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ncipidkg

NCI-PID 2.0 KG

The NCI-PID 2.0 Knowledge Graph converts NCI Pathway Interaction Database version 2.0 networks into RDF, capturing protein interactions, signaling pathways, and post-translational modifications enriched with INDRA evidence metadata.

968 triples
2 classes
14 properties
136 subjects

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.

List neighbors of HDAC1 protein 
PREFIX uniprot: <http://identifiers.org/uniprot/>
PREFIX RO: <http://purl.obolibrary.org/obo/RO_>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?relation ?neighbor ?neighborLabel
WHERE {
  uniprot:Q13547 ?relation ?neighbor .
  FILTER(STRSTARTS(STR(?relation), STR(RO:)))

  OPTIONAL { ?neighbor rdfs:label ?neighborLabel }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v2("?neighbor"):::projected 
  v3("?neighborLabel"):::projected 
  v1("?relation"):::projected 
  c2([http://identifiers.org/uniprot/Q13547]):::iri 
  f0[["starts-with(str(?relation),str(obo:RO_))"]]
  f0 --> v1
  c2 -->v1--> v2
  subgraph optional0["(optional)"]
  style optional0 fill:#bbf,stroke-dasharray: 5 5;
    v2 -."rdfs:label".->  v3
  end
Run in FRINK
List all labeled interactions 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX RO: <http://purl.obolibrary.org/obo/RO_>

SELECT ?sourceLabel ?relation ?targetLabel
WHERE {
  ?source ?relation ?target .
  FILTER(STRSTARTS(STR(?relation), STR(RO:)))

  OPTIONAL { ?source rdfs:label ?sourceLabel }
  OPTIONAL { ?target rdfs:label ?targetLabel }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?relation"):::projected 
  v2("?source")
  v4("?sourceLabel"):::projected 
  v3("?target")
  v5("?targetLabel"):::projected 
  f0[["starts-with(str(?relation),str(obo:RO_))"]]
  f0 --> v1
  v2 -->v1--> v3
  subgraph optional0["(optional)"]
  style optional0 fill:#bbf,stroke-dasharray: 5 5;
    v2 -."rdfs:label".->  v4
  end
  subgraph optional1["(optional)"]
  style optional1 fill:#bbf,stroke-dasharray: 5 5;
    v3 -."rdfs:label".->  v5
  end
Run in FRINK
List all proteins with labels 
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX SIO: <http://semanticscience.org/resource/SIO_>

SELECT ?protein ?label
WHERE {
  ?protein a SIO:010043 ;
           rdfs:label ?label .
}
ORDER BY ?label

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?label"):::projected 
  v2("?protein"):::projected 
  c2([http://semanticscience.org/resource/SIO_010043]):::iri 
  v2 --"a"-->  c2
  v2 --"rdfs:label"-->  v1
Run in FRINK
SPARQL Endpoint https://frink.apps.renci.org/ncipidkg/sparql
Triple Pattern Fragments https://frink.apps.renci.org/ldf/ncipidkg
ClassEntities
PropertyTriples