3 votes

The NCI-Nature Pathway Interaction Database: A cell signaling resource.

Shiva Krupa¹, Kira Anthony¹, Jeffrey R. Buchoff², Matthew Day¹, Timo Hannay³, & Carl F. Schaefer²

Correspondence: (Login to view email address)

1. Web Publishing, Nature Publishing Group
2. National Cancer Institute Center for Bioinformatics and Information Technology
3. Nature.com, Nature Publishing Group

PDF (1.1 MB)

Document Type:

Poster

Date:

Received 12 November 2007 16:17 UTC; Posted 12 November 2007

Subjects:

Cancer, Molecular Cell Biology, Bioinformatics

Tags:

• molecular interactions
• Signal transduction
• pathways
• database
• BioPax

Abstract:

The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely available
collection of curated and peer-reviewed signaling pathways composed of human
biomolecular interactions and cellular processes. Created in a collaboration between the
U.S. National Cancer Institute and Nature Publishing Group, the database is a research
tool for cell biologists, biochemists, computational biologists and bioinformaticians.
The PID offers a range of tools to facilitate pathway exploration. Users can browse the
pre-defi ned set of pathways and also create interaction network maps centered on
a single molecule of interest or an extensive list of molecules. In addition, users can
download complete data sets in extensible markup language (XML) and Biological
Pathway Exchange (BioPAX) Level 2 formats. The database is updated every month and
supplemented by a concise editorial section that provides synopses of recent noteworthy
papers in cell signaling and specially commissioned articles on the practical uses of
other relevant online tools. Users can sign up for free email alerts or RSS feeds to receive
database updates.

Presented at:

2nd International Biocuration Meeting, 25 October 2007

Discussion

Votes:

3 votes

(Login to vote)

Comments:

2 comments

Kojiro Yano on 12 November 2007 23:58 UTC

I find the pathway map quite difficult to view. Hope they make it more readable in the future.

Kira Anthony on 13 November 2007 21:40 UTC

Kojiro Yano,
If you zoom into the poster to 1200-1600% you will be able to resolve the participating molecules and interactions in the very large network map within the poster. This network map was generated from a list of 120 protein kinases. Hence, it includes interactions from numerous pathways, and is actually much larger than any of our individual pathway maps at http://pid.nci.nih.gov/PID/browse_pathways.shtml.

I am also pleased that you brought up this point, as developing network visualization tools is a growing field and is something that we are very interested in. We have just started working with the groups that are developing Cytoscape (http://www.cytoscape.org/), which is an open-source platform for visualizing network data.

(Login to post a comment)

Share:

(Login to share with a colleague)

Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Krupa, Shiva, Anthony, Kira, Buchoff, Jeffrey , Day, Matthew, Hannay, Timo, and Schaefer, Carl . The NCI-Nature Pathway Interaction Database: A cell signaling resource.. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2007.1311.1> (2007)

Version info:

Other versions of this document in Nature Precedings

None.

Other versions of this document elsewhere on the web

None known.

Submit a new version link