TOOLS_REFERENCE.md

Precision Medicine Stratification - Tools Reference

Tools Used by Phase

Phase 1: Disease Disambiguation & Profile Standardization

Tool	Parameters	Response	Purpose
OpenTargets_get_disease_id_description_by_name	diseaseName	{data: {search: {hits: [{id, name, description}]}}}	Resolve disease to EFO ID
MyGene_query_genes	query (NOT q)	{hits: [{_id, symbol, name, ensembl: {gene}}]}	Resolve gene to Ensembl/Entrez IDs
ensembl_lookup_gene	gene_id, species='homo_sapiens'	{data: {id, display_name, description, biotype}}	Gene details (REQUIRES species)
ols_search_terms	query, ontology	Ontology terms	Disease ontology resolution
OpenTargets_get_disease_ids_by_name	diseaseName	Disease cross-references	ICD-10, MONDO, OMIM mappings

Phase 2: Genetic Risk Assessment

Tool	Parameters	Response	Purpose
clinvar_search_variants	gene, significance, limit	Variant list with clinical significance	Pathogenic variant search
clinvar_get_variant_details	variant_id	Full variant details	Specific variant pathogenicity
clinvar_get_clinical_significance	variant_id	Clinical significance classification	Quick pathogenicity check
EnsemblVEP_annotate_rsid	variant_id (NOT rsid)	VEP annotation with SIFT/PolyPhen	Variant impact prediction
EnsemblVEP_annotate_hgvs	hgvs_notation, species	VEP annotation	HGVS variant annotation
OpenTargets_target_disease_evidence	ensemblId, efoId, size	Evidence items with scores	Gene-disease evidence strength
gwas_get_associations_for_trait	trait	GWAS associations	Disease-SNP associations
gwas_search_associations	query	GWAS associations	Broad GWAS search
GWAS_search_associations_by_gene	gene_name	Gene-trait associations	Gene-specific GWAS hits
gwas_get_snps_for_gene	gene	Associated SNPs	Gene GWAS variants
OpenTargets_search_gwas_studies_by_disease	diseaseIds (array), size	{data: {studies: {count, rows}}}	Disease GWAS studies
gnomad_get_variant	variant_id	Allele frequencies	Population frequency
gnomad_get_gene_constraints	gene_symbol	pLI, LOEUF scores	Gene constraint/intolerance

Phase 3: Disease-Specific Stratification

Cancer Tools

Tool	Parameters	Response	Purpose
cBioPortal_get_mutations	study_id, gene_list (STRING)	{status, data: [...]}	Somatic mutation landscape
HPA_get_cancer_prognostics_by_gene	gene_name	Prognostic data	Cancer prognosis markers
fda_pharmacogenomic_biomarkers	drug_name, biomarker, limit	{count, shown, results}	TMB-H, MSI-H FDA approvals
civic_search_variants	name, gene_name	{data: {variants: {nodes}}}	Variant clinical significance
civic_search_evidence_items	therapy_name, disease_name	{data: {evidenceItems: {nodes}}}	Biomarker-drug evidence

Metabolic/CVD Tools

Tool	Parameters	Response	Purpose
OpenTargets_get_associated_targets_by_disease_efoId	efoId, size	Target associations	Disease genetic architecture

Rare Disease Tools

Tool	Parameters	Response	Purpose
UniProt_get_disease_variants_by_accession	accession	Disease variants	Known pathogenic variants
UniProt_get_function_by_accession	accession	List of strings	Protein function

Phase 4: Pharmacogenomic Profiling

Tool	Parameters	Response	Purpose
PharmGKB_get_clinical_annotations	query	Clinical annotations	Drug-gene-phenotype PGx
PharmGKB_get_dosing_guidelines	query	Dosing guidelines	CPIC dosing recommendations
PharmGKB_search_variants	query	Variant PGx data	PGx variant annotations
PharmGKB_get_gene_details	query	Gene PGx details	PGx gene information
PharmGKB_get_drug_details	query	Drug PGx details	Drug PGx profile
fda_pharmacogenomic_biomarkers	drug_name, biomarker, limit	{count, shown, results}	FDA PGx biomarker labels
FDA_get_pharmacogenomics_info_by_drug_name	drug_name, limit	{meta, results}	FDA PGx label text
OpenTargets_drug_pharmacogenomics_data	chemblId	PGx data	OpenTargets PGx

Phase 5: Comorbidity & Drug Interaction Risk

Tool	Parameters	Response	Purpose
drugbank_get_drug_interactions_by_drug_name_or_id	query, case_sensitive, exact_match, limit	DDI data	Drug-drug interactions
FDA_get_drug_interactions_by_drug_name	drug_name, limit	{meta, results}	FDA DDI info
FDA_get_contraindications_by_drug_name	drug_name, limit	{meta, results}	Contraindications
PubMed_search_articles	query, max_results	List of dicts	Comorbidity literature

Phase 6: Molecular Pathway Analysis

Tool	Parameters	Response	Purpose
enrichr_gene_enrichment_analysis	gene_list (array), libs (array, REQUIRED)	Enrichment results	Pathway enrichment
ReactomeAnalysis_pathway_enrichment	identifiers (space-separated string)	{data: {pathways: [...]}}	Reactome enrichment
Reactome_map_uniprot_to_pathways	id (UniProt accession)	List of pathways	Gene-to-pathway mapping
STRING_get_interaction_partners	protein_ids (array), species (9606), limit	Interactions	PPI network
STRING_functional_enrichment	protein_ids (array), species (9606)	Functional enrichment	Network biology
OpenTargets_get_target_tractability_by_ensemblID	ensemblId	Tractability scores	Druggability assessment

Phase 7: Clinical Evidence & Guidelines

Tool	Parameters	Response	Purpose
PubMed_Guidelines_Search	query, max_results	List of guideline articles	Clinical guidelines
PubMed_search_articles	query, max_results	List of dicts	Literature evidence
OpenTargets_get_associated_drugs_by_disease_efoId	efoId, size	{data: {disease: {knownDrugs: {count, rows}}}}	Disease drug landscape
FDA_get_indications_by_drug_name	drug_name, limit	{meta, results}	FDA-approved indications
FDA_get_mechanism_of_action_by_drug_name	drug_name, limit	{meta, results}	Drug mechanism
FDA_get_clinical_studies_info_by_drug_name	drug_name, limit	{meta, results}	Clinical study data
OpenTargets_get_drug_mechanisms_of_action_by_chemblId	chemblId	{data: {drug: {mechanismsOfAction: {rows}}}}	Drug MOA
drugbank_get_drug_basic_info_by_drug_name_or_id	query, case_sensitive, exact_match, limit	Drug info	Drug details
drugbank_get_pharmacology_by_drug_name_or_drugbank_id	query, case_sensitive, exact_match, limit	Pharmacology	Drug pharmacology
civic_search_assertions	therapy_name, disease_name	{data: {assertions: {nodes}}}	Clinical assertions

Phase 8: Clinical Trial Matching

Tool	Parameters	Response	Purpose
clinical_trials_search	action='search_studies', condition, intervention, limit	{total_count, studies}	Trial search
search_clinical_trials	query_term (REQUIRED), condition, intervention, pageSize	{studies, total_count}	Alternative trial search
clinical_trials_get_details	action='get_study_details', nct_id	Full study	Trial details
get_clinical_trial_eligibility_criteria	nct_ids (array), eligibility_criteria='all'	Eligibility criteria	Biomarker eligibility

Total Tool Count

Phase	Tools	Category
Phase 1: Disease Disambiguation	5	OpenTargets, MyGene, Ensembl, OLS
Phase 2: Genetic Risk	13	ClinVar, VEP, GWAS, gnomAD, OpenTargets
Phase 3: Disease Stratification	5-8	cBioPortal, HPA, FDA, CIViC, UniProt
Phase 4: Pharmacogenomics	8	PharmGKB, FDA PGx, OpenTargets
Phase 5: Comorbidity/DDI	4	DrugBank, FDA, PubMed
Phase 6: Pathways	6	Enrichr, Reactome, STRING, OpenTargets
Phase 7: Evidence/Guidelines	10	PubMed, OpenTargets, FDA, DrugBank, CIViC
Phase 8: Clinical Trials	4	ClinicalTrials.gov
Total unique tools	~55	13 databases