NCI-Nature Pathway Interaction Database
Encyclopedia
The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways. The database contains information about the molecular interactions and reactions that take place in cells, with a particular focus on processes that might be relevant to cancer research and treatment. The database was established as collaboration between the U.S. National Cancer Institute
, NIH
and Nature Publishing Group
in 2005 and was launched in November 2006.
The NCI-Nature curated data is gathered from published research literature and reviewed by expert scientists before publication. Evidence codes are assigned to each molecular interaction, which allows users to evaluate the reliability of the interactions or to search for interactions identified by particular experimental techniques.
(including the standard pathway interchange format, BioPAX
). The entire database is also available for download.
National Cancer Institute
The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...
, NIH
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
and Nature Publishing Group
Nature Publishing Group
Nature Publishing Group is an international publishing company that publishes academic journals, online databases, and services across the life, physical, chemical and applied sciences and clinical medicine...
in 2005 and was launched in November 2006.
Database content
As of November 2007, the database contained 59 pathways (comprising 3309 molecular interactions) curated by the NCI-Nature editorial team. New pathways are added each month. The database also contains 254 pathways (comprising 3003 interactions) imported from the June 2004 edition of the BioCarta pathway database.The NCI-Nature curated data is gathered from published research literature and reviewed by expert scientists before publication. Evidence codes are assigned to each molecular interaction, which allows users to evaluate the reliability of the interactions or to search for interactions identified by particular experimental techniques.
Data output and download
The database content can be viewed in self-contained, pre-defined pathways. The database can also dynamically generate interaction networks to visualize the results of database searches. Pathways and dynamically generated networks are displayed in GIF and SVG images and can be downloaded as XMLXML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
(including the standard pathway interchange format, BioPAX
BioPAX
BioPAX is a RDF/OWL-basedstandard language to represent biological pathwaysat the molecular and cellular level. Its major use is to facilitate the exchange of pathway data....
). The entire database is also available for download.
Other references
- An Introduction to the NCI-Nature Pathway Interaction Database
- Identification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis
External links
- http://pid.nci.nih.gov
- UCSD-Nature Molecule Pages
- BioCarta
- PharmGKB