The Pathway Interaction Database is a highly-structured, curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. This was a collaborative project between the NCI and Nature Publishing Group (NPG) from 2006 until September 22nd, 2012. Future update will be performed by NCI.
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Citing the Pathway Interaction Database
To cite the NCI-Nature Pathway Interaction Database please use the following format:
Carl F. Schaefer, Kira Anthony, Shiva Krupa, Jeffrey Buchoff, Matthew Day, Timo Hannay & Kenneth H. Buetow. PID: The Pathway Interaction Database. Nucleic Acids Res. 37, D674-9 (2009)
Citing and linking to pathways:
All NCI-Nature curated pathways have stable URLs that can be used for citation and linking purposes.
Pathway citation should include the title of the pathway, the name of the publication ("NCI-Nature Pathway Interaction Database"), and the stable URL for the pathway. The following is an illustrative example:
Class I PI3K signaling events. NCI-Nature Pathway Interaction Database.
Thus, the URL for linking to PID pathways is:
http://pid.nci.nih.gov/search/pathway_landing.shtml?what=graphic&jpg=on&pathway_id=xxxxxx&source=NCI-Nature curated where xxxxxx is the Pathway ID found on each of the predefined pathway pages.
Links to pathways imported from BioCarta or Reactome can be constructed in a similar manner and are as follows where xxxxxx is the Pathway ID found on each of the pathway pages.
Linking to proteins:
In order to link to proteins found in the Pathway Interaction Database please use the following URL:
and populate xxxxx with the UniProt accession number. UniProt accession numbers found in the Pathway Interaction Database are available by downloading the file "NCI-Nature Curated Pathway-UniProt mapping (tab delimited file)" on the Download data page. UniProt accession numbers in the PID can also be found by entering the protein name or identifier in the search box on the homepage and clicking on the hyperlinked protein name in the Search results summary page. A list of permissible protein search terms can be found here.
Citing Bioinformatics primers:
Bioinformatics primer citation should include the names of all authors, the title of the article, the name of the publication ("NCI-Nature Pathway Interaction Database"), the digital object identifier (DOI) and the year of publication in parentheses. The following is an illustrative example:
Matthews L, D'Eustachio P, Gillespie G, Croft D, de Bono B, Gopinath G, Jassal B, Lewis S, Schmidt E, Vastrik I, Wu G, Birney E & Stein L. An Introduction to the Reactome Knowledgebase of Human Biological Pathways and Processes. NCI-Nature Pathway Interaction Database. doi:10.1038/pid.2007.3 (2007).