Biointelligence

September 24, 2009

Pathway Databases – A broader view

Filed under: Bioinformatics,Systems Biology — Biointelligence: Education,Training & Consultancy Services @ 7:58 am
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Studying Reactome, actually led me to explore some more databases of pathways and reactions. While browing I eventually landed on a paper “Pathway databases and tools for their exploitation: benefits, current limitations and challenges” authored by Anna Bauer-Mehren, Laura I Furlong & Ferran Sanz. So, my todays post gives an abstract of what this paper is talking about.

Cell signalling studies have been going on from over a decade. This process basically refers to the biochemical processes using which cells respond to cues in their internal or external environment. This eventually led to the creation of chain of reactions and development of databases to store them in a compiled manner. Several databases containing information on cell signalling pathways have now been developed in conjunction with methodologies to access and analyse the data. At present, there are several repositories of information on cell signalling pathways that cover a wide range of signal transduction mechanisms and include high quality data in terms of annotation and cross references to biological databases.

Some of the online pathway databases have been nicely listed here: http://www.nature.com/msb/journal/v5/n1/fig_tab/msb200947_T2.html

This table basically lists Reactome, KEGG, Wikipathways, Nature interaction databases, pathway commons and many more….

The paper also explains the main standards for representation of biological networks, BioPAX and SBML. Furthermore, the advantages and drawbacks of current methods for pathway retrieval and integration, using the EGFR signalling as an illustrative example, have been discussed.

The paper is available here: http://www.nature.com/msb/journal/v5/n1/full/msb200947.html

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1 Comment »

  1. I enjoy this site, it is worth me coming back

    Comment by Kelli Garner — October 4, 2009 @ 2:31 am | Reply


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