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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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The pathway ontology - updates and applications.

Victoria Petri1, Pushkala Jayaraman, Marek Tutaj

  • 1Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI, USA. vpetri@mcw.edu.

Journal of Biomedical Semantics
|February 7, 2014
PubMed
Summary
This summary is machine-generated.

The Pathway Ontology (PW) enriches biological pathway data through automated pipelines, increasing content by over 75% and enhancing gene annotation for research. This valuable resource is freely available for download and use.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Ontology Development

Background:

  • The Pathway Ontology (PW) from Rat Genome Database (RGD) standardizes biological pathway annotation for rat, human, and mouse genes.
  • It uses a directed acyclic graph to represent relationships between biological, altered, and disease pathways.
  • PW facilitates navigation between genes, pathways, and interactive diagrams.

Purpose of the Study:

  • To describe the ongoing development and content enrichment of the Pathway Ontology.
  • To highlight the role of automated pipelines in integrating external pathway data.
  • To showcase the expansion of PW's coverage of various pathway types.

Main Methods:

  • Development and implementation of automated annotation import pipelines (PID and KEGG).
  • Integration of pathway data from external databases and literature surveys.
  • Incorporation of user requests and mapping of pathways from other resources.

Main Results:

  • Released two pipelines (PID and KEGG) providing over 7,400 and 31,000 gene annotations, respectively.
  • Significant increase in pathway terms, particularly in signaling, immune/inflammatory diseases, infectious diseases, and drug pathways.
  • Overall content of the Pathway Ontology increased by over 75%.

Conclusions:

  • Ongoing development and pipeline implementation enhance pathway data provision.
  • The Pathway Ontology is freely accessible for download and use.
  • PW serves as a valuable, expanding resource for biological pathway information.