Ctd Tools#

Configuration File: ctd_tools.json Tool Type: Local Tools Count: 5

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

Available Tools#

CTD_get_chemical_diseases (Type: CTDTool)#

Get curated chemical-disease associations from CTD. Given a chemical name, returns diseases it is…

CTD_get_chemical_diseases tool specification

Tool Information:

  • Name: CTD_get_chemical_diseases

  • Type: CTDTool

  • Description: Get curated chemical-disease associations from CTD. Given a chemical name, returns diseases it is associated with, along with the underlying evidence type (marker/mechanism vs. therapeutic) and a supporting PubMed ID. Example: ‘bisphenol A’ returns associations with cancer, reproductive disorders, etc. Backed by mydisease.info’s cached copy of CTD’s curated chemical-disease data (CTD’s own native batchQuery.go is CAPTCHA-blocked for programmatic clients, and the RENCI Automat mirror this tool previously used has been fully decommissioned).

Parameters:

  • input_terms (string) (required) Chemical name, CAS Registry Number, or CTD/MeSH chemical ID (e.g., ‘C006780’, ‘D016729’, optionally prefixed ‘MESH:’). Examples: ‘arsenic’, ‘bisphenol A’, ‘C006780’, ‘80-05-7’. Matched by exact string against CTD’s canonical chemical name, not fuzzy-matched, so an uncommon synonym can fail even when the substance is covered. Other identifier systems (CHEBI, PubChem CID, etc.) are not supported – resolve to a name first.

Example Usage:

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

CTD_get_chemical_gene_interactions (Type: CTDTool)#

PERMANENTLY UNAVAILABLE: this tool always returns an error. CTD’s native batchQuery.go is CAPTCHA…

CTD_get_chemical_gene_interactions tool specification

Tool Information:

  • Name: CTD_get_chemical_gene_interactions

  • Type: CTDTool

  • Description: PERMANENTLY UNAVAILABLE: this tool always returns an error. CTD’s native batchQuery.go is CAPTCHA-blocked for programmatic clients, and the RENCI Automat mirror this tool used to fall back on has been fully decommissioned (its registry no longer lists a ‘ctd’ backend at all). No other free, live source of CTD’s curated chemical-gene interactions was found. Use DGIdb_get_drug_gene_interactions or ChEMBL/OpenTargets tools for target-compound bioactivity data instead.

Parameters:

  • input_terms (string) (required) Chemical name, CAS RN, or MeSH ID. Unused – this tool always returns an error; see the tool description.

Example Usage:

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

CTD_get_disease_chemicals (Type: CTDTool)#

Get curated disease-chemical associations from CTD. Given a disease name, MONDO CURIE, or MeSH di…

CTD_get_disease_chemicals tool specification

Tool Information:

  • Name: CTD_get_disease_chemicals

  • Type: CTDTool

  • Description: Get curated disease-chemical associations from CTD. Given a disease name, MONDO CURIE, or MeSH disease ID, returns chemicals associated with it, including the underlying evidence type (marker/mechanism vs. therapeutic) and a supporting PubMed ID. Example: ‘breast neoplasm’ returns chemicals linked to breast cancer including both therapeutic agents and toxicants. Backed by mydisease.info’s cached copy of CTD’s curated chemical-disease data (CTD’s own native batchQuery.go is CAPTCHA-blocked for programmatic clients, and the RENCI Automat mirror this tool previously used has been fully decommissioned).

Parameters:

  • input_terms (string) (required) Disease name, MONDO CURIE (e.g. ‘MONDO:0007254’), or MeSH disease ID (e.g. ‘D001249’, optionally prefixed ‘MESH:’). Examples: ‘breast neoplasm’, ‘asthma’, ‘MESH:D001249’. Free-text names are resolved via MONDO’s own text search, so common synonyms generally work; exact CURIEs are more reliable for ambiguous names.

Example Usage:

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

CTD_get_gene_chemicals (Type: CTDTool)#

PERMANENTLY UNAVAILABLE: this tool always returns an error. CTD’s native batchQuery.go is CAPTCHA…

CTD_get_gene_chemicals tool specification

Tool Information:

  • Name: CTD_get_gene_chemicals

  • Type: CTDTool

  • Description: PERMANENTLY UNAVAILABLE: this tool always returns an error. CTD’s native batchQuery.go is CAPTCHA-blocked for programmatic clients, and the RENCI Automat mirror this tool used to fall back on has been fully decommissioned (its registry no longer lists a ‘ctd’ backend at all). No other free, live source of CTD’s curated gene-chemical interactions was found. Use DGIdb_get_drug_gene_interactions or ChEMBL/OpenTargets tools for target-compound bioactivity data instead.

Parameters:

  • input_terms (string) (required) Gene symbol or NCBI Gene ID. Unused – this tool always returns an error; see the tool description.

Example Usage:

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

CTD_get_gene_diseases (Type: CTDTool)#

PERMANENTLY UNAVAILABLE: this tool always returns an error. No live, free source of CTD’s curated…

CTD_get_gene_diseases tool specification

Tool Information:

  • Name: CTD_get_gene_diseases

  • Type: CTDTool

  • Description: PERMANENTLY UNAVAILABLE: this tool always returns an error. No live, free source of CTD’s curated gene-disease associations was found (CTD’s native API is CAPTCHA-blocked, and the RENCI Automat mirror this tool previously fell back on has been fully decommissioned). This tool returns a structured error and redirects callers to OpenTargets_get_associated_diseases. Use that tool instead.

Parameters:

  • input_terms (string) (optional) Gene symbol or NCBI Gene ID. Examples: ‘TP53’, ‘BRCA1’, ‘CYP1A1’, ‘7157’ (Gene ID for TP53).

  • query (string) (optional) Gene symbol or name to search (alias for input_terms, e.g. TP53)

  • gene_symbol (string) (optional) Gene symbol (alias for input_terms, e.g. TP53)

Example Usage:

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