Civic Tools

Configuration File: civic_tools.json Tool Type: Local Tools Count: 12

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

Available Tools

civic_get_assertion (Type: CIViCTool)

Get detailed information about a specific assertion in CIViC database by assertion ID. Assertions…

civic_get_assertion tool specification

Tool Information:

• Name: civic_get_assertion

• Type: CIViCTool

• Description: Get detailed information about a specific assertion in CIViC database by assertion ID. Assertions are higher-level clinical interpretations that integrate multiple evidence items into formal statements about clinical actionability. Returns assertion description, evidence summary, and associated molecular profile or variant information.

Parameters:

• assertion_id (integer) (required) CIViC assertion ID (e.g., 101)

Example Usage:

query = {
    "name": "civic_get_assertion",
    "arguments": {
        "assertion_id": 10
    }
}
result = tu.run(query)

civic_get_evidence_item (Type: CIViCTool)

Get detailed information about a specific evidence item in CIViC database by evidence ID. Evidenc…

civic_get_evidence_item tool specification

Tool Information:

• Name: civic_get_evidence_item

• Type: CIViCTool

• Description: Get detailed information about a specific evidence item in CIViC database by evidence ID. Evidence items link molecular profiles or variants to clinical outcomes, therapies, or disease states with curated literature support. Returns evidence description, level (A-E), type (PREDICTIVE, DIAGNOSTIC, PROGNOSTIC), and associated information.

Parameters:

• evidence_id (integer) (required) CIViC evidence item ID (e.g., 116)

Example Usage:

query = {
    "name": "civic_get_evidence_item",
    "arguments": {
        "evidence_id": 10
    }
}
result = tu.run(query)

civic_get_molecular_profile (Type: CIViCTool)

Get detailed information about a specific molecular profile in CIViC database by molecular profil…

civic_get_molecular_profile tool specification

Tool Information:

• Name: civic_get_molecular_profile

• Type: CIViCTool

• Description: Get detailed information about a specific molecular profile in CIViC database by molecular profile ID. Molecular profiles represent combinations of variants or features (e.g., ‘BRAF V600E’) that serve as biomarkers for clinical interpretation. Returns profile name, description, and associated variants.

Parameters:

• molecular_profile_id (integer) (required) CIViC molecular profile ID (e.g., 12 for BRAF V600E)

Example Usage:

query = {
    "name": "civic_get_molecular_profile",
    "arguments": {
        "molecular_profile_id": 10
    }
}
result = tu.run(query)

civic_get_variant (Type: CIViCTool)

Get detailed information about a specific variant in CIViC database by variant ID. Variants repre…

civic_get_variant tool specification

Tool Information:

• Name: civic_get_variant

• Type: CIViCTool

• Description: Get detailed information about a specific variant in CIViC database by variant ID. Variants represent specific genetic alterations (SNVs, indels, structural variants, etc.) with clinical significance in cancer. Returns variant name, coordinates, gene association, and related information.

Parameters:

• variant_id (integer) (required) CIViC variant ID (e.g., 4170)

Example Usage:

query = {
    "name": "civic_get_variant",
    "arguments": {
        "variant_id": 10
    }
}
result = tu.run(query)

civic_get_variants_by_gene (Type: CIViCTool)

Get all variants associated with a specific gene in CIViC database. Returns variant information i…

civic_get_variants_by_gene tool specification

Tool Information:

• Name: civic_get_variants_by_gene

• Type: CIViCTool

• Description: Get all variants associated with a specific gene in CIViC database. Returns variant information including names, coordinates, and associated evidence. Use this after finding a gene ID with civic_search_genes to explore all cancer variants for that gene.

Parameters:

• gene_id (integer) (required) CIViC gene ID (e.g., 4244 for ABCB1). Find gene IDs using civic_search_genes.

• limit (integer) (optional) Maximum number of variants to return (default: 50, recommended max: 200)

Example Usage:

query = {
    "name": "civic_get_variants_by_gene",
    "arguments": {
        "gene_id": 10
    }
}
result = tu.run(query)

civic_search_assertions (Type: CIViCTool)

Search for assertions in CIViC database. Assertions are higher-level clinical interpretations tha…

civic_search_assertions tool specification

Tool Information:

• Name: civic_search_assertions

• Type: CIViCTool

• Description: Search for assertions in CIViC database. Assertions are higher-level clinical interpretations that integrate multiple evidence items into formal statements about clinical actionability. Returns a list of assertions with descriptions and associated molecular profiles or variants.

Parameters:

• limit (integer) (optional) Maximum number of assertions to return (default: 20, recommended max: 100)

Example Usage:

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

civic_search_diseases (Type: CIViCTool)

Search for diseases in CIViC database. Returns a list of cancer diseases and conditions (with IDs…

civic_search_diseases tool specification

Tool Information:

• Name: civic_search_diseases

• Type: CIViCTool

• Description: Search for diseases in CIViC database. Returns a list of cancer diseases and conditions (with IDs and names) that are associated with variants and evidence in CIViC. Use this to browse available disease entities before querying variants or evidence by disease.

Parameters:

• limit (integer) (optional) Maximum number of diseases to return (default: 20, recommended max: 100)

Example Usage:

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

civic_search_evidence_items (Type: CIViCTool)

Search for evidence items in CIViC database. Evidence items are curated statements linking varian…

civic_search_evidence_items tool specification

Tool Information:

• Name: civic_search_evidence_items

• Type: CIViCTool

• Description: Search for evidence items in CIViC database. Evidence items are curated statements linking variants or molecular profiles to clinical outcomes, therapies, or disease states. Returns a list of evidence items with descriptions, evidence levels (A-E), and evidence types (PREDICTIVE, DIAGNOSTIC, PROGNOSTIC).

Parameters:

• limit (integer) (optional) Maximum number of evidence items to return (default: 20, recommended max: 100)

Example Usage:

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

civic_search_genes (Type: CIViCTool)

Search for genes in CIViC (Clinical Interpretation of Variants in Cancer) database. CIViC is a co…

civic_search_genes tool specification

Tool Information:

• Name: civic_search_genes

• Type: CIViCTool

• Description: Search for genes in CIViC (Clinical Interpretation of Variants in Cancer) database. CIViC is a community knowledgebase for expert-curated interpretations of variants in cancer. Returns genes with their IDs, names, and descriptions. Use this to find genes of interest before querying variants or evidence.

Parameters:

• query (string) (optional) Optional search query to filter genes by name or description. If not provided, returns all genes up to the limit.

• limit (integer) (optional) Maximum number of genes to return (default: 10, recommended max: 100)

Example Usage:

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

civic_search_molecular_profiles (Type: CIViCTool)

Search for molecular profiles in CIViC database. Molecular profiles represent combinations of var…

civic_search_molecular_profiles tool specification

Tool Information:

• Name: civic_search_molecular_profiles

• Type: CIViCTool

• Description: Search for molecular profiles in CIViC database. Molecular profiles represent combinations of variants or features (e.g., ‘BRAF V600E’, ‘EGFR T790M’) that serve as biomarkers for clinical interpretation. Returns a list of molecular profiles with IDs, names, and descriptions.

Parameters:

• limit (integer) (optional) Maximum number of molecular profiles to return (default: 20, recommended max: 100)

Example Usage:

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

civic_search_therapies (Type: CIViCTool)

Search for therapies (drugs/treatments) in CIViC database. Returns a list of cancer therapies and…

civic_search_therapies tool specification

Tool Information:

• Name: civic_search_therapies

• Type: CIViCTool

• Description: Search for therapies (drugs/treatments) in CIViC database. Returns a list of cancer therapies and drugs (with IDs and names) that are associated with variants and evidence in CIViC. Use this to browse available therapies before querying evidence items or assertions by therapy.

Parameters:

• limit (integer) (optional) Maximum number of therapies to return (default: 20, recommended max: 100)

Example Usage:

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

civic_search_variants (Type: CIViCTool)

Search for variants in CIViC database. Returns a list of variants with their IDs and names. Varia…

civic_search_variants tool specification

Tool Information:

• Name: civic_search_variants

• Type: CIViCTool

• Description: Search for variants in CIViC database. Returns a list of variants with their IDs and names. Variants represent specific genetic alterations with clinical significance in cancer.

Parameters:

• limit (integer) (optional) Maximum number of variants to return (default: 20, recommended max: 100)

Example Usage:

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

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