monarch_kg — Monarch Initiative knowledge graph (2023-2026)

Description

The knowledge graph of the Monarch Initiative, which integrates data on genes, diseases and phenotypes across species, for the study of genetic diseases and model organisms. Nodes are biological entities of many kinds, given by their Biolink Model category, e.g. genes (of human and of model organisms such as mouse, rat, zebrafish, fruit fly, C. elegans, yeast), diseases (Mondo Disease Ontology), phenotypes (Human Phenotype Ontology and the phenotype ontologies of other species), genotypes, variants, anatomical entities, cell types, biological processes, molecular functions and cellular components (Gene Ontology), pathways (Reactome), chemicals and publications. A directed edge is an association between two entities with a Biolink predicate, e.g. a gene has_phenotype a phenotype, a gene causes a disease, a gene is orthologous_to another, a gene interacts_with another (STRING, BioGRID and other interaction databases), a gene expressed_in an anatomical entity, a term subclass_of a more general term of an ontology. The data are integrated from dozens of sources (e.g. the Alliance of Genome Resources, OMIM, Orphanet, ClinVar, ClinGen, HPO annotations, Gene Ontology annotations, PANTHER, Reactome, STRING, BioGRID, the PHENIO ontology), and both nodes and edges are normalized to common identifiers.

The Monarch knowledge graph is released monthly. One release per year is included, the first of each year (from the first release in the current format, of September 2023), and the latest one:

2023-09-28: 830,288 nodes and 8,076,791 edges (according to its statistics),
2024-01-13,
2025-01-15,
2026-01-11,
2026-10-07: 1,670,861 nodes and 16,433,147 edges.

Left out are the qualifiers of the edges (e.g. the frequency, onset or sex of a phenotype in a disease, the species or disease context), their supporting publications and evidence codes, and the synonyms, cross-references and descriptions of the nodes.

The networks have the following properties:

(Node) id: the identifier of the entity, as a compact URI, e.g. HGNC:11998 (the human gene TP53), MONDO:0007254 (breast cancer), HP:0001250 (seizure).
(Node) category: the Biolink category of the entity, e.g. biolink:Gene, biolink:Disease, biolink:PhenotypicFeature.
(Node) name: the name of the entity (empty if none).
(Node) symbol: the symbol of the gene (empty for other entities and if none).
(Node) taxon: the NCBI taxonomy identifier of the species of the entity, e.g. NCBITaxon:9606 (empty if none).
(Node) taxon_label: the name of the species, e.g. Homo sapiens (empty if none).
(Edge) predicate: the Biolink predicate of the association, e.g. biolink:has_phenotype, biolink:causes, biolink:interacts_with.
(Edge) category: the Biolink category of the association, e.g. biolink:GeneToPhenotypicFeatureAssociation.
(Edge) primary_knowledge_source: the original source of the association, e.g. infores:omim, infores:string.
(Edge) knowledge_level: e.g. knowledge_assertion, predicated or not_provided (empty in releases without it).
(Edge) agent_type: the kind of agent that made the assertion, e.g. manual_agent, automated_agent (empty in releases without it).
(Edge) negated: whether the association is negated (e.g. a gene that does not have a phenotype).
(Node) release (graph): the date of the release.
(Node) dangling_nodes (graph): the number of nodes that appear in edges but not in the list of nodes of the release (they have only an id).

Tags

Biological Informational Unweighted Multigraph Metadata

Added

2026-10-28

Citation

T. A. Putman et al., "The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species." Nucleic Acids Research 52, D938-D949 (2024) 10.1093/nar/gkad1082 Sci-Hub

Upstream URL OK

https://monarchinitiative.org/
https://data.monarchinitiative.org/monarch-kg/

Upstream license

CC BY 4.0 (the integrated sources keep their own licenses), https://creativecommons.org/licenses/by/4.0/

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	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
2023-09-28	830,288	8,076,791	9.73	301.52	373.78	585.98	-0.05	0.01	24	0.56	Directed	Unipartite	id category name symbol taxon taxon_label	negated predicate category primary_knowledge_source knowledge_level agent_type	18.7 MiB	45.4 MiB	45.1 MiB	41.8 MiB
2024-01-13	870,042	11,443,973	13.15	403.42	439.17	1238.09	-0.04	0.02	26	0.60	Directed	Unipartite	id category name symbol taxon taxon_label	negated predicate category primary_knowledge_source knowledge_level agent_type	27.1 MiB	65.5 MiB	65.2 MiB	58.8 MiB
2025-01-15	1,116,199	11,701,549	10.48	391.55	440.05	383.07	-0.04	0.02	24	0.66	Directed	Unipartite	id category name symbol taxon taxon_label	negated predicate category primary_knowledge_source knowledge_level agent_type	31.3 MiB	82.5 MiB	80.0 MiB	65.9 MiB
2026-01-11	1,379,605	15,356,321	11.13	422.20	469.32	433.98	-0.04	0.02	26	0.72	Directed	Unipartite	id category name symbol taxon taxon_label	negated predicate category primary_knowledge_source knowledge_level agent_type	47.3 MiB	124.0 MiB	120.4 MiB	99.7 MiB
2026-10-07	1,670,861	16,433,147	9.84	385.31	456.60	441.47	-0.04	0.02	25	0.70	Directed	Unipartite	id category name symbol taxon taxon_label	negated predicate category primary_knowledge_source knowledge_level agent_type	42.4 MiB	119.3 MiB	115.5 MiB	96.1 MiB