drug-discovery-prompts/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-clinical-trial-matching/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
Clinical Trial Matching - Tools Reference		import	https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-clinical-trial-matching/TOOLS_REFERENCE.md	e2520a96	2026-06-26	prompt	accepted	upstream	false

Clinical Trial Matching - Tools Reference

Summary

This skill uses 40+ ToolUniverse tools across 10 categories to perform comprehensive clinical trial matching.

Tool Inventory

Clinical Trial Tools (13 total, 11 primary)

Tool	Purpose	Key Parameters	Response
search_clinical_trials	Main trial search	query_term (REQ), condition, intervention, pageSize	{studies, nextPageToken, total_count}
ClinicalTrials_search_studies	Alternative search	action="search_studies" (REQ), condition, intervention, limit	{total_count, studies}
ClinicalTrials_get_study	Full trial details	action="get_study_details" (REQ), nct_id (REQ)	Full study object
get_clinical_trial_eligibility_criteria	Eligibility text	nct_ids (REQ array), eligibility_criteria (REQ)	[{NCT ID, eligibility_criteria}]
get_clinical_trial_locations	Site locations	nct_ids (REQ array), location (REQ)	[{NCT ID, locations}]
get_clinical_trial_descriptions	Title/summary	nct_ids (REQ array), description_type (REQ)	[{NCT ID, brief_title, ...}]
get_clinical_trial_status_and_dates	Status/dates	nct_ids (REQ array), status_and_date (REQ)	[{NCT ID, overall_status, dates}]
get_clinical_trial_conditions_and_interventions	Interventions	nct_ids (REQ array), condition_and_intervention (REQ)	[{NCT ID, condition, arm_groups, interventions}]
get_clinical_trial_outcome_measures	Outcomes	nct_ids (REQ array), outcome_measures	[{NCT ID, outcomes}]
extract_clinical_trial_outcomes	Result data	nct_ids (REQ array)	Outcome result data
extract_clinical_trial_adverse_events	AE data	nct_ids (REQ array)	Adverse event data

OpenTargets Tools (10 primary)

Tool	Purpose	Key Parameters
OpenTargets_get_disease_id_description_by_name	Resolve disease	diseaseName
OpenTargets_get_target_id_description_by_name	Resolve target	targetName
OpenTargets_get_drug_id_description_by_name	Resolve drug	drugName
OpenTargets_get_drug_mechanisms_of_action_by_chemblId	Drug MoA	chemblId
OpenTargets_get_associated_drugs_by_target_ensemblID	Drugs for target	ensemblId, size
OpenTargets_get_associated_drugs_by_disease_efoId	Drugs for disease	efoId, size
OpenTargets_get_approved_indications_by_drug_chemblId	Approved indications	chemblId
OpenTargets_get_drug_approval_status_by_chemblId	Approval status	chemblId
OpenTargets_target_disease_evidence	Target-disease evidence	ensemblId, efoId, size
OpenTargets_get_drug_description_by_chemblId	Drug description	chemblId

CIViC Tools (6 primary)

Tool	Purpose	Key Parameters
civic_get_variants_by_gene	Gene variants	gene_id (CIViC int), limit
civic_get_variant	Variant details	variant_id
civic_search_evidence_items	Evidence search	query, limit
civic_search_therapies	Therapy search	query, limit
civic_search_diseases	Disease search	query, limit
civic_get_molecular_profile	Molecular profile	molecular_profile_id

FDA Tools (5 primary)

Tool	Purpose	Key Parameters
fda_pharmacogenomic_biomarkers	Biomarker-drug list	(none)
FDA_get_indications_by_drug_name	Drug indications	drug_name, limit
FDA_get_mechanism_of_action_by_drug_name	Drug MoA	drug_name, limit
FDA_get_clinical_studies_info_by_drug_name	Clinical studies	drug_name, limit
FDA_get_adverse_reactions_by_drug_name	Drug safety	drug_name, limit

Gene/Disease Resolution Tools (4 primary)

Tool	Purpose	Key Parameters
MyGene_query_genes	Gene ID resolution	query, species
ols_search_efo_terms	Disease ontology	query, limit
ols_get_efo_term	Term details	term_id
ols_get_efo_term_children	Sub-diseases	term_id

Drug Information Tools (4 primary)

Tool	Purpose	Key Parameters
drugbank_get_targets_by_drug_name_or_drugbank_id	Drug targets	query, case_sensitive, exact_match, limit (ALL REQ)
drugbank_get_indications_by_drug_name_or_drugbank_id	Drug indications	query, case_sensitive, exact_match, limit (ALL REQ)
ChEMBL_search_drugs	Drug search	query, limit
ChEMBL_get_drug_mechanisms	Drug mechanisms	drug_chembl_id__exact

Literature Tools (2 primary)

Tool	Purpose	Key Parameters
PubMed_search_articles	Literature search	query, max_results
openalex_literature_search	Literature search	query, limit

PharmGKB Tools (2 primary)

Tool	Purpose	Key Parameters
PharmGKB_search_genes	Gene pharmacogenomics	query
PharmGKB_get_clinical_annotations	Clinical annotations	query

Critical Parameter Notes

1. DrugBank tools: ALL 4 parameters (query, case_sensitive, exact_match, limit) are REQUIRED
2. search_clinical_trials: query_term is REQUIRED even for disease-only searches
3. ClinicalTrials_search_studies: action must be exactly "search_studies"
4. ClinicalTrials_get_study: action must be exactly "get_study_details"
5. CIViC civic_search_variants: Does NOT filter by query - returns alphabetically
6. CIViC civic_get_variants_by_gene: Takes CIViC gene ID (integer), NOT gene symbol
7. OpenTargets drug lookup: Use drugName (NOT genericName)
8. Batch clinical trial tools: Accept arrays of NCT IDs
9. fda_pharmacogenomic_biomarkers: Takes no parameters

Response Structure Cheat Sheet

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

ClinicalTrials_search_studies:
  {total_count, studies: [{nctId, title, status, conditions: []}]}

get_clinical_trial_eligibility_criteria:
  [{NCT ID, eligibility_criteria: "Inclusion Criteria:\n...\nExclusion Criteria:\n..."}]

get_clinical_trial_locations:
  [{NCT ID, locations: [{facility, city, state, country}]}]

get_clinical_trial_conditions_and_interventions:
  [{NCT ID, condition: [], arm_groups: [{label, type, description, interventionNames}], interventions: [{type, name, description}]}]

get_clinical_trial_status_and_dates:
  [{NCT ID, overall_status, start_date, primary_completion_date, completion_date}]

OpenTargets_get_drug_mechanisms_of_action_by_chemblId:
  {data: {drug: {id, name, mechanismsOfAction: {rows: [{mechanismOfAction, actionType, targetName, targets: [{id, approvedSymbol}]}]}}}}

OpenTargets_get_associated_drugs_by_target_ensemblID:
  {data: {target: {id, approvedSymbol, knownDrugs: {count, rows: [{drug: {id, name, isApproved}, phase, mechanismOfAction, disease: {id, name}}]}}}}

fda_pharmacogenomic_biomarkers:
  {count, shown, results: [{Drug, TherapeuticArea, Biomarker, LabelingSection}]}

MyGene_query_genes:
  {hits: [{symbol, entrezgene, ensembl: {gene}, name}]}

PubMed_search_articles:
  [{pmid, title, abstract, authors, journal, pub_date}]