PID: the Pathway Interaction Database
Open accessAbstract
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 US 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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Three of the JAK2 trans-CDS pQTLs are proteins involved in the integrin β2 pathway: FCGR2A, GP1BA and ICAM2.
“Three of the JAK2 trans-CDS pQTLs are proteins involved in the integrin β2 pathway: FCGR2A, GP1BA and ICAM2 (ref. 45) (Fig. 3a).”
From Rare variant associations with plasma protein levels in the UK Biobank (2023) · cites this paper as [45]
The Introduction describes PID as a database of human signaling and regulatory pathways, and the Web Interface and Application section explains how to retrieve a pathway’s participating molecules (page numbers unavailable). Our copy does not identify FCGR2A, GP1BA or ICAM2 as members of an integrin β2 pathway, or discuss JAK2 trans-CDS pQTLs. Searches for those protein names, integrin β2 and JAK2 did not find a passage establishing the claim. (LLM, conf=0.74)
Experimental — accuracy not yet measuredReactome BioPAX formatted pathways are imported by the NCI/Nature Pathway Information Database (PID).
“For example, Reactome8 BioPAX formatted pathways are imported by the NCI/Nature Pathway Information Database (PID)9.”
From The BioPAX community standard for pathway data sharing (2010) · cites this paper as [9]
In the mTOR pathway, 67 genes are included.
“In the mTOR pathway are 67 genes included45.”
From A spatio-temporal brain miRNA expression atlas identifies sex-independent age-related microglial driven miR-155-5p increase (2025) · cites this paper as [45]
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“…from various sources, including pathways (Reactome [ 44], KEGG [ 45], BioCarta, WikiPathways [ 46], DMaps [ 47], SPIKE, NCI Nature Curated pathway [ 48], and GeoMx Cancer Transcriptome Atlas [ 49]), ontology annotations (Gene Ontology Annotation [ 50] also known as GOA and Human Phenotype…”
- Authors
- Schaefer, C. F., Anthony, K., Krupa, S., Buchoff, J., Day, M., Hannay, T., & Buetow, K. H.
- Affiliations
- National Cancer Institute (US)
- SRA International (United States) (US)
- Corresponding author
- Schaefer, Carl F.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-10-02
- Volume
- 37
- Issue
- suppl_1
- Pages
- D674-D679
- ISSN
- 1756-0357 (ISSN-L)
- 1362-4962
- 0305-1048
- PMC
- PMC2686461
- OpenAlex
- W2096766502
- Cited by
- 1,603
- References
- 15
- Citations by year
- 2026: 37 · 2025: 59 · 2024: 88 · 2023: 100 · 2022: 120 · 2021: 99 · 2020: 128 · 2019: 115 · 2018: 95 · 2017: 87 · 2016: 106 · 2015: 122 · 2014: 118 · 2013: 106 · 2012: 77
- Type
- posted content
- Language
- en
- Open access
- diamond
- doi.org
- Locations
- Nature Precedings (publishedVersion, cc-by)
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Nature Precedings (submittedVersion)
- Funders
- National Cancer Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Keywords
- biological pathways, molecular signaling, cellular processes, pathway curation, cancer research, pathway visualization
- MeSH terms
- Biological Transport, Cell Physiological Phenomena, Gene Expression Regulation, Humans, Proteins, RNA, User-Computer Interface, Signal Transduction, Databases, Factual, Internet, Protein Interaction Mapping
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