Omnipath Tools

Configuration File: omnipath_tools.json Tool Type: Local Tools Count: 8

This page contains all tools defined in the omnipath_tools.json configuration file.

Available Tools

OmniPath_get_cell_communication_annotations (Type: OmniPathTool)

Get cell-cell communication annotations for proteins from databases like CellPhoneDB, CellChatDB,…

OmniPath_get_cell_communication_annotations tool specification

Tool Information:

• Name: OmniPath_get_cell_communication_annotations

• Type: OmniPathTool

• Description: Get cell-cell communication annotations for proteins from databases like CellPhoneDB, CellChatDB, CellTalkDB, ICELLNET, and other curated resources integrated into OmniPath. Returns role classifications (ligand/receptor), signaling pathway assignments, categories (Secreted Signaling, Cell-Cell Contact, ECM-Receptor), and other cell communication metadata. Useful for understanding the functional context of proteins in intercellular signaling. Example: TGFB1 (P01137) is annotated as ‘ligand’ in CellChatDB pathway ‘TGFb’ category ‘Secreted Signaling’; TGFBR2 (P37173) is annotated as ‘receptor’ in multiple pathways.

Parameters:

• proteins (string) (required) UniProt accession(s) or gene symbol(s), comma-separated. Examples: ‘P01137,P37173’, ‘TGFB1,EGFR’, ‘P00533’.

• databases ([‘string’, ‘null’]) (optional) Filter by annotation database(s), comma-separated. Cell communication databases: CellPhoneDB, CellChatDB, CellTalkDB, ICELLNET, iTALK, scConnect, Cellinker, connectomeDB2020, Ramilowski2015, Baccin2019, LRdb, HPMR. Other databases: HPA_tissue, UniProt_tissue, PanglaoDB, CellTypist, DGIdb, Guide2Pharma. Default: CellPhoneDB,CellChatDB.

• genesymbols ([‘boolean’, ‘null’]) (optional) Whether to include gene symbols in output (default: true).

Example Usage:

query = {
    "name": "OmniPath_get_cell_communication_annotations",
    "arguments": {
        "proteins": "example_value"
    }
}
result = tu.run(query)

OmniPath_get_complexes (Type: OmniPathTool)

Get protein complex compositions from OmniPath’s comprehensive complex database. Integrates 22,00…

OmniPath_get_complexes tool specification

Tool Information:

• Name: OmniPath_get_complexes

• Type: OmniPathTool

• Description: Get protein complex compositions from OmniPath’s comprehensive complex database. Integrates 22,000+ complexes from CORUM, CellPhoneDB, CellChatDB, ComplexPortal, PDB, Guide2Pharma, SIGNOR, KEGG, and other resources. Returns complex names, component proteins with gene symbols, stoichiometry, and database identifiers. Essential for understanding multi-subunit ligand-receptor complexes in cell communication (e.g., heteromeric cytokine receptors). Example: TGFB1 (P01137) participates in 24 complexes including ‘TGF-beta receptor II-TGF-beta1 complex’ (TGFB1+TGFBR2) and ‘ITGAV-ITGB8-MMP14-TGFB1 complex’.

Parameters:

• proteins (string) (required) UniProt accession(s), comma-separated. Note: gene symbols are NOT supported for this endpoint; use UniProt IDs. Examples: ‘P01137’ (TGFB1), ‘P00533’ (EGFR), ‘P01137,P37173’ (TGFB1+TGFBR2).

• databases ([‘string’, ‘null’]) (optional) Filter by source database(s), comma-separated. Options: CORUM, CellPhoneDB, CellChatDB, ComplexPortal, Guide2Pharma, PDB, SIGNOR, KEGG-MEDICUS, Cellinker, ICELLNET, hu.MAP, Compleat. Default: all.

Example Usage:

query = {
    "name": "OmniPath_get_complexes",
    "arguments": {
        "proteins": "example_value"
    }
}
result = tu.run(query)

OmniPath_get_dorothea_regulon (Type: OmniPathTool)

Get the complete DoRothEA regulon for a transcription factor from OmniPath. Returns all target ge…

OmniPath_get_dorothea_regulon tool specification

Tool Information:

• Name: OmniPath_get_dorothea_regulon

• Type: OmniPathTool

• Description: Get the complete DoRothEA regulon for a transcription factor from OmniPath. Returns all target genes with mode of regulation (MoR: +1=activation, -1=repression), DoRothEA confidence levels, and source databases. Optionally filter by confidence levels (A, B, C). DoRothEA is the standard resource for TF activity estimation in tools like VIPER, decoupleR, and PROGENy. Use for: TF regulon retrieval for activity scoring, network analysis.

Parameters:

• tf_gene (string) (required) Transcription factor gene symbol (e.g., ‘TP53’, ‘MYC’, ‘STAT3’, ‘NF2’)

• confidence_levels ([‘string’, ‘null’]) (optional) Comma-separated DoRothEA confidence levels to include (e.g., ‘A,B’ for high confidence only). Options: A, B, C, D, E. Default: all levels.

Example Usage:

query = {
    "name": "OmniPath_get_dorothea_regulon",
    "arguments": {
        "tf_gene": "example_value"
    }
}
result = tu.run(query)

OmniPath_get_enzyme_substrate (Type: OmniPathTool)

Get enzyme-substrate (post-translational modification) interactions from OmniPath. Integrates dat…

OmniPath_get_enzyme_substrate tool specification

Tool Information:

• Name: OmniPath_get_enzyme_substrate

• Type: OmniPathTool

• Description: Get enzyme-substrate (post-translational modification) interactions from OmniPath. Integrates data from PhosphoSite, phosphoELM, dbPTM, SIGNOR, HPRD, KEA, and other PTM databases. Returns kinase/phosphatase->substrate relationships with specific residue positions, modification types, and supporting evidence. Critical for understanding signaling cascades downstream of receptor activation (e.g., RTK->SRC->downstream phosphorylation targets). Example: SRC kinase (P12931) has 200+ substrates with phosphorylation sites; LCK (P06239) phosphorylates SOCS3 at Y204 and Y221.

Parameters:

• enzymes ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) for enzyme/kinase. Comma-separated for multiple. Examples: ‘SRC’, ‘P12931’, ‘LCK,FYN’.

• substrates ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) for substrate. Examples: ‘STAT3’, ‘P40763’.

• types ([‘string’, ‘null’]) (optional) Modification type filter. Options include: phosphorylation, ubiquitination, acetylation, methylation, sumoylation, glycosylation. Default: all types.

• organisms ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID. Default: 9606 (human).

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return.

Example Usage:

query = {
    "name": "OmniPath_get_enzyme_substrate",
    "arguments": {
    }
}
result = tu.run(query)

OmniPath_get_intercell_roles (Type: OmniPathTool)

Get intercellular communication roles for proteins from OmniPath. Classifies proteins as ligands,…

OmniPath_get_intercell_roles tool specification

Tool Information:

• Name: OmniPath_get_intercell_roles

• Type: OmniPathTool

• Description: Get intercellular communication roles for proteins from OmniPath. Classifies proteins as ligands, receptors, transmembrane proteins, secreted factors, or extracellular matrix components based on evidence from 40+ databases. Returns functional categories (ligand/receptor/adhesion/transporter), locational annotations (secreted/transmembrane/peripheral), consensus scores, and supporting databases. Critical for identifying which genes act as senders vs receivers in cell-cell communication. Example: querying EGFR shows it is classified as ‘receptor’ by 10 databases with consensus_score 7, plasma_membrane_transmembrane=true; querying TGFB1 shows it is a ‘ligand’ (secreted=true, transmitter=true).

Parameters:

• proteins ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s), comma-separated. Examples: ‘EGFR’, ‘TGFB1,PDCD1’, ‘P00533,P01137’.

• categories ([‘string’, ‘null’]) (optional) Filter by intercellular role category. Examples: ‘ligand’, ‘receptor’, ‘adhesion’, ‘transporter’, ‘ecm’, ‘transmembrane’. Comma-separated for multiple.

• scope ([‘string’, ‘null’]) (optional) Filter by annotation scope: ‘generic’ (general role) or ‘specific’ (cell-type specific). Default: all.

• transmitter ([‘boolean’, ‘null’]) (optional) Filter for transmitter/sender proteins (true) or non-transmitters (false).

• receiver ([‘boolean’, ‘null’]) (optional) Filter for receiver proteins (true) or non-receivers (false).

• secreted ([‘boolean’, ‘null’]) (optional) Filter for secreted proteins (true) or non-secreted (false).

• limit ([‘integer’, ‘null’]) (optional) Maximum number of results to return. Default: no limit.

Example Usage:

query = {
    "name": "OmniPath_get_intercell_roles",
    "arguments": {
    }
}
result = tu.run(query)

OmniPath_get_ligand_receptor_interactions (Type: OmniPathTool)

Get ligand-receptor interaction pairs from OmniPath, the largest integrated intercellular communi…

OmniPath_get_ligand_receptor_interactions tool specification

Tool Information:

• Name: OmniPath_get_ligand_receptor_interactions

• Type: OmniPathTool

• Description: Get ligand-receptor interaction pairs from OmniPath, the largest integrated intercellular communication database. Combines data from CellPhoneDB, CellChatDB, CellTalkDB, connectomeDB, Ramilowski2015, Guide2Pharma, HPMR, and 20+ other curated resources. Returns source/target proteins with directionality, stimulation/inhibition flags, supporting databases, and curation effort scores. Essential for cell-cell communication analysis in single-cell transcriptomics (CellPhoneDB/CellChat/LIANA workflows). Example: querying TGFB1 returns 30 ligand-receptor interactions including TGFB1->TGFBR2 (135 curation effort, 34 databases), TGFB1->ACVRL1 (14 curation effort, 26 databases); querying CD274 (PD-L1) finds CD274->PDCD1 immune checkpoint interaction supported by 22 databases.

Parameters:

• partners ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) to query as interaction partners (either source or target). Comma-separated for multiple. Examples: ‘TGFB1’, ‘CD274,PDCD1’, ‘EGFR’, ‘P01137’.

• sources ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) for source (ligand) proteins only. Use instead of ‘partners’ to get outgoing interactions. Examples: ‘TGFB1’, ‘WNT3A’.

• targets ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) for target (receptor) proteins only. Use instead of ‘partners’ to get incoming interactions. Examples: ‘EGFR’, ‘PDCD1’.

• databases ([‘string’, ‘null’]) (optional) Filter by specific source database(s), comma-separated. Options include: CellPhoneDB, CellChatDB, CellTalkDB, connectomeDB2020, Ramilowski2015, Guide2Pharma, HPMR, iTALK, scConnect, Baccin2019, ICELLNET, LRdb, Cellinker. Default: all databases.

• organisms ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID for species filter. Default: 9606 (human). Options: 9606 (human), 10090 (mouse), 10116 (rat).

• limit ([‘integer’, ‘null’]) (optional) Maximum number of interactions to return. Default: no limit (returns all).

Example Usage:

query = {
    "name": "OmniPath_get_ligand_receptor_interactions",
    "arguments": {
    }
}
result = tu.run(query)

OmniPath_get_signaling_interactions (Type: OmniPathTool)

Get intracellular signaling pathway interactions from OmniPath’s curated datasets. Supports query…

OmniPath_get_signaling_interactions tool specification

Tool Information:

• Name: OmniPath_get_signaling_interactions

• Type: OmniPathTool

• Description: Get intracellular signaling pathway interactions from OmniPath’s curated datasets. Supports querying the main OmniPath signaling network (literature-curated, directed PPI), pathwayextra (activity flow from Reactome/KEGG/WikiPathways), kinaseextra (kinase-substrate from PhosphoSite/dbPTM), and more. Returns directed, signed interactions with stimulation/inhibition annotations and supporting evidence. Useful for reconstructing signaling cascades downstream of receptor activation. Example: NOTCH1 has 110 directed signaling interactions; SRC kinase connects to 200+ downstream substrates; TP53 has 500+ pathway interactions.

Parameters:

• partners ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) to query. Comma-separated for multiple. Examples: ‘TP53’, ‘NOTCH1’, ‘SRC,ABL1’.

• sources ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) for source/upstream proteins only.

• targets ([‘string’, ‘null’]) (optional) Gene symbol(s) or UniProt ID(s) for target/downstream proteins only.

• datasets ([‘string’, ‘null’]) (optional) Which OmniPath dataset(s) to query, comma-separated. Options: ‘omnipath’ (curated signaling, default), ‘pathwayextra’ (activity flow from pathway DBs), ‘kinaseextra’ (kinase-substrate), ‘dorothea’ (TF-target), ‘tf_target’ (TF regulation), ‘mirnatarget’ (miRNA targets), ‘lncrna_mrna’ (lncRNA regulation). Default: ‘omnipath’.

• directed ([‘boolean’, ‘null’]) (optional) Filter for directed interactions only (default: true for signaling).

• signed ([‘boolean’, ‘null’]) (optional) Filter for interactions with known stimulation/inhibition sign.

• organisms ([‘integer’, ‘null’]) (optional) NCBI taxonomy ID. Default: 9606 (human). Options: 9606, 10090, 10116.

• limit ([‘integer’, ‘null’]) (optional) Maximum number of interactions to return.

Example Usage:

query = {
    "name": "OmniPath_get_signaling_interactions",
    "arguments": {
    }
}
result = tu.run(query)

OmniPath_get_tf_target_interactions (Type: OmniPathTool)

Get transcription factor (TF) to target gene interactions from OmniPath DoRothEA and CollecTRI re…

OmniPath_get_tf_target_interactions tool specification

Tool Information:

• Name: OmniPath_get_tf_target_interactions

• Type: OmniPathTool

• Description: Get transcription factor (TF) to target gene interactions from OmniPath DoRothEA and CollecTRI regulons. Returns directed TF-target pairs with mode of regulation (activation/repression), DoRothEA confidence levels (A-E), and supporting evidence. Query by TF gene symbol or target gene. Use for: TF activity inference, regulatory network construction, identifying TF targets for VIPER/decoupleR analysis.

Parameters:

• tf_gene ([‘string’, ‘null’]) (optional) Transcription factor gene symbol (e.g., ‘TP53’, ‘MYC’, ‘STAT3’). Mutually exclusive with target_gene or can be combined.

• target_gene ([‘string’, ‘null’]) (optional) Target gene symbol to find regulating TFs (e.g., ‘CDKN1A’, ‘BCL2’). Mutually exclusive with tf_gene or can be combined.

• confidence_level ([‘string’, ‘null’]) (optional) DoRothEA confidence level filter: A=highest (1-2 sources), B=high (3+ sources), C=medium, D=low, E=lowest. A/B recommended for analysis.

Example Usage:

query = {
    "name": "OmniPath_get_tf_target_interactions",
    "arguments": {
    }
}
result = tu.run(query)

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