NCI-PID 2.0 KG

The NCI-PID 2.0 Knowledge Graph (NCI-PID 2.0 KG) is a semantic knowledge graph derived from the NCI Pathway Interaction Database (NCI-PID) version 2.0 networks. These networks represent curated biomolecular interactions and cellular signaling pathways, enhanced with evidence from the INDRA (Integrated Network and Dynamical Reasoning Assembler) system.

The knowledge graph is constructed by converting 196 NCI-PID 2.0 pathway networks from the Cytoscape CX2 format into RDF (Resource Description Framework) using standard biological ontologies. The source networks are publicly available on NDEx (Network Data Exchange).

Key Features

• Protein Interactions: Captures binding, activation, inhibition, and post-translational modification relationships between proteins identified by UniProt accessions
• Evidence Provenance: Each relationship is annotated with INDRA evidence counts, source database attribution (INDRA and/or NCI-PID), and links to supporting evidence
• Standard Ontologies: Uses Relations Ontology (RO) predicates for relationship semantics, Gene Ontology (GO) biological process terms for post-translational modification types, and Semanticscience Integrated Ontology (SIO) for entity typing
• RDF Reification: Relationships are reified to attach evidence metadata, enabling queries at multiple levels of abstraction

Ontologies Used

Prefix	Ontology	Usage
RO	Relations Ontology	Relationship predicates (binds, activates, inhibits, regulates)
GO	Gene Ontology	PTM process types (phosphorylation, ubiquitination, sumoylation)
SIO	Semanticscience Integrated Ontology	Entity types (protein, complex, gene product)
UniProt	UniProt	Protein entity identifiers
CHEBI	Chemical Entities of Biological Interest	Small molecule and chemical entity types

Funding

This work is supported by the NSF Proto-OKN (Prototype Open Knowledge Network) program, the NIH NCI NDEx project (5U24CA269436), and the NIH NHGRI Cytoscape project (5U24HG012107).

References

Pillich RT, Chen J, Churas C, Fong D, Gyori BM, Ideker T, Karis K, Liu SN, Ono K, Pico A, Pratt D. NDEx IQuery: a multi-method network gene set analysis leveraging the Network Data Exchange. Bioinformatics. 2023 Mar 1;39(3):btad118. doi: 10.1093/bioinformatics/btad118

Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. NDEx, the Network Data Exchange. Cell Syst. 2015 Oct 28;1(4):302-305. doi: 10.1016/j.cels.2015.10.001. PMID: 26594663; PMCID: PMC4649937.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003 Nov;13(11):2498-504. doi: 10.1101/gr.1239303. PMID: 14597658; PMCID: PMC403769.

Ono K, Fong D, Gao C, Churas C, Pillich R, Lenkiewicz J, Pratt D, Pico AR, Hanspers K, Xin Y, Morris J, Kucera M, Franz M, Lopes C, Bader G, Ideker T, Chen J. Cytoscape Web: bringing network biology to the browser. Nucleic Acids Res. 2025 Jul 7;53(W1):W203-W212. doi: 10.1093/nar/gkaf365. PMID: 40308211; PMCID: PMC12230733.

SPARQL Endpoint	https://frink.apps.renci.org/ncipidkg/sparql
Triple Pattern Fragments	https://frink.apps.renci.org/ldf/ncipidkg