The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways.
[{{cite journal , last=Schaefer, first=Carl F, author2=Anthony Kira , author3=Krupa Shiva , author4=Buchoff Jeffrey , author5=Day Matthew , author6=Hannay Timo , author7=Buetow Kenneth H , date=Jan 2009, title=PID: the Pathway Interaction Database, journal = Nucleic Acids Res., volume=37, issue=Database issue, pages=D674-9, location = England, pmid = 18832364, doi = 10.1093/nar/gkn653, pmc = 2686461 ] 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
The National Cancer Institute (NCI) coordinates the United States National Cancer Program and is part of the National Institutes of Health (NIH), which is one of eleven agencies that are part of the U.S. Department of Health and Human Services. T ...
,
NIH
The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late 1 ...
and
Nature Publishing Group
Nature Portfolio (formerly known as Nature Publishing Group and Nature Research) is a division of the international scientific publishing company Springer Nature that publishes academic journals, magazines, online databases, and services in scie ...
in 2005 and was launched in November 2006. In September 2012, active curation was stopped and the PID data are now available in th
Network Data Exchange, NDEx
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
XML
Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. ...
(including the standard pathway interchange format,
BioPAX BioPAX (Biological Pathway Exchange) is a RDF/ OWL-based
standard language to represent biological pathways
at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data.
Pathway data captures our understanding o ...
). The entire database is also available for download.
See also
*
Reactome
Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is au ...
*
KEGG
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis ...
*
Human Protein Reference Database
*
Cancer Genome Project
References
Other references
An Introduction to the NCI-Nature Pathway Interaction DatabaseIdentification of Key Processes Underlying Cancer Phenotypes Using Biologic Pathway Analysis
External links
*http://www.ndexbio.org
UCSD-Nature Molecule Pages
BioCarta
PharmGKB
Biological databases
Systems biology