drug-discovery-prompts/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-cancer-variant-interpretation/TOOLS_REFERENCE.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Cancer Variant Interpretation - Tools Reference		import	https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-cancer-variant-interpretation/TOOLS_REFERENCE.md	e2520a96	2026-06-26	prompt	accepted	upstream	false

Cancer Variant Interpretation - Tools Reference

Verified tool parameters and response structures for all tools used in this skill.

Gene Resolution Tools

MyGene_query_genes

Purpose: Resolve gene symbol to Ensembl, Entrez IDs Parameters:

• query (string, REQUIRED): Gene symbol, name, or ID (e.g., 'EGFR')
• species (string, default='human'): Species filter
• fields (string): Comma-separated fields to return

Response: {took, total, max_score, hits: [{_id, _score, ensembl: {gene}, entrezgene, name, symbol}]}

Example:

result = tu.tools.MyGene_query_genes(query='EGFR', species='human')
# hits[0] = {symbol: 'EGFR', ensembl: {gene: 'ENSG00000146648'}, entrezgene: '1956', name: 'epidermal growth factor receptor'}

UniProt_search

Purpose: Find protein accession Parameters:

• query (string, REQUIRED): e.g., 'gene:EGFR'
• organism (string): e.g., 'human'
• limit (integer)

Response: {total_results, returned, results: [{accession, id, protein_name, gene_names, organism, length}]}

UniProt_get_function_by_accession

Purpose: Get protein function description Parameters: accession (string, REQUIRED): e.g., 'P00533'

Response: Returns a list of strings (NOT a dict). Each string is a function description paragraph.

# Example: ['Receptor tyrosine kinase binding ligands of the EGF family...', ...]

UniProt_get_disease_variants_by_accession

Purpose: Get known disease-associated variants Parameters: accession (string, REQUIRED)

OpenTargets_get_target_id_description_by_name

Purpose: Resolve gene name to Ensembl ID in OpenTargets Parameters: targetName (string, REQUIRED)

Response: {data: {search: {hits: [{id (ensemblId), name, description}]}}}

OpenTargets_get_disease_id_description_by_name

Purpose: Resolve disease/cancer type to EFO ID Parameters: diseaseName (string, REQUIRED)

Response: {data: {search: {hits: [{id (efoId), name, description}]}}}

ensembl_lookup_gene

Purpose: Get gene details including version number Parameters:

• gene_id (string, REQUIRED): Ensembl ID or gene symbol
• species (string, REQUIRED for Ensembl IDs): e.g., 'homo_sapiens' -- will error without this!

Response: {status: 'success', data: {id, version, display_name, species, biotype, start, end, seq_region_name, strand, canonical_transcript, assembly_name}}

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CIViC Clinical Evidence Tools

civic_search_genes

Purpose: List genes in CIViC database Parameters:

• query (string): Filter query (NOTE: does NOT filter in GraphQL, returns all genes alphabetically)
• limit (integer, default=10, max=100): Number to return

Response: {data: {genes: {nodes: [{id, name, description, entrezId}]}}}

LIMITATION: Returns genes alphabetically, max 100 per call. No server-side filtering. Genes beyond alphabetical position 100 (E-Z) require multiple paginated calls or known CIViC gene IDs.

civic_get_variants_by_gene

Purpose: Get all variants for a gene in CIViC Parameters:

• gene_id (integer, REQUIRED): CIViC gene ID (NOT Entrez ID)
• limit (integer, default=50): Max variants to return

Response: {data: {gene: {variants: {nodes: [{id, name}]}}}}

civic_get_variant

Purpose: Get variant details Parameters: variant_id (integer, REQUIRED)

Response: {data: {variant: {id, name}}}

civic_get_molecular_profile

Purpose: Get molecular profile details Parameters: molecular_profile_id (integer, REQUIRED)

civic_search_evidence_items

Purpose: List evidence items Parameters: limit (integer, default=20)

Response: {data: {evidenceItems: {nodes: [{id, description, evidenceLevel, evidenceType}]}}}

civic_search_assertions

Purpose: List assertions Parameters: limit (integer, default=20)

civic_search_therapies

Purpose: List therapies Parameters: limit (integer, default=20)

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cBioPortal Mutation Prevalence Tools

cBioPortal_get_mutations

Purpose: Get mutation data for genes in a study Parameters:

• study_id (string): Cancer study ID (e.g., 'luad_tcga')
• gene_list (string): Comma-separated gene symbols (e.g., 'EGFR,KRAS')

Response: {status: 'success', data: [{proteinChange, mutationType, sampleId, entrezGeneId, studyId, mutationStatus, chr, startPosition, endPosition, ...}]}

IMPORTANT: Extract mutations via result.get('data', []), NOT treating result as a list directly.

cBioPortal_get_cancer_studies

Purpose: List available cancer studies Parameters: limit (integer, default=20)

Response: Array of [{studyId, name, description, cancerTypeId, ...}]

cBioPortal_get_molecular_profiles

Purpose: Get molecular profiles for a study Parameters: study_id (string, REQUIRED)

cBioPortal_get_gene_info

Purpose: Get gene info by Entrez ID Parameters: entrez_gene_id (integer, REQUIRED)

cBioPortal_get_samples

Purpose: Get samples from a study Parameters: study_id (string, REQUIRED)

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Drug Information Tools

OpenTargets_get_associated_drugs_by_target_ensemblID

Purpose: Get ALL drugs targeting a gene (approved + clinical trials) Parameters:

• ensemblId (string, REQUIRED): NOTE camelCase
• size (integer): Number of drug entries

Response: {data: {target: {id, approvedSymbol, knownDrugs: {count, rows: [{drug: {id, name, tradeNames, maximumClinicalTrialPhase, isApproved, hasBeenWithdrawn}, phase, mechanismOfAction, disease: {id, name}}]}}}}

OpenTargets_get_drug_chembId_by_generic_name

Purpose: Resolve drug name to ChEMBL ID Parameters: drugName (string, REQUIRED)

Response: {data: {search: {hits: [{id (ChEMBL ID), name, description}]}}}

OpenTargets_get_drug_mechanisms_of_action_by_chemblId

Purpose: Drug mechanism of action Parameters: chemblId (string, REQUIRED)

OpenTargets_get_drug_indications_by_chemblId

Purpose: Drug indications Parameters: chemblId (string, REQUIRED)

OpenTargets_get_drug_adverse_events_by_chemblId

Purpose: Drug adverse events Parameters: chemblId (string, REQUIRED)

OpenTargets_get_associated_drugs_by_disease_efoId

Purpose: Get drugs for a specific disease Parameters: efoId (string, REQUIRED), size (integer, REQUIRED)

FDA_get_indications_by_drug_name

Purpose: FDA-approved indications Parameters: drug_name (string), limit (integer)

Response: {meta: {skip, limit, total}, results: [{openfda.brand_name, openfda.generic_name, indications_and_usage}]}

FDA_get_mechanism_of_action_by_drug_name

Purpose: FDA mechanism of action Parameters: drug_name (string), limit (integer)

FDA_get_boxed_warning_info_by_drug_name

Purpose: FDA black box warnings Parameters: drug_name (string), limit (integer)

FDA_get_clinical_studies_info_by_drug_name

Purpose: FDA clinical study data Parameters: drug_name (string), limit (integer)

drugbank_get_drug_basic_info_by_drug_name_or_id

Purpose: Drug info from DrugBank Parameters (ALL REQUIRED):

• query (string): Drug name or DrugBank ID
• case_sensitive (boolean): Use False
• exact_match (boolean): Use False
• limit (integer): e.g., 3

Response: {query, total_matches, total_returned_results, results: [{drug_name, drugbank_id, description, ...}]}

drugbank_get_pharmacology_by_drug_name_or_drugbank_id

Purpose: Pharmacology details Parameters (ALL REQUIRED): query, case_sensitive, exact_match, limit

drugbank_get_targets_by_drug_name_or_drugbank_id

Purpose: Drug targets Parameters (ALL REQUIRED): query, case_sensitive, exact_match, limit

ChEMBL_get_drug_mechanisms

Purpose: Drug mechanisms from ChEMBL Parameters: drug_chembl_id__exact (string, REQUIRED), limit, offset

ChEMBL_search_drugs

Purpose: Search drugs Parameters: pref_name__contains (string), max_phase (integer), limit

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Clinical Trial Tools

search_clinical_trials

Purpose: Search ClinicalTrials.gov Parameters:

• query_term (string, REQUIRED): Search query
• condition (string): Disease/condition
• intervention (string): Drug/intervention
• pageSize (integer): Max results (default 10, max 1000)

Response: {studies: [{NCT ID, brief_title, brief_summary, overall_status, condition, phase}], nextPageToken, total_count}

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Literature & Pathway Tools

PubMed_search_articles

Purpose: Search PubMed literature Parameters:

• query (string, REQUIRED): PubMed search query
• limit (integer, default=10, max 200)
• include_abstract (boolean, default=False)

Response: Returns a plain list of article dicts (NOT wrapped in {articles: [...]}):

# [{pmid, title, authors, journal, pub_date, pub_year, doi, pmcid, article_type, url, abstract, ...}]

Reactome_map_uniprot_to_pathways

Purpose: Map protein to biological pathways Parameters: id (string, REQUIRED): UniProt accession (e.g., 'P00533')

GTEx_get_median_gene_expression

Purpose: Tissue expression data Parameters:

• gencode_id (string, REQUIRED): Versioned Ensembl ID (e.g., 'ENSG00000146648.12')
• operation (string): Use 'median'

OpenTargets_target_disease_evidence

Purpose: Evidence for target-disease association Parameters: efoId (string, REQUIRED), ensemblId (string, REQUIRED)

OpenTargets_get_publications_by_target_ensemblID

Purpose: Publications about target Parameters: ensemblId (string, REQUIRED)

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Known CIViC Gene IDs (Common Cancer Genes)

These are pre-verified CIViC gene IDs to bypass the search limitation:

Gene	CIViC Gene ID	Entrez ID
ABL1	4	25
ALK	1	238
BRAF	5	673

Note: For genes not in this table, use civic_search_genes(limit=100) and search results client-side. If gene starts with a letter beyond 'C', it may not be in the first 100 results.