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, and disease categories. Example: ‘bisphenol A’ returns associations with cancer, reproductive disorders, etc. Note: unlike the sibling CTD_get_chemical_gene_interactions tool, the RENCI mirror’s chemical-disease edges do not carry a direct evidence type (predicate/qualified_predicate) – those fields are consistently null here, not a query error. Backed by the RENCI Automat CTD mirror (June-2024 snapshot, biolink-categorized); CTD’s native batchQuery.go is currently CAPTCHA-blocked for programmatic clients.

Parameters:

  • input_terms (string) (required) Chemical name, MeSH name, synonym, CAS RN, or MeSH ID. Examples: ‘arsenic’, ‘bisphenol A’, ‘C006780’.

Example Usage:

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

CTD_get_chemical_gene_interactions (Type: CTDTool)#

Get curated chemical-gene interactions from CTD (Comparative Toxicogenomics Database). Given a ch…

CTD_get_chemical_gene_interactions tool specification

Tool Information:

  • Name: CTD_get_chemical_gene_interactions

  • Type: CTDTool

  • Description: Get curated chemical-gene interactions from CTD (Comparative Toxicogenomics Database). Given a chemical name, returns genes it interacts with, including organism, PubMed references, and interaction types. Example: ‘bisphenol A’ returns thousands of gene interactions across species. Note: the result’s top-level ‘predicate’ field is always null for this edge type – the real interaction-type signal is in ‘qualified_predicate’ (e.g. ‘biolink:causes’) and ‘object_direction_qualifier’. Backed by the RENCI Automat CTD mirror (June-2024 snapshot, biolink-categorized); CTD’s native batchQuery.go is currently CAPTCHA-blocked for programmatic clients.

Parameters:

  • input_terms (string) (required) Chemical name, CAS RN, or MeSH ID. Examples: ‘bisphenol A’, ‘paracetamol’ (the RENCI mirror’s canonical name – common synonyms like ‘acetaminophen’ may not resolve), ‘D000082’ (MeSH ID, prefix optional). CAS RN and MeSH/NCBI Gene IDs are matched by exact string against the graph’s canonical name/synonym list, not fuzzy-matched, so an uncommon synonym can fail even when the substance is covered.

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, returns chemicals assoc…

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, returns chemicals associated with it, including evidence type. Example: ‘breast neoplasm’ returns chemicals linked to breast cancer including both therapeutic agents and toxicants. Backed by the RENCI Automat CTD mirror (June-2024 snapshot, biolink-categorized); CTD’s native batchQuery.go is currently CAPTCHA-blocked for programmatic clients.

Parameters:

  • input_terms (string) (required) Disease name, MeSH/OMIM ID. Examples: ‘breast neoplasm’ (singular – the plural ‘Breast Neoplasms’ does not resolve), ‘asthma’, ‘MESH:D001249’. Matched by exact string against the graph’s canonical name, not fuzzy-matched, so an uncommon phrasing can fail even when the disease is covered.

Example Usage:

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

CTD_get_gene_chemicals (Type: CTDTool)#

Get curated gene-chemical interactions from CTD. Given a gene symbol, returns chemicals that inte…

CTD_get_gene_chemicals tool specification

Tool Information:

  • Name: CTD_get_gene_chemicals

  • Type: CTDTool

  • Description: Get curated gene-chemical interactions from CTD. Given a gene symbol, returns chemicals that interact with the gene product, with PubMed evidence. Example: ‘TP53’ returns over 2000 chemical interactions including drugs, environmental toxicants. Backed by the RENCI Automat CTD mirror (June-2024 snapshot, biolink-categorized); CTD’s native batchQuery.go is currently CAPTCHA-blocked for programmatic clients.

Parameters:

  • input_terms (string) (required) Gene symbol or NCBI Gene ID. Examples: ‘CYP1A1’, ‘TP53’, ‘ESR1’.

Example Usage:

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

CTD_get_gene_diseases (Type: CTDTool)#

Gene -> disease relationships are NOT served by the RENCI CTD mirror (chemical-centric snapshot)….

CTD_get_gene_diseases tool specification

Tool Information:

  • Name: CTD_get_gene_diseases

  • Type: CTDTool

  • Description: Gene -> disease relationships are NOT served by the RENCI CTD mirror (chemical-centric snapshot). 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)