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Nucleic Acids Research Advance Access published online on October 2, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn653
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Database issue

PID: the Pathway Interaction Database

Carl F. Schaefer1,*, Kira Anthony2, Shiva Krupa3, Jeffrey Buchoff4, Matthew Day5, Timo Hannay5 and Kenneth H. Buetow1

1National Cancer Institute, Center for Biomedical Informatics and Information Technology, Rockville MD, USA, 2Nature Publishing Group, Boston MA, USA, 3Novartis Knowledge Center, Cambridge MA, USA, 4SRA International, Inc., Health Research and Informatics, Fairfax VA, USA and 5Nature Publishing Group, London, UK

*To whom correspondence should be addressed. Tel: +1 301 435 1535; Fax:+1 301 480 6641; Email: schaefec{at}mail.nih.gov

Received August 15, 2008. Revised September 15, 2008. Accepted September 18, 2008.

The Pathway Interaction Database (PID, http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the US National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools.


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