/graph</ext-link>. The DAS registry and the DAS 1.53E specification is found at <ext-link ext-link-type="uri" xlink:href="http://www.dasregistry.org/">http://www.dasregistry.org/</ext-link>.</p><p><bold>Contact:</bold> <email>mario.albrecht@mpi-inf.mpg.de</email></p><p><bold>Supplementary information:</bold> <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btp142/DC1">Supplementary data</ext-link> and all figures in color are available at <italic>Bioinformatics</italic> online.</p></abstract></article-meta></front></pmc><affiliations><list><country><li>Allemagne</li><li>Royaume-Uni</li></country><region><li>Sarre (Land)</li></region><settlement><li>Sarrebruck</li></settlement></list><tree><noCountry><name sortKey="Finn, Robert D" sort="Finn, Robert D" uniqKey="Finn R" first="Robert D." last="Finn">Robert D. Finn</name><name sortKey="Prli, Andreas" sort="Prli, Andreas" uniqKey="Prli A" first="Andreas" last="Prli">Andreas Prli</name></noCountry><country name="Allemagne"><region name="Sarre (Land)"><name sortKey="Blankenburg, Hagen" sort="Blankenburg, Hagen" uniqKey="Blankenburg H" first="Hagen" last="Blankenburg">Hagen Blankenburg</name></region><name sortKey="Albrecht, Mario" sort="Albrecht, Mario" uniqKey="Albrecht M" first="Mario" last="Albrecht">Mario Albrecht</name><name sortKey="Buch, Joachim" sort="Buch, Joachim" uniqKey="Buch J" first="Joachim" last="Büch">Joachim Büch</name><name sortKey="Emig, Dorothea" sort="Emig, Dorothea" uniqKey="Emig D" first="Dorothea" last="Emig">Dorothea Emig</name><name sortKey="Lengauer, Thomas" sort="Lengauer, Thomas" uniqKey="Lengauer T" first="Thomas" last="Lengauer">Thomas Lengauer</name><name sortKey="Ramirez, Fidel" sort="Ramirez, Fidel" uniqKey="Ramirez F" first="Fidel" last="Ramírez">Fidel Ramírez</name><name sortKey="Schelhorn, Sven Eric" sort="Schelhorn, Sven Eric" uniqKey="Schelhorn S" first="Sven-Eric" last="Schelhorn">Sven-Eric Schelhorn</name></country><country name="Royaume-Uni"><noRegion><name sortKey="Jenkinson, Andrew M" sort="Jenkinson, Andrew M" uniqKey="Jenkinson A" first="Andrew M." last="Jenkinson">Andrew M. Jenkinson</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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