omnipath — OmniPath molecular interactions (2018-2026)

Description

Directed and signed networks of molecular interactions from OmniPath, a database that integrates more than 100 resources of literature-curated and predicted molecular interactions (mostly of human proteins): signaling pathways (post-translational interactions, e.g. SIGNOR, SignaLink, Reactome, KEGG, PhosphoSite), enzyme-substrate (kinase-substrate) relations, ligand-receptor interactions between cells, transcriptional regulation of genes by transcription factors (DoRothEA, CollecTRI), regulation by miRNAs and lncRNAs, and interactions of small molecules with proteins. Each edge is an interaction, from the source to the target of the interaction (e.g. from a kinase to its substrate), with its direction and sign (stimulation or inhibition) when they are known; the interactions whose direction is unknown are also listed from a source to a target, with is_directed false.

The networks are all the archived contents of the OmniPath web service (the interactions query, with all its datasets and organisms, i.e. human, and the interactions translated by homology to mouse and rat), each named by the date from which it was served, until the next one: 2018-06-14, 2018-11-14, 2019-04-25, 2019-06-26, 2019-08-26, 2019-10-18, 2019-11-27, 2020-02-17, 2020-05-19, 2020-08-03, 2020-09-09, 2020-09-21, 2021-01-21, 2021-03-29, 2021-06-16, 2021-06-21, 2021-11-13, 2022-01-14, 2023-03-30, 2023-05-18, 2023-05-24, 2023-07-28 (until 2025-08-13), 2025-08-13 (the last content of the legacy web service, until 2026-06-24) and 2026-06-25 (with the new CollecTRI 2 dataset as a separate dataset). No two of them have identical content (2023-05-24 and 2023-07-28 have the same interactions, resources and datasets, but differ in some gene symbols, directions, signs and further attributes). The current content of the web service (omnipath_webservice_interactions__latest, replaced in place at every update) is left out. Nodes are proteins (UniProt accessions), protein complexes (COMPLEX: followed by the accessions of their members), miRNAs, lncRNAs and small molecules.

The networks have the following properties (the columns of the web service; the later contents have more of them):

(Node) name: the identifier of the node in OmniPath (e.g. the UniProt accession P0DP23).
(Node) genesymbol: the gene symbol of the node (e.g. CALM1).
(Node) ncbi_tax_id: the NCBI taxonomy identifier of the organism of the node (e.g. 9606 for human; -1 if not given).
(Node) entity_type (from 2020-05-19): the kind of node, e.g. protein, complex, mirna, lncrna, small_molecule.
(Edge) is_directed, is_stimulation, is_inhibition: whether the interaction is directed, stimulatory and inhibitory, according to at least one resource.
(Edge) consensus_direction, consensus_stimulation, consensus_inhibition (from 2019-06-26): the same, according to the majority of the resources.
(Edge) sources: the resources of the interaction, separated by ;.
(Edge) references: the PubMed identifiers of the references of the interaction (prefixed by the resource in the later contents), separated by ;.
(Edge) type: the kind of interaction, e.g. post_translational, transcriptional, post_transcriptional, mirna_transcriptional, small_molecule_protein (PPI, TF and MTI until 2020-02-17).
(Edge) Dataset flags, e.g. omnipath (the core literature-curated signaling network), kinaseextra, ligrecextra, pathwayextra, mirnatarget, dorothea, collectri, collectri2, tf_target, lncrna_mrna, tf_mirna, small_molecule (tfregulons until 2020-02-17; ligrecextra and pathwayextra from 2019-06-26, tf_target, lncrna_mrna and tf_mirna from 2020-05-19, small_molecule from 2022-01-14, collectri from 2023-03-30, collectri2 in 2026-06-25): whether the interaction belongs to the dataset.
(Edge) dorothea_curated, dorothea_chipseq, dorothea_tfbs, dorothea_coexp, dorothea_level (tfregulons_... until 2020-02-17): the kinds of evidence and the confidence level (A to E) of the transcriptional regulation in DoRothEA.
(Edge) curation_effort (from 2020-02-17): the number of unique resource-reference pairs of the interaction.
(Edge) extra_attrs (from 2021-11-13): further attributes given by the resources, in JSON.
(Edge) evidences (from 2023-05-18): the provenance of the interaction by resource and dataset, with the references and the direction and sign given by each, in JSON.
(Edge) dip_url (until 2021-06-21): the URL of the interaction in DIP.

Tags

Biological Protein interactions Gene regulation Signed Unweighted Multigraph Metadata

Added

2026-10-31

Citation

D. Türei, T. Korcsmáros, J. Saez-Rodriguez, "OmniPath: guidelines and gateway for literature-curated signaling pathway resources." Nature Methods 13, 966-967 (2016) 10.1038/nmeth.4077 Sci-Hub
D. Türei, A. Valdeolivas, L. Gul, N. Palacio-Escat, M. Klein, O. Ivanova, M. Ölbei, A. Gábor, F. Theis, D. Módos, T. Korcsmáros, J. Saez-Rodriguez, "Integrated intra- and intercellular signaling knowledge for multicellular omics analysis." Molecular Systems Biology 17, e9923 (2021) 10.15252/msb.20209923 Sci-Hub

Upstream URL OK

https://omnipathdb.org/
https://archive.omnipathdb.org/

Upstream license

The licenses of the integrated resources (academic, non-profit or commercial use, depending on the resource), https://omnipathdb.org/info

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
2018-06-14	40,258	644,845	16.02	246.63	328.85	7.18	-0.29	0.02	7	0.48	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition sources references dip_url omnipath kinaseextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	2.9 MiB	7.1 MiB	6.9 MiB	5.0 MiB
2018-11-14	22,913	131,729	5.75	30.32	67.73	24.04	-0.07	0.09	13	0.46	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition sources references dip_url omnipath kinaseextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	1.5 MiB	2.8 MiB	2.8 MiB	2.8 MiB
2019-04-25	24,208	151,466	6.26	32.85	72.72	110.91	-0.07	0.08	13	0.97	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition sources references dip_url omnipath kinaseextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	1.7 MiB	3.1 MiB	3.0 MiB	3.1 MiB
2019-06-26	25,668	255,217	9.94	47.02	107.79	178.53	-0.05	0.15	13	0.98	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	2.0 MiB	4.4 MiB	4.3 MiB	3.8 MiB
2019-08-26	41,150	784,644	19.07	248.08	336.75	485.14	-0.24	0.02	7	1.00	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	3.5 MiB	9.2 MiB	9.1 MiB	6.5 MiB
2019-10-18	41,167	787,068	19.12	248.07	336.83	486.78	-0.24	0.02	7	1.00	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	3.5 MiB	9.3 MiB	9.1 MiB	6.5 MiB
2019-11-27	41,697	890,945	21.37	262.10	358.69	546.68	-0.25	0.02	8	1.00	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type	4.3 MiB	10.6 MiB	10.5 MiB	7.5 MiB
2020-02-17	41,446	853,058	20.58	263.04	358.99	4.49	-0.26	0.02	5	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget tfregulons tfregulons_curated tfregulons_chipseq tfregulons_tfbs tfregulons_coexp tfregulons_level type curation_effort	3.6 MiB	9.5 MiB	9.5 MiB	6.9 MiB
2020-05-19	41,575	902,937	21.72	263.40	362.13	3.91	-0.24	0.02	6	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	3.9 MiB	10.0 MiB	9.9 MiB	7.5 MiB
2020-08-03	41,564	896,325	21.56	263.05	360.83	13.39	-0.25	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	3.7 MiB	9.7 MiB	9.6 MiB	7.1 MiB
2020-09-09	41,556	853,373	20.54	261.53	357.22	13.04	-0.26	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	4.1 MiB	10.3 MiB	10.1 MiB	7.9 MiB
2020-09-21	41,563	853,390	20.53	261.52	357.16	13.04	-0.26	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	4.1 MiB	10.3 MiB	10.1 MiB	7.9 MiB
2021-01-21	41,613	856,178	20.57	261.36	357.29	13.04	-0.26	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	4.2 MiB	10.4 MiB	10.2 MiB	8.0 MiB
2021-03-29	41,633	861,177	20.68	261.49	358.44	13.04	-0.25	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	4.3 MiB	10.5 MiB	10.4 MiB	8.2 MiB
2021-06-16	41,638	856,641	20.57	261.38	358.17	13.04	-0.26	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	4.2 MiB	10.4 MiB	10.2 MiB	8.0 MiB
2021-06-21	41,630	860,143	20.66	261.47	358.40	13.04	-0.26	0.02	7	0.49	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references dip_url omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort	4.3 MiB	10.5 MiB	10.4 MiB	8.2 MiB
2021-11-13	51,824	1,173,654	22.65	285.01	358.23	9.16	-0.27	0.02	8	0.40	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs	5.9 MiB	14.7 MiB	14.9 MiB	12.8 MiB
2022-01-14	50,649	1,096,924	21.66	275.22	358.70	294.77	-0.27	0.02	8	0.43	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs	6.1 MiB	14.2 MiB	13.8 MiB	12.2 MiB
2023-03-30	50,122	1,225,778	24.46	275.11	378.16	98.99	-0.24	0.02	9	0.45	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea collectri tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs	8.0 MiB	16.3 MiB	15.9 MiB	15.0 MiB
2023-05-18	50,098	1,225,192	24.46	275.15	378.09	98.98	-0.24	0.02	9	0.45	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea collectri tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs evidences	18.0 MiB	27.8 MiB	27.5 MiB	31.2 MiB
2023-05-24	50,075	1,217,900	24.32	274.79	376.72	98.99	-0.24	0.02	9	0.45	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea collectri tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs evidences	18.0 MiB	27.7 MiB	27.5 MiB	31.4 MiB
2023-07-28	50,075	1,217,900	24.32	274.79	376.72	98.99	-0.24	0.02	9	0.45	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea collectri tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs evidences	17.9 MiB	27.7 MiB	27.4 MiB	31.3 MiB
2025-08-13	55,776	1,419,006	25.44	283.21	378.52	50.12	-0.23	0.02	10	0.40	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea collectri tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs evidences	22.9 MiB	34.2 MiB	34.0 MiB	39.0 MiB
2026-06-25	56,444	2,071,155	36.69	342.36	451.99	51.80	-0.23	0.06	12	0.41	Directed	Unipartite	name genesymbol ncbi_tax_id entity_type	is_directed is_stimulation is_inhibition consensus_direction consensus_stimulation consensus_inhibition sources references omnipath kinaseextra ligrecextra pathwayextra mirnatarget dorothea collectri collectri2 tf_target lncrna_mrna tf_mirna small_molecule dorothea_curated dorothea_chipseq dorothea_tfbs dorothea_coexp dorothea_level type curation_effort extra_attrs evidences	48.8 MiB	65.1 MiB	64.1 MiB	78.0 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.