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Getting Started in Biological Pathway Construction and Analysis

  • Ganesh A Viswanathan,
  • Jeremy Seto,
  • Sonali Patil,
  • German Nudelman,
  • Stuart C Sealfon mail

    To whom correspondence should be addressed. E-mail: Stuart.Sealfon@mssm.edu

    X
  • Published: February 29, 2008
  • DOI: 10.1371/journal.pcbi.0040016

Reader Comments (3)

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Completeness

Posted by LucaT on 27 Apr 2009 at 08:11 GMT

Dear Authors,
compliments for your introductory and yet very informative article. I was wondering about your opinion on the "wiki" approach, since I could not find much of it in your article (e.g. about wikpathways), and as well about other commercial providers (e.g. GeneGO, BioBase, GVK Bioscience,...)

No competing interests declared.

RE: Completeness

rsealfon replied to LucaT on 27 Apr 2009 at 16:58 GMT

The "wiki" approach seems to be a useful and promising tool for allowing large datasets, with individual pieces contributed by many people, to be contained in one place and represented in one format. In my opinion, the issues with reliability of information even on Wikipedia, where anyone can contribute, have been relatively minor and Wikipedia has been found to contain fewer factual errors, at any given time, than a professional encyclopedia article. Unlike peer-reviewed publications, which are difficult to correct after time of press, Wikipathways would allow users to instantaneously correct errors or add information to a preexisting pathway. An article about the validity and completeness of wikis (specifically Wikipedia) is over here, and has links to scholarly studies of wikis: http://en.wikipedia.org/w....

One of my concerns is that the wiki format, designed for communicating text-based and image-based information such as a review article on a particular pathway, seems to handle representations of the pathway itself relatively awkwardly. At present, editing on Wikipathways and viewing pathways are slow processes. Commercial software is, obviously, designed to represent the pathway per se and allow data to be curated and mined as easily as possible. I don't really know the individual differences between commercial providers, but our lab uses Ingenuity. I suspect the role of cheap software and freeware will increase as their quality improves and the data itself becomes less costly to collect and more accessible.

Commercial software, freeware and wikis could become complementary to one another, especially if the amount of data that needs to be added to or downloaded from an online (e.g. wiki) database is difficult to handle manually.

Competing interests declared: I am in the laboratory that produced this paper.