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dc.contributor.authorStobbe, Miranda D
dc.contributor.authorSwertz, Morris A
dc.contributor.authorThiele, Ines
dc.contributor.authorRengaw, Trebor
dc.contributor.authorvan Kampen, Antoine H C
dc.contributor.authorMoerland, Perry D
dc.date.accessioned2015-06-05T12:54:13Zen
dc.date.available2015-06-05T12:54:13Zen
dc.date.issued2013en
dc.identifier.citationBMC Syst Biol. 2013, 7:50en
dc.identifier.issn1752-0509en
dc.identifier.pmid23803311en
dc.identifier.doi10.1186/1752-0509-7-50en
dc.identifier.urihttp://hdl.handle.net/2336/556478en
dc.descriptionTo access publisher's full text version of this article click on the hyperlink at the bottom of the pageen
dc.description.abstractThe metabolic network of H. sapiens and many other organisms is described in multiple pathway databases. The level of agreement between these descriptions, however, has proven to be low. We can use these different descriptions to our advantage by identifying conflicting information and combining their knowledge into a single, more accurate, and more complete description. This task is, however, far from trivial.
dc.description.abstractWe introduce the concept of Consensus and Conflict Cards (C₂Cards) to provide concise overviews of what the databases do or do not agree on. Each card is centered at a single gene, EC number or reaction. These three complementary perspectives make it possible to distinguish disagreements on the underlying biology of a metabolic process from differences that can be explained by different decisions on how and in what detail to represent knowledge. As a proof-of-concept, we implemented C₂Cards(Human), as a web application http://www.molgenis.org/c2cards, covering five human pathway databases.
dc.description.abstractC₂Cards can contribute to ongoing reconciliation efforts by simplifying the identification of consensus and conflicts between pathway databases and lowering the threshold for experts to contribute. Several case studies illustrate the potential of the C₂Cards in identifying disagreements on the underlying biology of a metabolic process. The overviews may also point out controversial biological knowledge that should be subject of further research. Finally, the examples provided emphasize the importance of manual curation and the need for a broad community involvement.
dc.description.sponsorshipNetherlands Bioinformatics Centre (NBIC) SP1.2.4 4.1 'Molgenis' BSIK Netherlands Proteomics Center grants through The Netherlands Genomics Initiative (NGI) Netherlands Consortium for Systems Biology (NCSB), which is part of the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research info:eu-repo/grantAgreement/EC/FP7/232816 info:eu-repo/grantAgreement/EC/FP7/249261en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/249261en
dc.relationinfo:eu-repo/grantAgreement/EC/FP7/249261en
dc.relation.urlhttp://dx.doi.org/ 10.1186/1752-0509-7-50en
dc.relation.urlhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703255/en
dc.rightsopenAccessen
dc.subject.meshConflict (Psychology)en
dc.subject.meshConsensusen
dc.subject.meshData Miningen
dc.subject.meshDatabases, Geneticen
dc.subject.meshHumansen
dc.subject.meshMetabolic Networks and Pathwaysen
dc.titleConsensus and conflict cards for metabolic pathway databases.en
dc.typearticleen
dc.contributor.department[ 1 ] Univ Amsterdam, Acad Med Ctr, Bioinformat Lab, NL-1100 DE Amsterdam, Netherlands [ 2 ] Univ Amsterdam, Swammerdam Inst Life Sci, NL-1098 XH Amsterdam, Netherlands [ 3 ] Univ Luxembourg, Luxembourg Ctr Syst Biomed, L-4362 Esch Sur Alzette, Luxembourg [ 4 ] Univ Med Ctr Groningen, Genom Coordinat Ctr, NL-9700 RB Groningen, Netherlands [ 5 ] Univ Groningen, NL-9700 RB Groningen, Netherlands [ 6 ] Netherlands Bioinformat Ctr, NL-6525 GA Nijmegen, Netherlands [ 7 ] Univ Amsterdam, Netherlands Consortium Syst Biol, NL-1090 GE Amsterdam, Netherlandsen
dc.identifier.journalBMC systems biologyen
dc.rights.accessOpen Access - Opinn aðganguren
html.description.abstractThe metabolic network of H. sapiens and many other organisms is described in multiple pathway databases. The level of agreement between these descriptions, however, has proven to be low. We can use these different descriptions to our advantage by identifying conflicting information and combining their knowledge into a single, more accurate, and more complete description. This task is, however, far from trivial.
html.description.abstractWe introduce the concept of Consensus and Conflict Cards (C₂Cards) to provide concise overviews of what the databases do or do not agree on. Each card is centered at a single gene, EC number or reaction. These three complementary perspectives make it possible to distinguish disagreements on the underlying biology of a metabolic process from differences that can be explained by different decisions on how and in what detail to represent knowledge. As a proof-of-concept, we implemented C₂Cards(Human), as a web application http://www.molgenis.org/c2cards, covering five human pathway databases.
html.description.abstractC₂Cards can contribute to ongoing reconciliation efforts by simplifying the identification of consensus and conflicts between pathway databases and lowering the threshold for experts to contribute. Several case studies illustrate the potential of the C₂Cards in identifying disagreements on the underlying biology of a metabolic process. The overviews may also point out controversial biological knowledge that should be subject of further research. Finally, the examples provided emphasize the importance of manual curation and the need for a broad community involvement.


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