NCI-Nature Pathway Interaction Database

PID
Content
Description	Pathway Interaction Database.
Contact
Laboratory	National Cancer Institute; NIH; Nature Publishing Group
Primary citation	Schaefer & al. (2009)[1]
Release date	2005
Access
Standards	BioPAX
Data format	XML
Website	http://www.ndexbio.org

The Pathway Interaction Database (PID) is a free biomedical database of human cellular signaling pathways.[1] 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. In September 2012, active curation was stopped and the PID data are now available in the 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 (including the standard pathway interchange format, BioPAX). The entire database is also available for download.

gollark: Like the "online safety bill" and whatever policing things people are angry about here.

gollark: Yeeees, it seems like the particularly totalitarian stuff just gets shoved through without COVID-19 being hugely related.

gollark: But that seems inaccurate because politicians also probably look good/bad if they do well/badly against COVID-19 regardless.

gollark: If you were somewhat more cynical than me I guess you could think something like: updated vaccines aren't part of mainstream political discourse yet, they are unlikely to be unless there is deployment/development of them, and so politicians (who are optimizing for looking good according to said political discourse) don't care and don't do anything about the situation.

gollark: I said three things. Maybe I should retroactively use semicolons.

References

Schaefer, Carl F; Anthony Kira; Krupa Shiva; Buchoff Jeffrey; Day Matthew; Hannay Timo; Buetow Kenneth H (Jan 2009). "PID: the Pathway Interaction Database". Nucleic Acids Res. England. 37 (Database issue): D674-9. doi:10.1093/nar/gkn653. PMC 2686461. PMID 18832364.

Other references

External links

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[pmid18832364-1] Schaefer, Carl F; Anthony Kira; Krupa Shiva; Buchoff Jeffrey; Day Matthew; Hannay Timo; Buetow Kenneth H (Jan 2009). "PID: the Pathway Interaction Database". Nucleic Acids Res. England. 37 (Database issue): D674-9. doi:10.1093/nar/gkn653. PMC 2686461. PMID 18832364.