dgidb — DGIdb drug-gene interactions (2021-2026)

Description

Bipartite networks of drugs and genes from the Drug-Gene Interaction Database (DGIdb), which collects drug-gene interactions (e.g. a drug that inhibits the product of a gene) from about 40 sources (e.g. ChEMBL, DrugBank, the Guide to Pharmacology, TTD, CIViC, the FDA, clinical trial and cancer knowledge bases, the literature), and normalizes the drugs and genes they name to common concepts. Each edge is an interaction claim of a source, so that a drug and a gene are often connected by several edges, one per source (and the networks are multigraphs).

There is one network for each data release of DGIdb that is available for download, named by its date: 2021-05 and 2022-02 (DGIdb 4), 2023-12, 2024-06, 2024-12, 2026-06, 2026-06b (a corrected release of the same month) and 2026-10 (DGIdb 5); the release 2026-09 is identical to 2026-10, and is left out. The drugs and genes of the claims that DGIdb could not normalize (about a tenth of the claims) are kept as nodes identified by the name given by the source (with an empty concept_id), so that the same drug or gene may appear in several of these nodes.

The networks have the following properties:

(Node) is_drug: whether the node is a drug (otherwise it is a gene).
(Node) concept_id: the identifier of the normalized concept of the drug (e.g. rxcui:12574, chembl:CHEMBL296468, ncit:C70982) or of the gene (in DGIdb 5 its HGNC identifier, e.g. hgnc:5466; in DGIdb 4 its NCBI Gene identifier, written here as ncbigene:1022); empty for the drugs and genes that were not normalized.
(Node) name: the name of the normalized drug or the gene symbol, or the name given by the source if it was not normalized.
(Node) approved, immunotherapy, antineoplastic (from 2023-12): whether the drug is approved, an immunotherapy, and an antineoplastic drug (false if not given).
(Edge) source: the source of the claim, and source_version its version (from 2023-12).
(Edge) gene_claim, drug_claim: the names of the gene and the drug as given by the source.
(Edge) interaction_types: the types of the interaction, e.g. inhibitor, agonist, separated by | in DGIdb 5 and by , in DGIdb 4 (empty if not given).
(Edge) interaction_score: the interaction score of DGIdb, which grows with the number of sources and publications supporting the interaction, and with the specificity of the drug and the gene (NaN if not given).
(Edge) drug_specificity_score, gene_specificity_score, evidence_score (from 2024-12): the parts of the interaction score (NaN or -1 if not given).
(Edge) pmids (2021-05, 2022-02): the PubMed identifiers of the articles supporting the claim, separated by ,.

Tags

Biological Drug interactions Unweighted Multigraph Bipartite Metadata

Added

2026-10-31

Citation

M. Cannon, J. Stevenson, K. Stahl, R. Basu, A. Coffman, S. Kiwala, J. F. McMichael, K. Kuzma, D. Morrissey, K. Cotto, E. R. Mardis, O. L. Griffith, M. Griffith, A. H. Wagner, "DGIdb 5.0: rebuilding the drug-gene interaction database for precision medicine and drug discovery platforms." Nucleic Acids Research 52, D1227-D1235 (2024) 10.1093/nar/gkad1040 Sci-Hub
S. L. Freshour, S. Kiwala, K. C. Cotto, A. C. Coffman, J. F. McMichael, J. J. Song, M. Griffith, O. L. Griffith, A. H. Wagner, "Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts." Nucleic Acids Research 49, D1144-D1151 (2021) 10.1093/nar/gkaa1084 Sci-Hub

Upstream URL OK

https://dgidb.org/
https://github.com/dgidb/dgidb-data/releases

Upstream license

Open access data, collected from sources with their own licenses (DGIdb code: MIT), https://dgidb.org/about/overview/data-accessibility

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$: Mean degree
$\sigma_k$: Standard deviation of the degrees
$\lambda_h$: Largest eigenvalue of the Hashimoto (non-backtracking) matrix
$\tau$: Random walk mixing time
$r$: Degree assortativity
$c$: Global clustering coefficient
$\oslash$: (Pseudo-) diameter
$S$: Relative size of the largest component
NPs: Node properties
EPs: Edge properties

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
2021-05	35,558	100,273	5.64	23.05	47.70	246.67	-0.22	17	0.93	Undirected	Bipartite	is_drug concept_id name	source source_version gene_claim drug_claim interaction_types interaction_score pmids	1.8 MiB	2.5 MiB	2.5 MiB	2.5 MiB
2022-02	31,226	85,460	5.47	22.19	46.88	332.74	-0.21	16	0.92	Undirected	Bipartite	is_drug concept_id name	source source_version gene_claim drug_claim interaction_types interaction_score pmids	1.4 MiB	2.1 MiB	2.1 MiB	2.1 MiB
2023-12	26,151	81,129	6.20	23.19	59.68	321.37	-0.20	16	0.91	Undirected	Bipartite	is_drug concept_id name approved immunotherapy antineoplastic	source source_version gene_claim drug_claim interaction_types interaction_score	1.2 MiB	1.8 MiB	1.8 MiB	1.8 MiB
2024-06	33,306	98,239	5.90	21.60	59.68	136.47	-0.17	20	0.92	Undirected	Bipartite	is_drug concept_id name approved immunotherapy antineoplastic	source source_version gene_claim drug_claim interaction_types interaction_score	1.6 MiB	2.3 MiB	2.3 MiB	2.4 MiB
2024-12	33,621	98,920	5.88	21.56	61.88	140.16	-0.17	20	0.92	Undirected	Bipartite	is_drug concept_id name approved immunotherapy antineoplastic	source source_version gene_claim drug_claim interaction_types interaction_score drug_specificity_score gene_specificity_score evidence_score	1.6 MiB	2.4 MiB	2.4 MiB	2.6 MiB
2026-06	34,290	99,834	5.82	22.48	62.69	230.58	-0.21	16	0.92	Undirected	Bipartite	is_drug concept_id name approved immunotherapy antineoplastic	source source_version gene_claim drug_claim interaction_types interaction_score drug_specificity_score gene_specificity_score evidence_score	1.6 MiB	2.4 MiB	2.4 MiB	2.7 MiB
2026-06b	35,007	101,060	5.77	22.29	62.69	258.71	-0.21	18	0.93	Undirected	Bipartite	is_drug concept_id name approved immunotherapy antineoplastic	source source_version gene_claim drug_claim interaction_types interaction_score drug_specificity_score gene_specificity_score evidence_score	1.6 MiB	2.5 MiB	2.4 MiB	2.7 MiB
2026-10	39,596	122,904	6.21	24.07	62.70	145.36	-0.21	16	0.94	Undirected	Bipartite	is_drug concept_id name approved immunotherapy antineoplastic	source source_version gene_claim drug_claim interaction_types interaction_score drug_specificity_score gene_specificity_score evidence_score	2.0 MiB	2.9 MiB	2.9 MiB	3.2 MiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.