Consensus and conflict cards for metabolic pathway databases

Miranda D. Stobbe, Morris A. Swertz, Ines Thiele, Trebor Rengaw, Antoine H. C. van Kampen, Perry D. Moerland*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

10 Citations (Scopus)
269 Downloads (Pure)

Abstract

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 (C(2)Cards) 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 C(2)Cards(Human), as a web application http://www.molgenis.org/c2cards, covering five human pathway databases.

Conclusions: C(2)Cards 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 C(2)Cards 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.

Original languageEnglish
Article number50
Number of pages14
JournalBMC Systems Biology
Volume7
DOIs
Publication statusPublished - 26-Jun-2013

Keywords

  • Metabolic network
  • Consensus
  • Community support
  • Human
  • Pathway database
  • GLOBAL RECONSTRUCTION
  • COMMUNITY APPROACH
  • SYSTEMS BIOLOGY
  • GENOME
  • NETWORK
  • INTEGRATION
  • KNOWLEDGE

Fingerprint

Dive into the research topics of 'Consensus and conflict cards for metabolic pathway databases'. Together they form a unique fingerprint.

Cite this