Format

Send to

Choose Destination
See comment in PubMed Commons below
Methods Mol Biol. 2010;609:129-44. doi: 10.1007/978-1-60327-241-4_8.

Biomolecular pathway databases.

Author information

1
Bioinformatics Institute, Agency for science, Technology, and Research, Singapore.

Abstract

From the database point of view, biomolecular pathways are sets of proteins and other biomacromolecules that represent spatio-temporally organized cascades of interactions with the involvement of low-molecular compounds and are responsible for achieving specific phenotypic biological outcomes. A pathway is usually associated with certain subcellular compartments. In this chapter, we analyze the major public biomolecular pathway databases. Special attention is paid to database scope, completeness, issues of annotation reliability, and pathway classification. In addition, systems for information retrieval, tools for mapping user-defined gene sets onto the information in pathway databases, and their typical research applications are reviewed. Whereas today, pathway databases contain almost exclusively qualitative information, the desired trend is toward quantitative description of interactions and reactions in pathways, which will gradually enable predictive modeling and transform the pathway databases into analytical workbenches.

PMID:
20221917
DOI:
10.1007/978-1-60327-241-4_8
[Indexed for MEDLINE]
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Springer
    Loading ...
    Support Center