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PID: The Pathway Interaction Database

Carl F. Schaefer¹, Kira Anthony², Shiva Krupa³, Jeffrey Buchoff⁴, Matthew Day², Timo Hannay², & Kenneth H. Buetow¹

Correspondence: (Login to view email address)

1. National Cancer Institute, Center for Biomedical Informatics and Information Technology
2. Nature Publishing Group
3. Novartis Institutes for Biomedical Research Inc., Novartis Knowledge Center
4. SRA International, Inc., Health Research and Informatics

DOC (311.5 KB) PDF (338.3 KB)

Document Type:

Manuscript

Date:

Received 29 August 2008 01:06 UTC; Posted 29 August 2008

Subjects:

Cancer, Molecular Cell Biology, Bioinformatics

Tags:

• Cell Signaling
• Signal transduction
• pathway
• database

Abstract:

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 U.S. 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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Additional information

License:

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

How to cite this document:

Schaefer, Carl, Anthony, Kira, Krupa, Shiva, Buchoff, Jeffrey, Day, Matthew, Hannay, Timo, and Buetow, Kenneth. PID: The Pathway Interaction Database. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2008.2243.1> (2008)

Version info:

Published version:

10.1093/nar/gkn653 (Peer Reviewed) Published in Nucleic Acids Research (Advance Access published online: October 2, 2008) by Oxford University Press. All rights reserved.

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