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title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Target Intelligence Tool Reference		import	https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-target-research/REFERENCE.md	e2520a96	2026-06-26	prompt	accepted	upstream	false

Target Intelligence Tool Reference

Complete reference of 225+ ToolUniverse tools for target research, organized by category.

1. Core Protein Information (UniProt)

Tool	Parameters	Returns
`UniProt_get_entry_by_accession`	`accession`	Complete protein entry
`UniProt_get_function_by_accession`	`accession`	Functional annotations
`UniProt_get_recommended_name_by_accession`	`accession`	Official protein name
`UniProt_get_alternative_names_by_accession`	`accession`	Aliases and synonyms
`UniProt_get_organism_by_accession`	`accession`	Species info
`UniProt_get_subcellular_location_by_accession`	`accession`	Cellular localization
`UniProt_get_disease_variants_by_accession`	`accession`	Disease variants
`UniProt_get_ptm_processing_by_accession`	`accession`	PTMs, active sites
`UniProt_get_sequence_by_accession`	`accession`	Amino acid sequence
`UniProt_get_isoform_ids_by_accession`	`accession`	Splice isoforms
`UniProt_search`	`query`, `organism`, `limit`, `fields`	Search results
`UniProt_id_mapping`	`ids`, `from_db`, `to_db`	ID mappings
`UniProt_get_proteome`	`proteome_id`	Proteome info
`UniProt_get_uniref_cluster`	`cluster_id`	UniRef cluster
`UniProt_search_uniref`	`query`, `cluster_type`, `limit`	UniRef search
`UniProt_get_uniparc_entry`	`upi`	UniParc entry
`UniProt_search_uniparc`	`query`, `limit`	UniParc search

EBI Proteins API

Tool	Parameters	Returns
`proteins_api_get_protein`	`accession`, `format`	Comprehensive protein info
`proteins_api_get_features`	`accession`	Protein features
`proteins_api_get_variants`	`accession`	Protein variants
`proteins_api_get_comments`	`accession`	Annotations/comments
`proteins_api_get_epitopes`	`accession`	Epitope data
`proteins_api_get_proteomics`	`accession`	Proteomics data
`proteins_api_get_xrefs`	`accession`	Cross-references
`proteins_api_get_publications`	`accession`	Related publications
`proteins_api_get_genome_mappings`	`accession`	Genome mappings
`proteins_api_search`	`query`	Search proteins

2. Gene Information

MyGene (BioThings)

Tool	Parameters	Returns
`MyGene_get_gene_annotation`	`gene_id`, `fields`	Detailed gene annotation
`MyGene_query_genes`	`query`, `species`, `fields`, `size`	Gene search
`MyGene_batch_query`	`gene_ids`, `species`, `fields`	Batch gene query

Ensembl

Tool	Parameters	Returns
`ensembl_lookup_gene`	`gene_id`, `species`	Gene lookup
`ensembl_get_sequence`	`id`, `type`, `species`	DNA/protein sequence
`ensembl_get_variants`	`region`, `species`	Variants in region
`ensembl_get_variation`	`id`, `species`	Variation details
`ensembl_get_variation_phenotypes`	`id`, `species`	Phenotype associations
`ensembl_get_xrefs`	`id`, `external_db`	Cross-references
`ensembl_get_xrefs_by_name`	`name`, `species`	Xrefs by gene name
`ensembl_get_regulatory_features`	`region`, `species`	Regulatory features
`ensembl_get_genetree`	`id`, `prune_species`	Gene tree
`ensembl_get_homology`	`species`, `symbol`, `target_species`	Orthologs/paralogs
`ensembl_get_alignment`	`species`, `region`	Genomic alignments
`ensembl_get_taxonomy`	`id`	Taxonomy info
`ensembl_vep_region`	`species`, `region`, `allele`	Variant effect prediction

Other Gene Resources

Tool	Parameters	Returns
`kegg_get_gene_info`	`gene_id`	KEGG gene info
`kegg_find_genes`	`keyword`, `organism`	KEGG gene search
`cBioPortal_get_genes`	`keyword`	Cancer gene search
`civic_search_genes`	`gene_symbol`	CIViC gene info
`gnomad_get_gene`	`gene_symbol`	gnomAD gene data
`gnomad_search_variants`	`query`	gnomAD gene search
`gnomad_get_gene_constraints`	`gene_symbol`	Constraint scores

3. Drug-Target Interactions

DGIdb

Tool	Parameters	Returns
`DGIdb_get_drug_gene_interactions`	`genes`, `interaction_sources`, `interaction_types`	Drug-gene interactions
`DGIdb_get_gene_druggability`	`genes`	Druggability categories
`DGIdb_get_gene_info`	`genes`	Gene info from DGIdb
`DGIdb_get_drug_info`	`drugs`	Drug info from DGIdb

ChEMBL

Tool	Parameters	Returns
`ChEMBL_get_target`	`target_chembl_id`, `format`	Target details
`ChEMBL_search_targets`	`pref_name__contains`, `organism`, `target_type`, `limit`	Target search
`ChEMBL_get_target_activities`	`target_chembl_id__exact`, `limit`	Bioactivity data
`ChEMBL_get_target_assays`	`target_chembl_id__exact`, `limit`	Target assays
`ChEMBL_get_molecule_targets`	`molecule_chembl_id__exact`, `limit`	Molecule targets
`ChEMBL_search_binding_sites`	`target_chembl_id`	Binding sites
`ChEMBL_search_mechanisms`	`molecule_chembl_id`, `target_chembl_id`	Mechanisms of action
`ChEMBL_get_molecule`	`chembl_id`, `format`	Molecule details
`ChEMBL_search_molecules`	`pref_name__contains`, `limit`	Molecule search
`ChEMBL_get_assay`	`assay_chembl_id`	Assay details
`ChEMBL_search_activities`	`molecule_chembl_id`, `target_chembl_id`, `standard_type`	Activity search

DrugBank & GtoPdb

Tool	Parameters	Returns
`drugbank_get_targets_by_drug_name_or_drugbank_id`	`query`, `exact_match`, `limit`	Drug targets
`drugbank_get_drug_name_and_description_by_target_name`	`target_name`	Drugs for target
`GtoPdb_search_targets`	`target_id`	GtoPdb target info
`GtoPdb_search_targets`	`family_id`	List targets
`GtoPdb_search_ligands`	`target_id`	Target-ligand interactions
`GtoPdb_get_interactions`	`query`	Interaction search

STITCH

Tool	Parameters	Returns
`STITCH_get_chemical_protein_interactions`	`identifiers`, `species`, `required_score`, `limit`	Chemical-protein links
`STITCH_get_interaction_partners`	`identifiers`, `species`	Interaction network
`STITCH_resolve_identifier`	`identifier`, `species`	ID resolution

GPCRdb (NEW - for GPCR Targets)

~35% of approved drugs target GPCRs. GPCRdb provides specialized data for G protein-coupled receptors.

Tool	Parameters	Returns
`GPCRdb_get_protein`	`operation="get_protein"`, `protein` (entry name)	GPCR family, class, sequence info
`GPCRdb_list_proteins`	`operation="list_proteins"`, `family` (optional)	List GPCR families/proteins
`GPCRdb_get_structures`	`operation="get_structures"`, `protein`, `state` (optional)	Structures with receptor state (active/inactive)
`GPCRdb_get_ligands`	`operation="get_ligands"`, `protein`	Known ligands (agonists/antagonists)
`GPCRdb_get_mutations`	`operation="get_mutations"`, `protein`	Mutation effects on binding/signaling

Entry name format: {gene_lower}_human (e.g., adrb2_human, drd2_human)

Key advantages:

Active vs. inactive state structures
Ballesteros-Weinstein residue numbering
Curated ligand binding data
Experimental mutation effects

Pharos/TCRD (NEW - Target Development Level)

NIH's Illuminating the Druggable Genome (IDG) portal provides TDL classification.

Tool	Parameters	Returns
`Pharos_get_target`	`gene` OR `uniprot`	TDL, family, novelty, description
`Pharos_search_targets`	`query`, `top`	Target list with TDL
`Pharos_get_tdl_summary`	-	TDL level descriptions
`Pharos_get_disease_targets`	`disease`, `top`	Targets for disease with TDL

TDL Classification:

Level	Description	Druggability
Tclin	Approved drug targets	Highest
Tchem	Small molecule activities (IC50 < 30nM)	Good
Tbio	Biological annotations only	Moderate
Tdark	Understudied proteins	Unknown

Example:

result = tu.tools.Pharos_get_target(gene="EGFR")
# Returns: tdl="Tclin", fam="Kinase", novelty=0.2, publicationCount=45000

DepMap (NEW - Target Essentiality)

CRISPR knockout essentiality data from cancer cell lines.

Tool	Parameters	Returns
`DepMap_get_gene_dependencies`	`gene_symbol`	Gene essentiality data
`DepMap_get_cell_lines`	`tissue`, `cancer_type`, `page_size`	Cell line metadata
`DepMap_search_cell_lines`	`query`	Search cell lines
`DepMap_get_cell_line`	`model_id` OR `model_name`	Detailed cell line info
Drug sensitivity (GDSC)	`drug` / `cell-line` / `target`	No TU tool — run the precision-oncology skill's `scripts/gdsc_drug_response.py` (GDSC bulk data, IC50/AUC)

Effect Score Interpretation:

Score	Meaning
< -1.0	Strongly essential
-0.5 to -1.0	Essential
-0.5 to 0	Weakly essential
> 0	Not essential

Example:

deps = tu.tools.DepMap_get_gene_dependencies(gene_symbol="KRAS")
# Returns: Gene info, note about essentiality

cells = tu.tools.DepMap_get_cell_lines(cancer_type="Lung Cancer", page_size=10)
# Returns: Cell line names, cancer types, MSI status

InterProScan (NEW - Domain Prediction)

De novo domain/family prediction for novel sequences.

Tool	Parameters	Returns
`InterProScan_scan_sequence`	`sequence`, `go_terms`, `pathways`	Domains, GO terms, pathways
`InterProScan_get_job_status`	`job_id`	Job status
`InterProScan_get_job_results`	`job_id`	Completed results

When to use: Novel proteins, Tdark targets, custom sequences.

Example:

# Submit sequence for analysis
result = tu.tools.InterProScan_scan_sequence(
    sequence="MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH...",
    go_terms=True,
    pathways=True
)
# Returns: job_id (if running) or domains/GO/pathways (if complete)

# Check job if still running
status = tu.tools.InterProScan_get_job_status(job_id="iprscan5-xxx")
results = tu.tools.InterProScan_get_job_results(job_id="iprscan5-xxx")

BindingDB (NEW - Ligand Binding Data)

Experimental binding affinity data (Ki, IC50, Kd) for target-ligand pairs.

Tool	Parameters	Returns
`BindingDB_get_ligands_by_uniprot`	`uniprot`, `affinity_cutoff`	Ligands with affinities
`BindingDB_get_ligands_by_uniprots`	`uniprots`, `affinity_cutoff`	Multi-target ligands
`BindingDB_get_ligands_by_pdb`	`pdb_ids`, `affinity_cutoff`, `sequence_identity`	Structure-based ligands
`BindingDB_get_targets_by_compound`	`smiles`, `similarity_cutoff`	Polypharmacology

Example:

# Get ligands for EGFR
ligands = tu.tools.BindingDB_get_ligands_by_uniprot(
    uniprot="P00533",
    affinity_cutoff=100  # Only potent ligands <100 nM
)
# Returns: SMILES, affinity_type (Ki/IC50/Kd), affinity value, PMID

# Find targets for a compound
targets = tu.tools.BindingDB_get_targets_by_compound(
    smiles="CC(=O)Nc1ccc(cc1)O",
    similarity_cutoff=0.85
)
# Returns: proteins with similar compound activities

Affinity Interpretation:

Range	Level	Drug Potential
<1 nM	Ultra-potent	Clinical candidate
1-30 nM	Tchem threshold	Drug-like
30-100 nM	Potent	Good start
100-1000 nM	Moderate	Needs optimization

Human Protein Atlas (NEW - Expression)

Protein and RNA expression across tissues and cell lines.

Tool	Parameters	Returns
`HPA_search_genes_by_query`	`search_query`	Gene info, Ensembl ID
`HPA_generic_search`	`search_query`, `columns`	Custom data fields
`HPA_get_comparative_expression_by_gene_and_cellline`	`gene_name`, `cell_line`	Cancer vs normal

Example:

# Search gene
gene = tu.tools.HPA_search_genes_by_query(search_query="EGFR")
# Returns: Gene name, Ensembl ID, synonyms

# Compare cancer cell line vs normal tissue
expr = tu.tools.HPA_get_comparative_expression_by_gene_and_cellline(
    gene_name="EGFR",
    cell_line="a549"  # Lung cancer
)
# Returns: expression comparison

Supported Cell Lines: a549, mcf7, hela, hepg2, pc3, jurkat, rh30, siha, u251, ishikawa

PubChem BioAssay (NEW - Screening Data)

HTS screening data and dose-response curves.

Tool	Parameters	Returns
`PubChem_search_assays_by_target_gene`	`gene_symbol`	AIDs for gene
`PubChem_get_assay_summary`	`aid`	Assay statistics
`PubChem_get_assay_targets`	`aid`	Target info
`PubChem_get_assay_active_compounds`	`aid`	Active CIDs
`PubChem_get_assay_dose_response`	`aid`	IC50/EC50 data

Example:

# Find assays for target
assays = tu.tools.PubChem_search_assays_by_target_gene(gene_symbol="EGFR")
# Returns: list of AIDs

# Get assay summary
summary = tu.tools.PubChem_get_assay_summary(aid=504526)
# Returns: active/inactive counts, target info

# Get active compounds
actives = tu.tools.PubChem_get_assay_active_compounds(aid=504526)
# Returns: CIDs of active compounds

4. Open Targets Platform

Target-Centric

Tool	Parameters	Returns
`OpenTargets_get_target_id_description_by_name`	`targetName`	Target ID lookup
`OpenTargets_get_associated_drugs_by_target_ensemblID`	`ensemblID`	Drugs for target
`OpenTargets_get_diseases_phenotypes_by_target_ensembl`	`ensemblID`	Diseases for target
`OpenTargets_get_target_safety_profile_by_ensemblID`	`ensemblID`	Safety info
`OpenTargets_get_target_tractability_by_ensemblID`	`ensemblID`	Tractability
`OpenTargets_get_target_interactions_by_ensemblID`	`ensemblID`	PPI via Open Targets
`OpenTargets_get_target_gene_ontology_by_ensemblID`	`ensemblID`	GO terms
`OpenTargets_get_target_synonyms_by_ensemblID`	`ensemblID`	Target synonyms
`OpenTargets_get_target_classes_by_ensemblID`	`ensemblID`	Classifications
`OpenTargets_get_target_constraint_info_by_ensemblID`	`ensemblID`	Constraint data
`OpenTargets_get_target_genomic_location_by_ensemblID`	`ensemblID`	Genomic location
`OpenTargets_get_target_subcell_locations_by_ensembl_ID`	`ensemblID`	Subcellular location
`OpenTargets_get_target_homologues_by_ensemblID`	`ensemblID`	Homologs
`OpenTargets_get_target_enabling_packages_by_ensemblID`	`ensemblID`	TEP info
`OpenTargets_get_chemical_probes_by_target_ensemblID`	`ensemblID`	Chemical probes
`OpenTargets_get_biological_mouse_models_by_ensemblID`	`ensemblID`	Mouse models
`OpenTargets_get_publications_by_target_ensemblID`	`ensemblID`	Publications
`OpenTargets_get_similar_entities_by_target_ensemblID`	`ensemblID`	Similar targets

Disease-Target Evidence

Tool	Parameters	Returns
`OpenTargets_get_associated_targets_by_disease_efoId`	`efoId`	Targets for disease
`OpenTargets_target_disease_evidence`	`ensemblID`, `efoId`	Evidence details
`disease_target_score`	`efoId`, `datasourceId`	Disease-target scores

5. Protein Structure

RCSB PDB

Tool	Parameters	Returns
`get_protein_metadata_by_pdb_id`	`pdb_id`	Basic metadata
`get_protein_classification_by_pdb_id`	`pdb_id`	Protein classification
`get_sequence_by_pdb_id`	`pdb_id`	PDB sequence
`get_binding_affinity_by_pdb_id`	`pdb_id`	Binding affinity data
`get_target_cofactor_info`	`pdb_id`	Cofactor info
`get_polymer_entity_annotations`	`entity_id`	Polymer annotations
`get_uniprot_accession_by_entity_id`	`entity_id`	UniProt from PDB
`get_gene_name_by_entity_id`	`entity_id`	Gene name from PDB
`PDB_search_similar_structures`	`pdb_id`	Similar structures
`get_polymer_entity_ids_by_pdb_id`	`pdb_id`	Polymer entity IDs
`get_source_organism_by_pdb_id`	`pdb_id`	Source organism
`get_citation_info_by_pdb_id`	`pdb_id`	Citation info
`get_mutation_annotations_by_pdb_id`	`pdb_id`	Mutation annotations
`get_assembly_info_by_pdb_id`	`pdb_id`	Biological assembly
`get_taxonomy_by_pdb_id`	`pdb_id`	Taxonomy
`get_crystallographic_properties_by_pdb_id`	`pdb_id`	Crystal properties
`get_structure_validation_metrics_by_pdb_id`	`pdb_id`	Validation metrics
`get_ligand_smiles_by_chem_comp_id`	`chem_comp_id`	Ligand SMILES
`visualize_protein_structure_3d`	`pdb_id`	3D visualization

PDBe

Tool	Parameters	Returns
`pdbe_get_entry_summary`	`pdb_id`	Entry summary
`pdbe_get_entry_quality`	`pdb_id`	Quality metrics
`pdbe_get_entry_publications`	`pdb_id`	Publications
`pdbe_get_entry_assemblies`	`pdb_id`	Biological assemblies
`pdbe_get_entry_secondary_structure`	`pdb_id`	Secondary structure
`pdbe_get_entry_molecules`	`pdb_id`	Molecule info
`pdbe_get_entry_status`	`pdb_id`	Entry status
`pdbe_get_entry_experiment`	`pdb_id`	Experimental details

AlphaFold

Tool	Parameters	Returns
`alphafold_get_prediction`	`qualifier` (UniProt)	Full 3D predictions
`alphafold_get_summary`	`qualifier`	Summary/metadata
`alphafold_get_annotations`	`qualifier`	Annotations

EMDB

Tool	Parameters	Returns
`EMDB_search_structures`	`query`	EM structure search
`EMDB_get_structure`	`emdb_id`	EM structure details

6. Protein-Protein Interactions

STRING

Tool	Parameters	Returns
`STRING_get_protein_interactions`	`protein_ids`, `species`, `confidence_score`, `network_type`, `limit`	PPI network

IntAct

Tool	Parameters	Returns
`intact_get_interactions`	`identifier`, `format`	Interactions
`intact_search_interactions`	`query`, `first`, `max`	Interaction search
`intact_get_interactor`	`identifier`, `format`	Interactor details
`intact_get_interaction_network`	`identifier`, `depth`	Interaction network
`intact_get_interaction_details`	`interaction_id`	Interaction details
`intact_get_interactions_by_organism`	`taxid`, `size`	Organism interactions
`intact_get_interactions_by_complex`	`complex_id`	Complex interactions
`intact_get_complex_details`	`complex_ac`	Complex details

Other PPI Sources

Tool	Parameters	Returns
`BioGRID_get_interactions`	`gene_names`, `organism`, `interaction_type`, `limit`	BioGRID PPI
`HPA_get_protein_interactions_by_gene`	`gene_symbol`	HPA interactions
`humanbase_ppi_analysis`	`genes`, `tissue`	HumanBase PPI
`Reactome_get_interactor`	`id`	Reactome interactors
`pc_get_interactions`	`source`, `target`	Pathway Commons

7. Functional Annotations

Gene Ontology

Tool	Parameters	Returns
`GO_get_annotations_for_gene`	`gene_id`	GO annotations
`GO_get_genes_for_term`	`go_id`, `taxon`, `rows`	Genes for GO term
`GO_search_terms`	`query`	GO term search
`GO_get_term_details`	`id`	GO term details
`GO_get_term_by_id`	`id`	GO term info
`OpenTargets_get_gene_ontology_terms_by_goID`	`goId`	GO term via OT

InterPro & Pfam

Tool	Parameters	Returns
`InterPro_get_protein_domains`	`protein_id`	Domain annotations
`InterPro_search_domains`	`query`, `page_size`	Domain search
`InterPro_get_domain_details`	`accession`	Domain details

Gene Set Enrichment

Tool	Parameters	Returns
`enrichr_gene_enrichment_analysis`	`genes`, `gene_set_library`	Enrichment analysis

8. Pathways

Reactome

Tool	Parameters	Returns
`Reactome_map_uniprot_to_pathways`	`id` (UniProt)	Pathways for protein
`Reactome_map_uniprot_to_reactions`	`id`	Reactions for protein
`Reactome_get_pathway`	`stId`	Pathway details
`Reactome_get_pathway_reactions`	`stId`	Pathway reactions
`Reactome_get_pathway_hierarchy`	`stId`	Parent pathways
`Reactome_list_top_pathways`	`species`	Top-level pathways
`Reactome_get_participants`	`stId`	Reaction participants
`Reactome_get_reaction`	`stId`	Reaction details
`Reactome_get_complex`	`stId`	Complex details
`Reactome_list_species`	-	All species
`Reactome_query_by_ids`	`ids`, `species`	ID query
`Reactome_get_events_hierarchy`	`species`	Full hierarchy
`Reactome_get_diseases`	-	Disease pathways

KEGG

Tool	Parameters	Returns
`kegg_get_pathway_info`	`pathway_id`	Pathway details
`kegg_search_pathway`	`keyword`, `org`	Pathway search
`kegg_list_organisms`	-	All organisms

WikiPathways

Tool	Parameters	Returns
`WikiPathways_get_pathway`	`wpid`, `format`	Pathway content
`WikiPathways_search`	`query`, `organism`	Pathway search

Pathway Commons

Tool	Parameters	Returns
`pc_search_pathways`	`query`	Pathway search

9. Gene Expression

GTEx

Tool	Parameters	Returns
`GTEx_get_gene_expression`	`gencode_id`, `tissue_site_detail_id`	Expression data
`GTEx_get_median_gene_expression`	`gencode_id`	Median by tissue
`GTEx_get_top_expressed_genes`	`tissue_id`	Top genes in tissue
`GTEx_get_expression_summary`	`gencode_id`	Expression summary
`GTEx_get_eqtl_genes`	`tissue_id`	eQTL genes
`GTEx_get_single_tissue_eqtls`	`gencode_id`, `tissue_id`	Single tissue eQTL
`GTEx_get_multi_tissue_eqtls`	`gencode_id`	Multi-tissue eQTL
`GTEx_calculate_eqtl`	`gencode_id`, `variant_id`	Calculate eQTL

Human Protein Atlas (HPA)

Tool	Parameters	Returns
`HPA_search_genes_by_query`	`search_query`	Gene search
`HPA_get_gene_basic_info_by_ensembl_id`	`ensembl_id`	Basic gene info
`HPA_get_comprehensive_gene_details_by_ensembl_id`	`ensembl_id`	Comprehensive details
`HPA_get_rna_expression_in_specific_tissues`	`ensembl_id`, `tissue`	Tissue RNA expression
`HPA_get_rna_expression_by_source`	`ensembl_id`	Expression by source
`HPA_get_subcellular_location`	`ensembl_id`	Subcellular location
`HPA_get_disease_expression_by_gene_tissue_disease`	`ensembl_id`, `tissue`, `disease`	Disease expression
`HPA_get_cancer_prognostics_by_gene`	`gene_symbol`	Cancer prognostics
`HPA_get_biological_processes_by_gene`	`gene_symbol`	Biological processes

Single-Cell

Tool	Parameters	Returns
`CELLxGENE_get_expression_data`	`gene_id`, `dataset_id`	Single-cell expression
`CELLxGENE_get_gene_metadata`	`gene_id`	Gene metadata

10. Variants & Mutations

ClinVar

Tool	Parameters	Returns
`ClinVar_search_variants`	`gene`, `condition`, `variant_id`, `max_results`	Variant search
`ClinVar_get_variant_details`	`variant_id`	Variant details
`ClinVar_get_clinical_significance`	`variant_id`	Clinical significance

dbSNP

Tool	Parameters	Returns
`dbsnp_get_variant_by_rsid`	`rsid`	dbSNP variant
`dbsnp_search_by_gene`	`gene_symbol`	dbSNP by gene
`dbsnp_get_frequencies`	`rsid`	Allele frequencies

gnomAD

Tool	Parameters	Returns
`gnomad_get_variant`	`variant_id`	gnomAD variant
`gnomad_search_variants`	`query`	Variant search
`gnomad_get_region`	`chrom`, `start`, `stop`	Variants in region

CIViC

Tool	Parameters	Returns
`civic_get_variant`	`variant_id`	CIViC variant
`civic_get_variants_by_gene`	`gene_symbol`	Variants for gene
`civic_search_variants`	`query`	Variant search

Other Variant Sources

Tool	Parameters	Returns
`MyVariant_get_variant_annotation`	`variant_id`	MyVariant annotation
`MyVariant_query_variants`	`query`	Variant query
`PharmGKB_search_variants`	`query`	PharmGKB variants
`cBioPortal_get_mutations`	`gene_symbol`, `study_id`	Cancer mutations
`RegulomeDB_query_variant`	`variant_id`	Regulatory annotation
`gwas_search_snps`	`query`	GWAS SNPs
`gwas_get_snp_by_id`	`snp_id`	GWAS SNP details
`gwas_get_snps_for_gene`	`gene_symbol`	GWAS SNPs for gene

11. Literature

PubMed

Tool	Parameters	Returns
`PubMed_search_articles`	`query`, `limit`, `api_key`	Article search
`PubMed_get_article`	`pmid`, `api_key`	Article metadata
`PubMed_get_related`	`pmid`, `limit`	Related articles
`PubMed_get_cited_by`	`pmid`, `limit`	Citing articles
`PubMed_get_links`	`pmid`	External links

Europe PMC

Tool	Parameters	Returns
`EuropePMC_search_articles`	`query`, `limit`	Article search
`EuropePMC_get_citations`	`source`, `article_id`	Citations
`EuropePMC_get_references`	`source`, `article_id`	References

Other Literature

Tool	Parameters	Returns
`PMC_search_papers`	`query`	PMC full-text search
`PubTator3_LiteratureSearch`	`query`	PubTator with NER
`PubTator3_EntityAutocomplete`	`query`	Entity autocomplete
`openalex_search_works`	`query`	OpenAlex publications
`openalex_literature_search`	`query`	Literature search

12. Pharmacogenomics

PharmGKB

Tool	Parameters	Returns
`PharmGKB_get_gene_details`	`gene_symbol`	Gene info
`PharmGKB_search_genes`	`query`	Gene search
`PharmGKB_get_drug_details`	`drug_name`	Drug details
`PharmGKB_search_drugs`	`query`	Drug search
`PharmGKB_get_clinical_annotations`	`gene_symbol`	Clinical annotations
`PharmGKB_get_dosing_guidelines`	`gene_symbol`	Dosing guidelines
`OpenTargets_drug_pharmacogenomics_data`	`chemblId`	OT pharmacogenomics
`fda_pharmacogenomic_biomarkers`	-	FDA biomarkers

13. Disease Associations

Tool	Parameters	Returns
`OpenTargets_get_disease_ids_by_name`	`diseaseName`	Disease ID lookup
`OpenTargets_get_disease_description_by_efoId`	`efoId`	Disease description
`OpenTargets_get_associated_drugs_by_disease_efoId`	`efoId`	Drugs for disease
`OpenTargets_get_publications_by_disease_efoId`	`efoId`	Disease publications
`OpenTargets_get_disease_therapeutic_areas_by_efoId`	`efoId`	Therapeutic areas
`gwas_search_studies`	`query`	GWAS studies
`gwas_get_studies_for_trait`	`trait`	Studies for trait
`gwas_search_associations`	`query`	GWAS associations
`gwas_get_associations_for_trait`	`trait`	Associations for trait
`GtoPdb_search_diseases`	-	GtoPdb diseases
`GtoPdb_search_diseases`	`disease_id`	Disease details
`Reactome_get_diseases`	-	Reactome diseases
`OSL_get_efo_id_by_disease_name`	`disease_name`	EFO ID lookup

DisGeNET (NEW - Gene-Disease Associations)

DisGeNET integrates gene-disease associations from curated repositories, GWAS catalogs, animal models, and literature. Requires: DISGENET_API_KEY

Tool	Parameters	Returns
`DisGeNET_search_gene`	`operation="search_gene"`, `gene` (symbol/ID), `limit`	Diseases associated with gene
`DisGeNET_search_disease`	`operation="search_disease"`, `disease` (name/UMLS CUI), `limit`	Genes associated with disease
`DisGeNET_get_gda`	`operation="get_gda"`, `gene`, `disease`, `min_score`	Gene-disease association details
`DisGeNET_get_vda`	`operation="get_vda"`, `variant` (rsID), `limit`	Variant-disease associations
`DisGeNET_get_disease_genes`	`operation="get_disease_genes"`, `disease`, `limit`	All genes for a disease

Key metrics:

GDA Score: 0-1 confidence score for gene-disease association
Evidence Index: Number and diversity of sources
Disease Specificity Index: How specific is gene to this disease
Disease Pleiotropy Index: How many diseases gene is linked to

Interpretation:

Score ≥0.7: Strong association (consider T2 evidence)
Score 0.4-0.7: Moderate association
Score <0.4: Weak/limited evidence

14. ID Conversion & Cross-References

Tool	Parameters	Returns
`UniProt_id_mapping`	`ids`, `from_db`, `to_db`	ID conversion
`OpenTargets_map_any_disease_id_to_all_other_ids`	`diseaseId`	Disease ID mapping
`ebi_cross_reference_search`	`identifier`, `source`	EBI cross-refs
`Reactome_query_by_ids`	`ids`	Reactome ID lookup

Common ID Mapping Combinations

From	To	Tool Call
Gene Symbol → UniProt	`UniProt_search(query='gene:EGFR AND organism_id:9606')`
UniProt → Ensembl	`UniProt_id_mapping(ids=['P00533'], from_db='UniProtKB_AC-ID', to_db='Ensembl')`
Ensembl → UniProt	`UniProt_id_mapping(ids=['ENSG00000146648'], from_db='Ensembl', to_db='UniProtKB')`
UniProt → PDB	Extract from UniProt entry cross-references
Gene Symbol → Entrez	`MyGene_query_genes(query='symbol:EGFR', species='human')`
UniProt → ChEMBL Target	`ChEMBL_search_targets(pref_name__contains='EGFR', organism='Homo sapiens')`

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Target Intelligence Tool Reference

1. Core Protein Information (UniProt)

EBI Proteins API

2. Gene Information

MyGene (BioThings)

Ensembl

Other Gene Resources

3. Drug-Target Interactions

DGIdb

ChEMBL

DrugBank & GtoPdb

STITCH

GPCRdb (NEW - for GPCR Targets)

Pharos/TCRD (NEW - Target Development Level)

DepMap (NEW - Target Essentiality)

InterProScan (NEW - Domain Prediction)

BindingDB (NEW - Ligand Binding Data)

Human Protein Atlas (NEW - Expression)

PubChem BioAssay (NEW - Screening Data)

4. Open Targets Platform

Target-Centric

Disease-Target Evidence

5. Protein Structure

RCSB PDB

PDBe

AlphaFold

EMDB

6. Protein-Protein Interactions

STRING

IntAct

Other PPI Sources

7. Functional Annotations

Gene Ontology

InterPro & Pfam

Gene Set Enrichment

8. Pathways

Reactome

KEGG

WikiPathways

Pathway Commons

9. Gene Expression

GTEx

Human Protein Atlas (HPA)

Single-Cell

10. Variants & Mutations

ClinVar

dbSNP

gnomAD

CIViC

Other Variant Sources

11. Literature

PubMed

Europe PMC

Other Literature

12. Pharmacogenomics

PharmGKB

13. Disease Associations

DisGeNET (NEW - Gene-Disease Associations)

14. ID Conversion & Cross-References

Common ID Mapping Combinations

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