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Living cells constantly carry out various chemical reactions which are necessary for their proper functioning. These reactions are interlinked to one another via multiple pathways. The collection of these chemical reactions is known as metabolism.
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Related Experiment Video

Updated: May 10, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

Consensus and conflict cards for metabolic pathway databases.

Miranda D Stobbe1, Morris A Swertz, Ines Thiele

  • 1Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, Amsterdam 1100 DE, the Netherlands.

BMC Systems Biology
|June 28, 2013
PubMed
Summary

Pathway databases show low agreement. Consensus and Conflict Cards (C₂Cards) identify discrepancies, aiding in creating more accurate metabolic network descriptions for human biology research.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Metabolic Networks

Background:

  • Metabolic networks are described in multiple pathway databases with low agreement.
  • Discrepancies between databases present challenges but offer opportunities for knowledge integration.
  • Reconciling conflicting information is crucial for a comprehensive understanding of metabolic processes.

Purpose of the Study:

  • To introduce a novel method for identifying consensus and conflicts between metabolic pathway databases.
  • To develop a tool that simplifies the comparison and reconciliation of biological pathway information.
  • To facilitate the integration of knowledge from diverse pathway databases.

Main Methods:

  • Concept of Consensus and Conflict Cards (C₂Cards) introduced.
  • C₂Cards provide concise overviews centered on genes, EC numbers, or reactions.
  • Implementation of C₂Cards(Human) as a web application covering five human pathway databases.

Main Results:

  • C₂Cards effectively highlight areas of agreement and disagreement across pathway databases.
  • The three-perspective approach (gene, EC number, reaction) distinguishes biological conflicts from representational differences.
  • A functional web application (http://www.molgenis.org/c2cards) was developed as a proof-of-concept.

Conclusions:

  • C₂Cards simplify the identification of consensus and conflicts, lowering the barrier for expert contribution.
  • The tool aids in pinpointing disagreements in metabolic process biology and controversial knowledge.
  • Emphasizes the importance of manual curation and community involvement in pathway database reconciliation.