Reference : Consensus and conflict cards for metabolic pathway databases.
Scientific journals : Article
Life sciences : Multidisciplinary, general & others
http://hdl.handle.net/10993/13030
Consensus and conflict cards for metabolic pathway databases.
English
Stobbe, Miranda D. [University of Amsterdam > Bioinformatics Laboratory, Academic Medical Center > > ; Netherlands Bioinformatics Centre > > > ; University of Amsterdam > Netherlands Consortium for Systems Biology]
Swertz, Morris A. [University Medical Center Groningen & University of Groningen > Genomics Coordination Center > > ; Netherlands Bioinformatics Centre]
Thiele, Ines mailto [University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) > >]
Rengaw, Trebor [University Medical Center Groningen & University Groningen > Genomics Coordination Center > > ; Netherlands Bioinformatics Centre]
van Kampen, Antoine Hc [University of Amsterdam > Bioinformatics Laboratory, Academic Medical Center > > ; University of Amsterdam > Biosystems Data Analysis, Swammerdam Institute for Life Sciences > > ; Netherlands Bioinformatics Centre]
Moerland, Perry D. [University of Amsterdam > Bioinformatics Laboratory, Academic Medical Center > > ; Netherlands Bioinformatics Centre]
26-Jun-2013
BMC Systems Biology
7
50
Yes (verified by ORBilu)
1752-0509
England
[en] Metabolic network ; Consensus ; Community support ; Human ; Pathway database
[en] BACKGROUND: The 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. RESULTS: We 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 C2CardsHuman, as a web application http://www.molgenis.org/c2cards, covering five human pathway databases. CONCLUSIONS: C2Cards 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.
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group)
http://hdl.handle.net/10993/13030
10.1186/1752-0509-7-50

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