"""Default tool configuration files mapping.
Separated from __init__.py to avoid circular imports.
"""
import os
import json
from pathlib import Path
# Get the current directory where this file is located
current_dir = os.path.dirname(os.path.abspath(__file__))
default_tool_files = {
"special_tools": os.path.join(current_dir, "data", "special_tools.json"),
"tool_finder": os.path.join(current_dir, "data", "finder_tools.json"),
# 'tool_finder_llm': os.path.join(current_dir, 'data', 'tool_finder_llm_config.json'),
"opentarget": os.path.join(current_dir, "data", "opentarget_tools.json"),
"fda_drug_label": os.path.join(current_dir, "data", "fda_drug_labeling_tools.json"),
"monarch": os.path.join(current_dir, "data", "monarch_tools.json"),
"clinical_trials": os.path.join(
current_dir, "data", "clinicaltrials_gov_tools.json"
),
"fda_drug_adverse_event": os.path.join(
current_dir, "data", "fda_drug_adverse_event_tools.json"
),
"fda_drug_adverse_event_detail": os.path.join(
current_dir, "data", "fda_drug_adverse_event_detail_tools.json"
),
"ChEMBL": os.path.join(current_dir, "data", "chembl_tools.json"),
"EuropePMC": os.path.join(current_dir, "data", "europe_pmc_tools.json"),
"semantic_scholar": os.path.join(
current_dir, "data", "semantic_scholar_tools.json"
),
"pubtator": os.path.join(current_dir, "data", "pubtator_tools.json"),
"EFO": os.path.join(current_dir, "data", "efo_tools.json"),
"Enrichr": os.path.join(current_dir, "data", "enrichr_tools.json"),
"HumanBase": os.path.join(current_dir, "data", "humanbase_tools.json"),
"OpenAlex": os.path.join(current_dir, "data", "openalex_tools.json"),
# Literature search tools
"literature_search": os.path.join(
current_dir, "data", "literature_search_tools.json"
),
"arxiv": os.path.join(current_dir, "data", "arxiv_tools.json"),
"crossref": os.path.join(current_dir, "data", "crossref_tools.json"),
"simbad": os.path.join(current_dir, "data", "simbad_tools.json"),
"dblp": os.path.join(current_dir, "data", "dblp_tools.json"),
"pubmed": os.path.join(current_dir, "data", "pubmed_tools.json"),
"ncbi_nucleotide": os.path.join(current_dir, "data", "ncbi_nucleotide_tools.json"),
"ncbi_sra": os.path.join(current_dir, "data", "ncbi_sra_tools.json"),
"doaj": os.path.join(current_dir, "data", "doaj_tools.json"),
"unpaywall": os.path.join(current_dir, "data", "unpaywall_tools.json"),
"biorxiv": os.path.join(current_dir, "data", "biorxiv_tools.json"),
"medrxiv": os.path.join(current_dir, "data", "medrxiv_tools.json"),
"hal": os.path.join(current_dir, "data", "hal_tools.json"),
"core": os.path.join(current_dir, "data", "core_tools.json"),
"pmc": os.path.join(current_dir, "data", "pmc_tools.json"),
"zenodo": os.path.join(current_dir, "data", "zenodo_tools.json"),
"openaire": os.path.join(current_dir, "data", "openaire_tools.json"),
"osf_preprints": os.path.join(current_dir, "data", "osf_preprints_tools.json"),
"fatcat": os.path.join(current_dir, "data", "fatcat_tools.json"),
"wikidata_sparql": os.path.join(current_dir, "data", "wikidata_sparql_tools.json"),
"wikipedia": os.path.join(current_dir, "data", "wikipedia_tools.json"),
"dbpedia": os.path.join(current_dir, "data", "dbpedia_tools.json"),
"agents": os.path.join(current_dir, "data", "agentic_tools.json"),
# Smolagents tool wrapper configs
"smolagents": os.path.join(current_dir, "data", "smolagent_tools.json"),
"tool_discovery_agents": os.path.join(
current_dir, "data", "tool_discovery_agents.json"
),
"web_search_tools": os.path.join(current_dir, "data", "web_search_tools.json"),
"package_discovery_tools": os.path.join(
current_dir, "data", "package_discovery_tools.json"
),
"pypi_package_inspector_tools": os.path.join(
current_dir, "data", "pypi_package_inspector_tools.json"
),
"drug_discovery_agents": os.path.join(
current_dir, "data", "drug_discovery_agents.json"
),
"dataset": os.path.join(current_dir, "data", "dataset_tools.json"),
# 'mcp_clients': os.path.join(current_dir, 'data', 'mcp_client_tools_example.json'),
"mcp_auto_loader_txagent": os.path.join(
current_dir, "data", "txagent_client_tools.json"
),
"mcp_auto_loader_expert_feedback": os.path.join(
current_dir, "data", "expert_feedback_tools.json"
),
"adverse_event": os.path.join(current_dir, "data", "adverse_event_tools.json"),
"dailymed": os.path.join(current_dir, "data", "dailymed_tools.json"),
"fda_orange_book": os.path.join(current_dir, "data", "fda_orange_book_tools.json"),
"faers_analytics": os.path.join(current_dir, "data", "faers_analytics_tools.json"),
"cdc": os.path.join(current_dir, "data", "cdc_tools.json"),
"nhanes": os.path.join(current_dir, "data", "nhanes_tools.json"),
"health_disparities": os.path.join(
current_dir, "data", "health_disparities_tools.json"
),
"hpa": os.path.join(current_dir, "data", "hpa_tools.json"),
"reactome": os.path.join(current_dir, "data", "reactome_tools.json"),
"pubchem": os.path.join(current_dir, "data", "pubchem_tools.json"),
"medlineplus": os.path.join(current_dir, "data", "medlineplus_tools.json"),
"rxnorm": os.path.join(current_dir, "data", "rxnorm_tools.json"),
"loinc": os.path.join(current_dir, "data", "loinc_tools.json"),
"uniprot": os.path.join(current_dir, "data", "uniprot_tools.json"),
"cellosaurus": os.path.join(current_dir, "data", "cellosaurus_tools.json"),
# 'software': os.path.join(current_dir, 'data', 'software_tools.json'),
# Package tools - categorized software tools
"software_bioinformatics": os.path.join(
current_dir, "data", "packages", "bioinformatics_core_tools.json"
),
"software_genomics": os.path.join(
current_dir, "data", "packages", "genomics_tools.json"
),
"software_single_cell": os.path.join(
current_dir, "data", "packages", "single_cell_tools.json"
),
"software_structural_biology": os.path.join(
current_dir, "data", "packages", "structural_biology_tools.json"
),
"software_cheminformatics": os.path.join(
current_dir, "data", "packages", "cheminformatics_tools.json"
),
"software_machine_learning": os.path.join(
current_dir, "data", "packages", "machine_learning_tools.json"
),
"software_visualization": os.path.join(
current_dir, "data", "packages", "visualization_tools.json"
),
# Scientific visualization tools
"visualization_protein_3d": os.path.join(
current_dir, "data", "protein_structure_3d_tools.json"
),
"visualization_molecule_2d": os.path.join(
current_dir, "data", "molecule_2d_tools.json"
),
# New database tools
"interpro": os.path.join(current_dir, "data", "interpro_tools.json"),
"ebi_search": os.path.join(current_dir, "data", "ebi_search_tools.json"),
"intact": os.path.join(current_dir, "data", "intact_tools.json"),
"metabolights": os.path.join(current_dir, "data", "metabolights_tools.json"),
"proteins_api": os.path.join(current_dir, "data", "proteins_api_tools.json"),
"arrayexpress": os.path.join(current_dir, "data", "arrayexpress_tools.json"),
"biostudies": os.path.join(current_dir, "data", "biostudies_tools.json"),
"dbfetch": os.path.join(current_dir, "data", "dbfetch_tools.json"),
"pdbe_api": os.path.join(current_dir, "data", "pdbe_api_tools.json"),
"ena_browser": os.path.join(current_dir, "data", "ena_browser_tools.json"),
"blast": os.path.join(current_dir, "data", "blast_tools.json"),
"cbioportal": os.path.join(current_dir, "data", "cbioportal_tools.json"),
"regulomedb": os.path.join(current_dir, "data", "regulomedb_tools.json"),
"jaspar": os.path.join(current_dir, "data", "jaspar_tools.json"),
"remap": os.path.join(current_dir, "data", "remap_tools.json"),
"screen": os.path.join(current_dir, "data", "screen_tools.json"),
"pride": os.path.join(current_dir, "data", "pride_tools.json"),
"emdb": os.path.join(current_dir, "data", "emdb_tools.json"),
"sasbdb": os.path.join(current_dir, "data", "sasbdb_tools.json"),
"gtopdb": os.path.join(current_dir, "data", "gtopdb_tools.json"),
"mpd": os.path.join(current_dir, "data", "mpd_tools.json"),
"worms": os.path.join(current_dir, "data", "worms_tools.json"),
"paleobiology": os.path.join(current_dir, "data", "paleobiology_tools.json"),
"visualization_molecule_3d": os.path.join(
current_dir, "data", "molecule_3d_tools.json"
),
"software_scientific_computing": os.path.join(
current_dir, "data", "packages", "scientific_computing_tools.json"
),
"software_physics_astronomy": os.path.join(
current_dir, "data", "packages", "physics_astronomy_tools.json"
),
"software_earth_sciences": os.path.join(
current_dir, "data", "packages", "earth_sciences_tools.json"
),
"software_image_processing": os.path.join(
current_dir, "data", "packages", "image_processing_tools.json"
),
"software_neuroscience": os.path.join(
current_dir, "data", "packages", "neuroscience_tools.json"
),
"go": os.path.join(current_dir, "data", "gene_ontology_tools.json"),
"compose": os.path.join(current_dir, "data", "compose_tools.json"),
"python_executor": os.path.join(current_dir, "data", "python_executor_tools.json"),
"idmap": os.path.join(current_dir, "data", "idmap_tools.json"),
"disease_target_score": os.path.join(
current_dir, "data", "disease_target_score_tools.json"
),
"mcp_auto_loader_uspto_downloader": os.path.join(
current_dir, "data", "uspto_downloader_tools.json"
),
"uspto": os.path.join(current_dir, "data", "uspto_tools.json"),
"xml": os.path.join(current_dir, "data", "xml_tools.json"),
"mcp_auto_loader_boltz": os.path.join(
current_dir, "data", "boltz_mcp_loader_tools.json"
),
"mcp_auto_loader_esm": os.path.join(
current_dir, "data", "mcp_auto_loader_esm.json"
),
"url": os.path.join(current_dir, "data", "url_fetch_tools.json"),
"file_download": os.path.join(current_dir, "data", "file_download_tools.json"),
# 'langchain': os.path.join(current_dir, 'data', 'langchain_tools.json'),
"rcsb_pdb": os.path.join(current_dir, "data", "rcsb_pdb_tools.json"),
"rcsb_search": os.path.join(current_dir, "data", "rcsb_search_tools.json"),
"tool_composition": os.path.join(
current_dir, "data", "tool_composition_tools.json"
),
"embedding": os.path.join(current_dir, "data", "embedding_tools.json"),
"gwas": os.path.join(current_dir, "data", "gwas_tools.json"),
"admetai": os.path.join(current_dir, "data", "admetai_tools.json"),
# duplicate key removed
"alphafold": os.path.join(current_dir, "data", "alphafold_tools.json"),
"output_summarization": os.path.join(
current_dir, "data", "output_summarization_tools.json"
),
"odphp": os.path.join(current_dir, "data", "odphp_tools.json"),
"who_gho": os.path.join(current_dir, "data", "who_gho_tools.json"),
# Marine Regions - VLIZ geographic authority file for oceans, seas, and marine regions worldwide
"marine_regions": os.path.join(current_dir, "data", "marine_regions_tools.json"),
# ERDDAP - NOAA CoastWatch ocean/atmospheric dataset search and metadata (SST, chlorophyll, currents)
"erddap": os.path.join(current_dir, "data", "erddap_tools.json"),
# MET Norway - Norwegian Meteorological Institute weather forecasts (global, no auth)
"metnorway": os.path.join(current_dir, "data", "metnorway_tools.json"),
"umls": os.path.join(current_dir, "data", "umls_tools.json"),
"icd": os.path.join(current_dir, "data", "icd_tools.json"),
"euhealth": os.path.join(current_dir, "data", "euhealth_tools.json"),
"markitdown": os.path.join(current_dir, "data", "markitdown_tools.json"),
# Guideline and health policy tools
"guidelines": os.path.join(current_dir, "data", "unified_guideline_tools.json"),
# Clinical guidelines - MAGICapp, NCI R4R, NCI Drug Dict extended, DailyMed drug classes
"clinical_guidelines": os.path.join(
current_dir, "data", "clinical_guidelines_tools.json"
),
# FDA drug labels - official prescribing information with clinical recommendations
"openfda_labels": os.path.join(current_dir, "data", "openfda_label_tools.json"),
# Database tools
"kegg": os.path.join(current_dir, "data", "kegg_tools.json"),
"ensembl": os.path.join(current_dir, "data", "ensembl_tools.json"),
"clinvar": os.path.join(current_dir, "data", "clinvar_tools.json"),
"geo": os.path.join(current_dir, "data", "geo_tools.json"),
"dbsnp": os.path.join(current_dir, "data", "dbsnp_tools.json"),
"gnomad": os.path.join(current_dir, "data", "gnomad_tools.json"),
# Newly added database tools
"gbif": os.path.join(current_dir, "data", "gbif_tools.json"),
"obis": os.path.join(current_dir, "data", "obis_tools.json"),
"wikipathways": os.path.join(current_dir, "data", "wikipathways_tools.json"),
"rnacentral": os.path.join(current_dir, "data", "rnacentral_tools.json"),
"mirna": os.path.join(current_dir, "data", "mirna_tools.json"),
"lncrna": os.path.join(current_dir, "data", "lncrna_tools.json"),
"encode": os.path.join(current_dir, "data", "encode_tools.json"),
"gtex": os.path.join(current_dir, "data", "gtex_tools.json"),
"mgnify": os.path.join(current_dir, "data", "mgnify_tools.json"),
"gdc": os.path.join(current_dir, "data", "gdc_tools.json"),
# Ontology tools
"ols": os.path.join(current_dir, "data", "ols_tools.json"),
"optimizer": os.path.join(current_dir, "data", "optimizer_tools.json"),
# Compact mode core tools
"compact_mode": os.path.join(current_dir, "data", "compact_mode_tools.json"),
# New Life Science Tools
"hca_tools": os.path.join(current_dir, "data", "hca_tools.json"),
"iedb_tools": os.path.join(current_dir, "data", "iedb_tools.json"),
"pathway_commons_tools": os.path.join(
current_dir, "data", "pathway_commons_tools.json"
),
"biomodels_tools": os.path.join(current_dir, "data", "biomodels_tools.json"),
# BioThings APIs (MyGene, MyVariant, MyChem)
"biothings": os.path.join(current_dir, "data", "biothings_tools.json"),
# FDA Pharmacogenomic Biomarkers
"fda_pharmacogenomic_biomarkers": os.path.join(
current_dir, "data", "fda_pharmacogenomic_biomarkers_tools.json"
),
# Metabolomics Workbench
"metabolomics_workbench": os.path.join(
current_dir, "data", "metabolomics_workbench_tools.json"
),
# PharmGKB - Pharmacogenomics
"pharmgkb": os.path.join(current_dir, "data", "pharmgkb_tools.json"),
# DisGeNET - Gene-Disease Associations
# DGIdb - Drug Gene Interactions
"dgidb": os.path.join(current_dir, "data", "dgidb_tools.json"),
# STITCH - Chemical-Protein Interactions
"stitch": os.path.join(current_dir, "data", "stitch_tools.json"),
# CIViC - Clinical Interpretation of Variants in Cancer
"civic": os.path.join(current_dir, "data", "civic_tools.json"),
# Single-cell RNA-seq data
"cellxgene_census": os.path.join(
current_dir, "data", "cellxgene_census_tools.json"
),
# Chromatin and epigenetics data
"chipatlas": os.path.join(current_dir, "data", "chipatlas_tools.json"),
# 4DN Data Portal - 3D genome organization
"fourdn": os.path.join(current_dir, "data", "fourdn_tools.json"),
# GTEx Portal API V2 - Tissue-specific gene expression and eQTLs
"gtex_v2": os.path.join(current_dir, "data", "gtex_v2_tools.json"),
# Rfam Database API - RNA families (v15.1, January 2026)
"rfam": os.path.join(current_dir, "data", "rfam_tools.json"),
# BiGG Models API - Genome-scale metabolic models
"bigg_models": os.path.join(current_dir, "data", "bigg_models_tools.json"),
# Protein-Protein Interaction (PPI) tools - STRING and BioGRID
"ppi": os.path.join(current_dir, "data", "ppi_tools.json"),
# BioGRID - Genetic and Protein Interactions, Chemical-Protein, PTMs
"biogrid": os.path.join(current_dir, "data", "biogrid_tools.json"),
# NVIDIA NIM Healthcare APIs - Structure prediction, molecular docking, genomics
"nvidia_nim": os.path.join(current_dir, "data", "nvidia_nim_tools.json"),
# COSMIC - Catalogue of Somatic Mutations in Cancer
"cosmic": os.path.join(current_dir, "data", "cosmic_tools.json"),
# OncoKB - Precision Oncology Knowledge Base
"oncokb": os.path.join(current_dir, "data", "oncokb_tools.json"),
# OMIM - Online Mendelian Inheritance in Man
"omim": os.path.join(current_dir, "data", "omim_tools.json"),
# Orphanet - Rare Disease Encyclopedia
"orphanet": os.path.join(current_dir, "data", "orphanet_tools.json"),
# DisGeNET - Gene-Disease Associations
"disgenet": os.path.join(current_dir, "data", "disgenet_tools.json"),
# BindingDB - Protein-Ligand Binding Affinities
"bindingdb": os.path.join(current_dir, "data", "bindingdb_tools.json"),
# GPCRdb - G Protein-Coupled Receptor Database
"gpcrdb": os.path.join(current_dir, "data", "gpcrdb_tools.json"),
# BRENDA - Enzyme Kinetics Database
"brenda": os.path.join(current_dir, "data", "brenda_tools.json"),
# SAbDab - Structural Antibody Database
"sabdab": os.path.join(current_dir, "data", "sabdab_tools.json"),
# IMGT - International ImMunoGeneTics Information System
"imgt": os.path.join(current_dir, "data", "imgt_tools.json"),
# HMDB - Human Metabolome Database
"hmdb": os.path.join(current_dir, "data", "hmdb_tools.json"),
# MetaCyc - Metabolic Pathway Database
"metacyc": os.path.join(current_dir, "data", "metacyc_tools.json"),
# ZINC - Virtual Screening Library
"zinc": os.path.join(current_dir, "data", "zinc_tools.json"),
# Enamine - Make-on-Demand Compounds
"enamine": os.path.join(current_dir, "data", "enamine_tools.json"),
# eMolecules - Vendor Aggregator
"emolecules": os.path.join(current_dir, "data", "emolecules_tools.json"),
# Pharos/TCRD - NIH IDG Understudied Proteins Database
"pharos": os.path.join(current_dir, "data", "pharos_tools.json"),
# AlphaMissense - DeepMind Pathogenicity Predictions
"alphamissense": os.path.join(current_dir, "data", "alphamissense_tools.json"),
# CADD - Combined Annotation Dependent Depletion
"cadd": os.path.join(current_dir, "data", "cadd_tools.json"),
# DepMap - Cancer Dependency Map (Sanger Cell Model Passports)
"depmap": os.path.join(current_dir, "data", "depmap_tools.json"),
# InterProScan - Protein Domain/Family Prediction
"interproscan": os.path.join(current_dir, "data", "interproscan_tools.json"),
# EVE - Evolutionary Variant Effect Predictions
"eve": os.path.join(current_dir, "data", "eve_tools.json"),
# Thera-SAbDab - Therapeutic Structural Antibody Database
"therasabdab": os.path.join(current_dir, "data", "therasabdab_tools.json"),
# DeepGO - Protein Function Prediction
"deepgo": os.path.join(current_dir, "data", "deepgo_tools.json"),
# ClinGen - Gene-Disease Validity, Dosage Sensitivity, Actionability
"clingen": os.path.join(current_dir, "data", "clingen_tools.json"),
# SpliceAI - Deep Learning Splice Prediction
"spliceai": os.path.join(current_dir, "data", "spliceai_tools.json"),
# IMPC - International Mouse Phenotyping Consortium (mouse KO phenotypes)
"impc": os.path.join(current_dir, "data", "impc_tools.json"),
# Complex Portal - Curated protein complexes (includes CORUM mammalian complexes)
"complex_portal": os.path.join(current_dir, "data", "complex_portal_tools.json"),
# Expression Atlas - EBI GXA baseline + differential gene expression
"expression_atlas": os.path.join(
current_dir, "data", "expression_atlas_tools.json"
),
# ProteinsPlus - Protein-ligand docking and binding site analysis
"proteinsplus": os.path.join(current_dir, "data", "proteinsplus_tools.json"),
# SwissDock - Molecular docking with AutoDock Vina and Attracting Cavities
"swissdock": os.path.join(current_dir, "data", "swissdock_tools.json"),
# LIPID MAPS - Lipid Structure Database (lipidomics)
"lipidmaps": os.path.join(current_dir, "data", "lipidmaps_tools.json"),
# USDA FoodData Central - Food composition and nutrient database
"fooddata_central": os.path.join(
current_dir, "data", "fooddata_central_tools.json"
),
# CTD - Comparative Toxicogenomics Database (chemical-gene-disease interactions)
"ctd": os.path.join(current_dir, "data", "ctd_tools.json"),
# NeuroMorpho - Neuronal morphology database (neuron reconstructions, morphometrics)
"neuromorpho": os.path.join(current_dir, "data", "neuromorpho_tools.json"),
# Allen Brain Atlas - Brain gene expression and structure data
"allen_brain": os.path.join(current_dir, "data", "allen_brain_tools.json"),
# GlyGen - Glycoinformatics (glycan structures, glycoproteins, glycosylation sites)
"glygen": os.path.join(current_dir, "data", "glygen_tools.json"),
# MGnify Expanded - Metagenomics genome catalog, biomes, study details
"mgnify_expanded": os.path.join(current_dir, "data", "mgnify_expanded_tools.json"),
# SGD - Saccharomyces Genome Database (yeast genes, phenotypes, interactions)
"sgd": os.path.join(current_dir, "data", "sgd_tools.json"),
# NCBI Datasets API v2 - Gene info, orthologs, taxonomy, genome metadata
"ncbi_datasets": os.path.join(current_dir, "data", "ncbi_datasets_tools.json"),
# EBI Taxonomy - Taxonomic classification, lineage, name resolution
"ebi_taxonomy": os.path.join(current_dir, "data", "ebi_taxonomy_tools.json"),
# Alliance of Genome Resources - Cross-species gene data from 7 model organisms
"alliance_genome": os.path.join(current_dir, "data", "alliance_genome_tools.json"),
# Open Targets Genetics - GWAS variant annotation, credible sets, L2G predictions
"opentarget_genetics": os.path.join(
current_dir, "data", "opentarget_genetics_tools.json"
),
# HGNC - HUGO Gene Nomenclature Committee (authoritative human gene naming)
"hgnc": os.path.join(current_dir, "data", "hgnc_tools.json"),
# BV-BRC - Bacterial and Viral Bioinformatics Resource Center (pathogen genomics, AMR)
"bvbrc": os.path.join(current_dir, "data", "bvbrc_tools.json"),
# BioImage Archive - EBI biological imaging data (microscopy, cryo-EM, fluorescence)
"bioimage_archive": os.path.join(
current_dir, "data", "bioimage_archive_tools.json"
),
# Plant Reactome - Gramene plant metabolic and regulatory pathways (140+ species)
"plant_reactome": os.path.join(current_dir, "data", "plant_reactome_tools.json"),
# Ensembl VEP - Variant Effect Predictor (HGVS, rsID annotation, variant recoding)
"ensembl_vep": os.path.join(current_dir, "data", "ensembl_vep_tools.json"),
# ITIS - Integrated Taxonomic Information System (US taxonomy, hierarchy, common names)
"itis": os.path.join(current_dir, "data", "itis_tools.json"),
# QuickGO - EBI Gene Ontology annotation browser (annotations, term details, hierarchy)
"quickgo": os.path.join(current_dir, "data", "quickgo_tools.json"),
# Bgee - Comparative gene expression across 29+ animal species (RNA-Seq, Affymetrix, EST)
"bgee": os.path.join(current_dir, "data", "bgee_tools.json"),
# OMA - Orthologous MAtrix Browser (orthology across 2,600+ genomes, HOGs, OMA Groups)
"oma": os.path.join(current_dir, "data", "oma_tools.json"),
# CATH - Protein Structure Classification (Class, Architecture, Topology, Homologous superfamily)
"cath": os.path.join(current_dir, "data", "cath_tools.json"),
# MeSH - Medical Subject Headings (NLM controlled vocabulary for PubMed indexing)
"mesh": os.path.join(current_dir, "data", "mesh_tools.json"),
# HPO - Human Phenotype Ontology (phenotype terms, hierarchy, clinical genetics)
"hpo": os.path.join(current_dir, "data", "hpo_tools.json"),
# Reactome Analysis Service - Pathway enrichment/overrepresentation analysis
"reactome_analysis": os.path.join(
current_dir, "data", "reactome_analysis_tools.json"
),
# Rhea - Expert-curated biochemical reactions (SIB, linked to ChEBI and EC)
"rhea": os.path.join(current_dir, "data", "rhea_tools.json"),
# PubChem BioAssay - Biological screening data (drug discovery, toxicology)
"pubchem_bioassay": os.path.join(
current_dir, "data", "pubchem_bioassay_tools.json"
),
# ENA Portal API - European Nucleotide Archive search (studies, samples, sequences)
"ena_portal": os.path.join(current_dir, "data", "ena_portal_tools.json"),
# PomBase - Fission yeast (S. pombe) genome database (gene info, phenotypes, domains)
"pombase": os.path.join(current_dir, "data", "pombase_tools.json"),
# EBI BioSamples - Biological sample metadata hub (60M+ samples, cross-archive)
"biosamples": os.path.join(current_dir, "data", "biosamples_tools.json"),
# GNPS - Mass spectrometry spectral library (metabolomics, natural products)
"gnps": os.path.join(current_dir, "data", "gnps_tools.json"),
# WormBase - C. elegans genome database (gene info, phenotypes, expression)
"wormbase": os.path.join(current_dir, "data", "wormbase_tools.json"),
# SWISS-MODEL Repository - Pre-computed protein homology models (ExPASy/SIB)
"swissmodel": os.path.join(current_dir, "data", "swissmodel_tools.json"),
# ProteomeXchange - Proteomics data consortium (PRIDE, MassIVE, jPOST)
"proteomexchange": os.path.join(current_dir, "data", "proteomexchange_tools.json"),
# PDBe Search - PDB structure search via EBI Solr (full-text, compounds, organisms)
"pdbe_search": os.path.join(current_dir, "data", "pdbe_search_tools.json"),
# Nextstrain - Pathogen phylogenetics and molecular epidemiology tracking
"nextstrain": os.path.join(current_dir, "data", "nextstrain_tools.json"),
# UCSC Genome Browser - Genome sequences, gene search, annotation tracks (220+ genomes)
"ucsc_genome": os.path.join(current_dir, "data", "ucsc_genome_tools.json"),
# ChEBI - Chemical Entities of Biological Interest (EBI chemical ontology, 195K+ compounds)
"chebi": os.path.join(current_dir, "data", "chebi_tools.json"),
# UniChem - EBI unified chemical cross-referencing across 40+ databases
"unichem": os.path.join(current_dir, "data", "unichem_tools.json"),
# PANTHER - Protein classification, gene enrichment, and ortholog analysis (144 organisms)
"panther": os.path.join(current_dir, "data", "panther_tools.json"),
# Ensembl LD - Linkage disequilibrium from 1000 Genomes (population genetics)
"ensembl_ld": os.path.join(current_dir, "data", "ensembl_ld_tools.json"),
# Ensembl Regulation - TF binding motifs, constrained elements, binding matrices
"ensembl_regulation": os.path.join(
current_dir, "data", "ensembl_regulation_tools.json"
),
# Ensembl Phenotypes - Gene/region/variant phenotype associations (GWAS, ClinVar, OMIM)
"ensembl_phenotype": os.path.join(
current_dir, "data", "ensembl_phenotype_tools.json"
),
# Europe PMC Annotations - Text-mined entities from articles (chemicals, organisms, GO)
"europepmc_annotations": os.path.join(
current_dir, "data", "europepmc_annotations_tools.json"
),
# WFGY ProblemMap - LLM/RAG failure triage prompt bundle (local, no API call)
"wfgy_promptbundle": os.path.join(
current_dir, "data", "wfgy_promptbundle_tools.json"
),
# UniProt ID Mapping - Cross-database identifier conversion (100+ databases)
"uniprot_idmapping": os.path.join(
current_dir, "data", "uniprot_idmapping_tools.json"
),
# Open Tree of Life - Phylogenetic tree of life (name resolution, taxonomy, MRCA, subtrees)
"opentree": os.path.join(current_dir, "data", "opentree_tools.json"),
# iNaturalist - Citizen science biodiversity observations (taxa, observations, species counts)
"inaturalist": os.path.join(current_dir, "data", "inaturalist_tools.json"),
# NCI Thesaurus - National Cancer Institute terminology (cancer diseases, drugs, genes)
"nci_thesaurus": os.path.join(current_dir, "data", "nci_thesaurus_tools.json"),
# ClinGen Allele Registry - Standardized allele IDs (HGVS normalization, cross-references)
"clingen_ar": os.path.join(current_dir, "data", "clingen_ar_tools.json"),
# NDEx - Network Data Exchange (biological network repository, PPI, signaling, regulatory networks)
"ndex": os.path.join(current_dir, "data", "ndex_tools.json"),
# Gene Ontology API - GO term details, gene functional annotations, gene-function associations
"go_api": os.path.join(current_dir, "data", "go_api_tools.json"),
# Ensembl Compara - Comparative genomics (orthologues, paralogues, gene trees)
"ensembl_compara": os.path.join(current_dir, "data", "ensembl_compara_tools.json"),
# Monarch Initiative V3 - Cross-species gene-disease-phenotype associations
"monarch_v3": os.path.join(current_dir, "data", "monarch_v3_tools.json"),
# EBI Proteins API Extended - Mutagenesis experiments and PTM proteomics evidence
"ebi_proteins_ext": os.path.join(
current_dir, "data", "ebi_proteins_ext_tools.json"
),
# PDBe-KB Graph API - Aggregated structural knowledge base (ligand sites, PPI interfaces, stats)
"pdbe_kb": os.path.join(current_dir, "data", "pdbe_kb_tools.json"),
# UniProt Reference Datasets - Diseases, keywords, and proteomes controlled vocabularies
"uniprot_ref": os.path.join(current_dir, "data", "uniprot_ref_tools.json"),
# Disease Ontology - Standardized human disease classification (DO terms, hierarchy, cross-refs)
"disease_ontology": os.path.join(
current_dir, "data", "disease_ontology_tools.json"
),
# RCSB PDB Data API - Direct REST access to PDB entry details, assemblies, non-polymer entities
"rcsb_data": os.path.join(current_dir, "data", "rcsb_data_tools.json"),
# EBI Proteins Features - Domain/site annotations, molecule processing, secondary structure
"ebi_proteins_features": os.path.join(
current_dir, "data", "ebi_proteins_features_tools.json"
),
# InterPro Extended - Reverse lookup: find proteins containing a specific domain
"interpro_ext": os.path.join(current_dir, "data", "interpro_ext_tools.json"),
# STRING Extended - Per-protein functional annotations (GO, KEGG, disease, tissue)
"string_ext": os.path.join(current_dir, "data", "string_ext_tools.json"),
# Ensembl Info - Genome assembly metadata and species catalog
"ensembl_info": os.path.join(current_dir, "data", "ensembl_info_tools.json"),
# Epigenomics - Histone marks, DNA methylation, chromatin accessibility, regulatory elements
"epigenomics": os.path.join(current_dir, "data", "epigenomics_tools.json"),
# 3D Beacons - Aggregated 3D structure models from PDBe, AlphaFold, SWISS-MODEL, PED
"three_d_beacons": os.path.join(current_dir, "data", "three_d_beacons_tools.json"),
# Reactome Content Service - Pathway search, contained events, enhanced details
"reactome_content": os.path.join(
current_dir, "data", "reactome_content_tools.json"
),
# InterPro Entry - Protein-to-domain mappings and keyword-based entry search
"interpro_entry": os.path.join(current_dir, "data", "interpro_entry_tools.json"),
# Ensembl Sequence - Region DNA and ID-based protein/cDNA sequence retrieval
"ensembl_sequence": os.path.join(
current_dir, "data", "ensembl_sequence_tools.json"
),
# MyDisease.info - BioThings disease annotation aggregator (MONDO, DO, CTD, HPO, DisGeNET)
"mydisease": os.path.join(current_dir, "data", "mydisease_tools.json"),
# EBI OxO - Ontology cross-reference mappings across biomedical databases
"oxo": os.path.join(current_dir, "data", "oxo_tools.json"),
# InterPro Domain Architecture - Protein domain positions, structure mapping, clan members
"interpro_domain_arch": os.path.join(
current_dir, "data", "interpro_domain_arch_tools.json"
),
# WikiPathways Extended - Gene lists from pathways and gene-to-pathway lookups
"wikipathways_ext": os.path.join(
current_dir, "data", "wikipathways_ext_tools.json"
),
# EBI Gene Expression Atlas (GxA) - Baseline/differential gene expression experiments
"gxa": os.path.join(current_dir, "data", "gxa_tools.json"),
# CellxGene Discovery - Single-cell RNA-seq dataset/collection browsing
"cellxgene_discovery": os.path.join(
current_dir, "data", "cellxgene_discovery_tools.json"
),
# Ensembl Archive - Stable ID versioning and history tracking
"ensembl_archive": os.path.join(current_dir, "data", "ensembl_archive_tools.json"),
# KEGG Extended - Gene-pathway links, pathway gene lists, compound details
"kegg_ext": os.path.join(current_dir, "data", "kegg_ext_tools.json"),
# EOL - Encyclopedia of Life (biodiversity knowledge aggregator: species, taxonomy, media)
"eol": os.path.join(current_dir, "data", "eol_tools.json"),
# Ensembl Map - Coordinate system conversion and assembly mapping
"ensembl_map": os.path.join(current_dir, "data", "ensembl_map_tools.json"),
# Ensembl Overlap - Features overlapping a genomic region (genes, variants, regulatory)
"ensembl_overlap": os.path.join(current_dir, "data", "ensembl_overlap_tools.json"),
# Ensembl Xrefs - External database cross-references for genes and proteins
"ensembl_xrefs": os.path.join(current_dir, "data", "ensembl_xrefs_tools.json"),
# Ensembl Variation Extended - Population genetics, linkage disequilibrium, haplotypes
"ensembl_variation_ext": os.path.join(
current_dir, "data", "ensembl_variation_ext_tools.json"
),
# EBI Proteins Coordinates - Protein 3D structural coordinates
"ebi_proteins_coordinates": os.path.join(
current_dir, "data", "ebi_proteins_coordinates_tools.json"
),
# EBI Proteins Epitope - Immunological epitope annotations
"ebi_proteins_epitope": os.path.join(
current_dir, "data", "ebi_proteins_epitope_tools.json"
),
# EBI Proteins Interactions - Protein-protein interaction evidence
"ebi_proteins_interactions": os.path.join(
current_dir, "data", "ebi_proteins_interactions_tools.json"
),
# PDBe Compound - Small molecule compound summaries and cross-references
"pdbe_compound": os.path.join(current_dir, "data", "pdbe_compound_tools.json"),
# PDBe Ligands - Structure-level ligand lists and residue details
"pdbe_ligands": os.path.join(current_dir, "data", "pdbe_ligands_tools.json"),
# PDBe SIFTS - Structure-to-sequence mappings (UniProt, Pfam, CATH, EC)
"pdbe_sifts": os.path.join(current_dir, "data", "pdbe_sifts_tools.json"),
# PDBe Validation - Experimental validation reports (R-factor, clashscore, geometry)
"pdbe_validation": os.path.join(current_dir, "data", "pdbe_validation_tools.json"),
# RCSB Advanced Search - Complex multi-attribute PDB queries
"rcsb_advanced_search": os.path.join(
current_dir, "data", "rcsb_advanced_search_tools.json"
),
# RCSB GraphQL - Flexible PDB data retrieval via GraphQL schema
"rcsb_graphql": os.path.join(current_dir, "data", "rcsb_graphql_tools.json"),
# Reactome Interactors - Protein interaction data from IntAct/ChEMBL
"reactome_interactors": os.path.join(
current_dir, "data", "reactome_interactors_tools.json"
),
# UniParc - UniProt Archive cross-references across sequence databases
"uniparc": os.path.join(current_dir, "data", "uniparc_tools.json"),
# UniProt Locations - Subcellular location controlled vocabulary
"uniprot_locations": os.path.join(
current_dir, "data", "uniprot_locations_tools.json"
),
# UniProt Taxonomy - Taxonomy nodes and lineage data from UniProt
"uniprot_taxonomy": os.path.join(
current_dir, "data", "uniprot_taxonomy_tools.json"
),
# UniRef - UniProt Reference Clusters (100/90/50 identity clusters)
"uniref": os.path.join(current_dir, "data", "uniref_tools.json"),
# ClinGen Dosage Sensitivity - Haploinsufficiency and triplosensitivity scores
"clingen_dosage": os.path.join(
current_dir, "data", "clingen_dosage_api_tools.json"
),
# Dfam - Repetitive DNA element database (transposons, SINEs, LINEs)
"dfam": os.path.join(current_dir, "data", "dfam_tools.json"),
# DisProt - Intrinsically disordered protein regions database
"disprot": os.path.join(current_dir, "data", "disprot_tools.json"),
# Genome Nexus - Cancer variant annotation aggregator (VEP, COSMIC, ClinVar)
"genome_nexus": os.path.join(current_dir, "data", "genome_nexus_tools.json"),
# g:Profiler - Functional enrichment, gene ID conversion, ortholog mapping
"gprofiler": os.path.join(current_dir, "data", "gprofiler_tools.json"),
# Harmonizome - Aggregated gene-attribute associations from 114 datasets
"harmonizome": os.path.join(current_dir, "data", "harmonizome_tools.json"),
# MobiDB - Intrinsic disorder and mobility annotations for proteins
"mobidb": os.path.join(current_dir, "data", "mobidb_tools.json"),
# OmniPath - Signaling network (ligand-receptor, enzyme-substrate, complexes)
"omnipath": os.path.join(current_dir, "data", "omnipath_tools.json"),
# OrthoDB - Hierarchical orthology database (orthologs, paralogs across 1,300+ species)
"orthodb": os.path.join(current_dir, "data", "orthodb_tools.json"),
# SynBioHub - Synthetic biology parts and designs repository (SBOL standard)
"synbiohub": os.path.join(current_dir, "data", "synbiohub_tools.json"),
# BioPortal - NCBO ontology browser and annotation service
"bioportal": os.path.join(current_dir, "data", "bioportal_tools.json"),
# FlyBase - Drosophila melanogaster genetics (via Alliance of Genome Resources)
"flybase": os.path.join(current_dir, "data", "flybase_tools.json"),
# ZFIN - Zebrafish Information Network (via Alliance of Genome Resources)
"zfin": os.path.join(current_dir, "data", "zfin_tools.json"),
# Pfam - Protein families database (via InterPro API)
"pfam": os.path.join(current_dir, "data", "pfam_tools.json"),
# PubChem Toxicity - Chemical toxicity, GHS hazard, carcinogen classification, LD50 data
"pubchem_tox": os.path.join(current_dir, "data", "pubchem_tox_tools.json"),
# ClinicalTrials.gov - World's largest clinical trial registry (572,000+ trials)
# EpiGraphDB - Mendelian Randomization, genetic correlations, drug repurposing via GWAS
"epigraphdb": os.path.join(current_dir, "data", "epigraphdb_tools.json"),
# Bio.tools - ELIXIR bioinformatics tool/software registry (30,000+ entries)
"biotools_registry": os.path.join(
current_dir, "data", "biotools_registry_tools.json"
),
# Identifiers.org - ELIXIR biological identifier resolution service (800+ namespaces)
"identifiers_org": os.path.join(current_dir, "data", "identifiers_org_tools.json"),
# Europe PMC Citations - Citation network traversal (who cites / is cited by)
"europepmc_citations": os.path.join(
current_dir, "data", "europepmc_citations_tools.json"
),
# TCIA - The Cancer Imaging Archive (medical imaging datasets)
"tcia": os.path.join(current_dir, "data", "tcia_tools.json"),
# OpenNeuro - Neuroimaging data repository (BIDS datasets)
"openneuro": os.path.join(current_dir, "data", "openneuro_tools.json"),
# ModelDB - Computational neuroscience model repository (Yale/SenseLab)
"modeldb": os.path.join(current_dir, "data", "modeldb_tools.json"),
# KEGG BRITE - Hierarchical functional classification (enzymes, kinases, transporters, GPCRs)
"kegg_brite": os.path.join(current_dir, "data", "kegg_brite_tools.json"),
# OmicsDI - Omics Discovery Index (integrated multi-omics repository search)
"omicsdi": os.path.join(current_dir, "data", "omicsdi_tools.json"),
# CPIC - Clinical Pharmacogenomics Implementation Consortium
"cpic": os.path.join(current_dir, "data", "cpic_tools.json"),
# PDB-REDO - Re-refined PDB structures with improved quality metrics
"pdb_redo": os.path.join(current_dir, "data", "pdb_redo_tools.json"),
# BMRB - Biological Magnetic Resonance Data Bank (NMR data for proteins and metabolites)
"bmrb": os.path.join(current_dir, "data", "bmrb_tools.json"),
# PharmVar - Pharmacogene Variation Consortium (star allele definitions)
"pharmvar": os.path.join(current_dir, "data", "pharmvar_tools.json"),
# Catalogue of Life - Global species index (2M+ species from 165+ databases)
"col": os.path.join(current_dir, "data", "col_tools.json"),
# MassBank Europe - Open-access MS spectral library for metabolomics and environmental chemistry
"massbank": os.path.join(current_dir, "data", "massbank_tools.json"),
# LOTUS - Natural products database (750K+ structure-organism pairs)
"lotus": os.path.join(current_dir, "data", "lotus_tools.json"),
# MSigDB - Molecular Signatures Database (33K+ gene sets for GSEA)
"msigdb": os.path.join(current_dir, "data", "msigdb_tools.json"),
# HumanMine - InterMine data warehouse for human/mouse/rat genomics
"humanmine": os.path.join(current_dir, "data", "humanmine_tools.json"),
# VariantValidator - HGVS variant validation and nomenclature conversion
"variant_validator": os.path.join(
current_dir, "data", "variant_validator_tools.json"
),
# IDR - Image Data Resource, public imaging datasets from published studies
"idr": os.path.join(current_dir, "data", "idr_tools.json"),
# OpenFDA - FDA drug labels, adverse events, and NDC directory
"openfda": os.path.join(current_dir, "data", "openfda_tools.json"),
# KLIFS - Kinase-Ligand Interaction Fingerprints and Structures
"klifs": os.path.join(current_dir, "data", "klifs_tools.json"),
# GeneNetwork - systems genetics QTL and gene expression for genetic crosses
"genenetwork": os.path.join(current_dir, "data", "genenetwork_tools.json"),
# ChannelsDB - protein channel, tunnel, and pore data for PDB structures
"channelsdb": os.path.join(current_dir, "data", "channelsdb_tools.json"),
# FlyMine - InterMine data warehouse for Drosophila melanogaster genomics
"flymine": os.path.join(current_dir, "data", "flymine_tools.json"),
# MouseMine - InterMine data warehouse for mouse genomics from MGI
"mousemine": os.path.join(current_dir, "data", "mousemine_tools.json"),
# TargetMine - InterMine data warehouse for drug target discovery
"targetmine": os.path.join(current_dir, "data", "targetmine_tools.json"),
# iCite - NIH citation metrics, RCR, APT scores for PubMed publications
"icite": os.path.join(current_dir, "data", "icite_tools.json"),
# scite - smart citation tallies (supporting/contradicting/mentioning)
"scite": os.path.join(current_dir, "data", "scite_tools.json"),
# VEuPathDB - eukaryotic pathogen, vector and host genomics
"veupathdb": os.path.join(current_dir, "data", "veupathdb_tools.json"),
# GeneNetwork Extended - trait and dataset detail info
"genenetwork_ext": os.path.join(current_dir, "data", "genenetwork_ext_tools.json"),
# Open Food Facts - commercial food products with barcodes, Nutri-Score, NOVA, ingredients
"openfoodfacts": os.path.join(current_dir, "data", "openfoodfacts_tools.json"),
# MIBiG - Minimum Information about a Biosynthetic Gene Cluster (natural product BGCs)
"mibig": os.path.join(current_dir, "data", "mibig_tools.json"),
# ScanProsite - Protein motif scanning against PROSITE patterns (ExPASy/SIB)
"scanprosite": os.path.join(current_dir, "data", "scanprosite_tools.json"),
# PDBe Graph API - Bound molecules, UniProt mappings, compound details, FunPDBe
"pdbe_graph": os.path.join(current_dir, "data", "pdbe_graph_tools.json"),
# NCBI Gene - E-utilities gene search and summary (Entrez Gene)
"ncbi_gene": os.path.join(current_dir, "data", "ncbi_gene_tools.json"),
# DataCite - research data DOIs for datasets, software, samples across repositories
"datacite": os.path.join(current_dir, "data", "datacite_tools.json"),
# Figshare - open-access research repository for datasets, figures, code, posters
"figshare": os.path.join(current_dir, "data", "figshare_tools.json"),
# Human Protein Atlas - protein expression across tissues, subcellular location, disease, cancer
# FPbase - fluorescent protein database with spectral properties, sequences, structures
"fpbase": os.path.join(current_dir, "data", "fpbase_tools.json"),
# ROR - Research Organization Registry for institution identifiers and metadata
"ror": os.path.join(current_dir, "data", "ror_tools.json"),
# ORCID - researcher identifiers, profiles, and publication lists
"orcid": os.path.join(current_dir, "data", "orcid_tools.json"),
# PanelApp - Genomics England gene panels for clinical genetic testing
"panelapp": os.path.join(current_dir, "data", "panelapp_tools.json"),
# Semantic Scholar Extended - paper details, author profiles, recommendations
"semantic_scholar_ext": os.path.join(
current_dir, "data", "semantic_scholar_ext_tools.json"
),
# bioRxiv Extended - list recent preprints by date range
"biorxiv_ext": os.path.join(current_dir, "data", "biorxiv_ext_tools.json"),
# World Bank - World Development Indicators (GDP, population, health, education, 200+ countries)
"worldbank": os.path.join(current_dir, "data", "worldbank_tools.json"),
# IMF - World Economic Outlook macroeconomic data (GDP growth, inflation, unemployment, debt)
# Open-Meteo - Free weather forecast, historical climate, air quality, and geocoding
"open_meteo": os.path.join(current_dir, "data", "open_meteo_tools.json"),
# EVA - European Variation Archive (EBI) for population variant data
"eva": os.path.join(current_dir, "data", "eva_tools.json"),
# eQTL Catalogue - Expression quantitative trait loci associations
"eqtl": os.path.join(current_dir, "data", "eqtl_tools.json"),
# OSDR - NASA Open Science Data Repository (space biology studies)
"osdr": os.path.join(current_dir, "data", "osdr_tools.json"),
# Gene2Phenotype - EBI curated gene-disease associations for clinical genetics
"gene2phenotype": os.path.join(current_dir, "data", "gene2phenotype_tools.json"),
# NASA Exoplanet Archive - ADQL queries for 5500+ confirmed exoplanets and stellar hosts
"nasa_exoplanet": os.path.join(current_dir, "data", "nasa_exoplanet_tools.json"),
# OpenStreetMap Nominatim - Free geocoding and reverse geocoding worldwide
"nominatim": os.path.join(current_dir, "data", "nominatim_tools.json"),
# REST Countries - Comprehensive country metadata (population, languages, currencies, borders)
# eBird - Cornell Lab bird taxonomy and regional species lists (no API key)
"ebird_taxonomy": os.path.join(current_dir, "data", "ebird_taxonomy_tools.json"),
# CRAN R Package Database - Metadata for 20,000+ R packages including versions and dependencies
"cran": os.path.join(current_dir, "data", "cran_tools.json"),
# NASA CMR - Common Metadata Repository for 40,000+ Earth observation datasets
"nasa_cmr": os.path.join(current_dir, "data", "nasa_cmr_tools.json"),
# DataONE - Federation of 43+ environmental data repositories (3.2M+ datasets)
"dataone": os.path.join(current_dir, "data", "dataone_tools.json"),
# Dryad - Open research data repository for life sciences and other disciplines
"dryad": os.path.join(current_dir, "data", "dryad_tools.json"),
# Dataverse (Harvard) - Open-source research data repository platform
"dataverse": os.path.join(current_dir, "data", "dataverse_tools.json"),
# SDSS - Sloan Digital Sky Survey DR18, SQL queries for 500M+ astronomical objects
"sdss": os.path.join(current_dir, "data", "sdss_tools.json"),
# NASA NED - NASA/IPAC Extragalactic Database for galaxies, quasars, and AGN
"nasa_ned": os.path.join(current_dir, "data", "nasa_ned_tools.json"),
# GitHub - Public repository search and metadata via GitHub API
"github": os.path.join(current_dir, "data", "github_tools.json"),
# LitVar2 - NCBI variant-literature linking (search variants, get publications)
"litvar": os.path.join(current_dir, "data", "litvar_tools.json"),
# PubTator3 Extended - entity annotation extraction from PubMed articles
"pubtator3_ext": os.path.join(current_dir, "data", "pubtator3_ext_tools.json"),
# RCSB Chemical Components - PDB ligand/small molecule chemical info
"rcsb_chemcomp": os.path.join(current_dir, "data", "rcsb_chemcomp_tools.json"),
# NCI Drug Dictionary - cancer drug definitions, aliases, and NCI concept IDs
"nci_drugdict": os.path.join(current_dir, "data", "nci_drugdict_tools.json"),
# Eurostat - EU statistical office data (GDP, population, health, environment)
"eurostat": os.path.join(current_dir, "data", "eurostat_tools.json"),
# USGS Earthquake - Real-time and historical earthquake data from USGS FDSN
"usgs_earthquake": os.path.join(current_dir, "data", "usgs_earthquake_tools.json"),
# JPL Horizons - Solar system body lookup and physical data from NASA JPL
"jpl_horizons": os.path.join(current_dir, "data", "jpl_horizons_tools.json"),
# NASA SBDB - Small Body Database for asteroids and comets (1.3M+ objects)
"nasa_sbdb": os.path.join(current_dir, "data", "nasa_sbdb_tools.json"),
# Space - ISS position/crew tracker and sunrise/sunset times (Open Notify API)
# COD - Crystallography Open Database for 500K+ crystal structures
"cod_crystal": os.path.join(current_dir, "data", "cod_crystal_tools.json"),
# HuggingFace Hub - ML model/dataset search and metadata (500K+ models)
"huggingface": os.path.join(current_dir, "data", "huggingface_tools.json"),
# OpenML - Open machine learning benchmark datasets and tasks
"openml": os.path.join(current_dir, "data", "openml_tools.json"),
# Metropolitan Museum of Art - 400K+ open-access artworks (search and object detail)
# Victoria and Albert Museum - 5000 years of art and design (search and object detail)
# Europeana - 50M+ European cultural heritage items (museums, libraries, archives)
# Exchange Rate - live currency exchange rates for 150+ currencies (no auth)
# Crates.io - Rust package registry (150K+ crates with search and details)
# Internet Archive - Digital library of 40M+ items (books, audio, video, web, software)
# Anaconda.org - Conda package registry (conda-forge, bioconda, 200K+ packages)
"anaconda": os.path.join(current_dir, "data", "anaconda_tools.json"),
# NASA EONET - Natural event tracker (wildfires, storms, volcanoes, floods)
"nasa_eonet": os.path.join(current_dir, "data", "nasa_eonet_tools.json"),
# POWO - Plants of the World Online by Kew Gardens (1.3M+ plant names)
"powo": os.path.join(current_dir, "data", "powo_tools.json"),
# NeuroVault - Neuroimaging statistical maps repository (16K+ collections, 650K+ images)
"neurovault": os.path.join(current_dir, "data", "neurovault_tools.json"),
# Disease.sh - COVID-19 and public health statistics (231 countries, historical data)
"diseasesh": os.path.join(current_dir, "data", "diseasesh_tools.json"),
# OpenCitations COCI - Open scholarly citation index (references, citations, counts)
"opencitations": os.path.join(current_dir, "data", "opencitations_tools.json"),
# Wikidata Entity API - search and retrieve Wikidata items/entities by ID
"wikidata_entity": os.path.join(current_dir, "data", "wikidata_entity_tools.json"),
# iDigBio - Integrated Digitized Biocollections (130M+ natural history specimens)
"idigbio": os.path.join(current_dir, "data", "idigbio_tools.json"),
# ELIXIR TeSS - Bioinformatics training materials and events aggregator
"elixir_tess": os.path.join(current_dir, "data", "elixir_tess_tools.json"),
# Wikimedia Stats - Wikipedia page views and top articles analytics
# Art Institute of Chicago - 130K+ artworks open access collection
# Cleveland Museum of Art - 61K+ open access artworks
# Open Notify - ISS real-time position and astronauts in space
# CEDA - UK Centre for Environmental Data Analysis climate datasets
"ceda": os.path.join(current_dir, "data", "ceda_tools.json"),
# Sunrise-Sunset API - solar event times for any location
"sunrise_sunset": os.path.join(current_dir, "data", "sunrise_sunset_tools.json"),
# Openverse - Creative Commons licensed images (700M+ from Flickr, Wikimedia, museums)
# US College Scorecard - higher education data (6000+ schools, admission rates, costs)
# FEC - US Federal Election Commission candidate and financial data
# Smithsonian Open Access - 5M+ digitized museum objects from 19 Smithsonian institutions
# Library of Congress - 21M+ digitized historical items (photos, maps, manuscripts)
# SoilGrids - global soil property predictions at any location (ISRIC)
"soilgrids": os.path.join(current_dir, "data", "soilgrids_tools.json"),
# US Treasury Fiscal Data - national debt, exchange rates, interest rates, debt breakdown
# Chronicling America - historic US newspaper search (LOC, 1777-1963)
# GBIF Extended - species detail by key and species name autocomplete
"gbif_ext": os.path.join(current_dir, "data", "gbif_ext_tools.json"),
# Frankfurter - real-time and historical currency exchange rates (ECB data)
# Datamuse - word-finding API (synonyms, antonyms, rhymes, semantic similarity)
# National Weather Service (NWS) - US weather forecasts, alerts, and point metadata
"nws": os.path.join(current_dir, "data", "nws_tools.json"),
# SpaceX - rocket launches, rockets, launchpads, and crew data
# USGS Water Services - real-time streamflow, water level, and temperature data
"usgs_water": os.path.join(current_dir, "data", "usgs_water_tools.json"),
# Spaceflight News API - 30K+ space news articles from major sites
# Launch Library 2 - upcoming rocket launches worldwide (all providers)
# US Census Bureau - population and demographic data (no key required)
"uscensus": os.path.join(current_dir, "data", "uscensus_tools.json"),
# Open-Meteo Marine - ocean wave/swell forecasts for any coastal location
"open_meteo_marine": os.path.join(
current_dir, "data", "open_meteo_marine_tools.json"
),
# Open-Meteo Flood - river discharge and flood forecasts (GloFAS/Copernicus)
"open_meteo_flood": os.path.join(
current_dir, "data", "open_meteo_flood_tools.json"
),
# NASA DONKI - space weather events (CME, flares, storms, particles, shocks)
"nasa_donki": os.path.join(current_dir, "data", "nasa_donki_tools.json"),
# OpenTopoData - terrain elevation data for any global location (SRTM/ASTER/NED)
"opentopodata": os.path.join(current_dir, "data", "opentopodata_tools.json"),
# Disease.sh - COVID-19 global and country-level statistics
# NASA NeoWs - Near Earth Object data (asteroids, close approaches)
"nasa_neows": os.path.join(current_dir, "data", "nasa_neows_tools.json"),
# REST Countries Extended - country details by name, region, language
# STRING Network - protein-protein interaction networks
"string_network": os.path.join(current_dir, "data", "string_network_tools.json"),
# UniProt Proteomes - proteome reference data
"uniprot_proteomes": os.path.join(
current_dir, "data", "uniprot_proteomes_tools.json"
),
# wttr.in - current weather in JSON format for any city or coordinates
# TimeAPI.io - current time by timezone or geographic coordinates
# ExchangeRate-API - current foreign exchange rates for 166 currencies
# BigDataCloud - reverse geocode lat/lng to country, city, region (no auth)
# Open-Meteo Climate - historical climate data from 1950 via ERA5/CMIP6 models
"open_meteo_climate": os.path.join(
current_dir, "data", "open_meteo_climate_tools.json"
),
# Open-Meteo Air Quality - hourly PM2.5/PM10/ozone forecast and history
"open_meteo_airquality": os.path.join(
current_dir, "data", "open_meteo_airquality_tools.json"
),
# Open Elevation - terrain elevation data from lat/lon coordinates
# Disease.sh extended - COVID historical and vaccine coverage data
"disease_sh_ext": os.path.join(current_dir, "data", "disease_sh_ext_tools.json"),
# Where the ISS At - real-time ISS position and velocity
# Wikipedia extended - featured daily content and on-this-day events
"wikipedia_ext": os.path.join(current_dir, "data", "wikipedia_ext_tools.json"),
# Data.gov - U.S. government open data catalog search
# WAQI - World Air Quality Index real-time AQI data
"waqi": os.path.join(current_dir, "data", "waqi_tools.json"),
# BLS - Bureau of Labor Statistics economic time series (CPI, unemployment, etc.)
# SEC EDGAR - SEC filing search and company financial facts (XBRL)
# InspireHEP - high energy physics literature database
"inspirehep": os.path.join(current_dir, "data", "inspirehep_tools.json"),
# Federal Register - US government regulations, rules, notices, presidential documents
# NASA TechPort - NASA technology development projects and investments
# Crates.io - Rust package registry (search crates, version history, downloads)
# MyMemory Translation - free machine translation for 200+ language pairs
# IETF Datatracker - Internet standards (RFCs, Internet-Drafts, protocol specs)
# Gutendex - Project Gutenberg ebooks catalog search
# Bioconductor - R/Bioconductor bioinformatics package search and metadata (via R-universe)
"bioconductor": os.path.join(current_dir, "data", "bioconductor_tools.json"),
# ArtIC - Art Institute of Chicago open-access artwork search and metadata
"artic": os.path.join(current_dir, "data", "artic_tools.json"),
# ADA/AHA/ACC/NCCN - Clinical society guidelines (diabetes, cardiology, oncology)
"ada_aha_nccn": os.path.join(current_dir, "data", "ada_aha_nccn_tools.json"),
# CLUE.io - L1000 Connectivity Map perturbation signatures
"clue": os.path.join(current_dir, "data", "clue_tools.json"),
# TIMER2.0 - Tumor immune estimation and gene-immune correlations
"timer": os.path.join(current_dir, "data", "timer_tools.json"),
# PROTAC-DB - PROTAC compound database
"protacdb": os.path.join(current_dir, "data", "protacdb_tools.json"),
# DNA Design Tools - Local restriction site, ORF, GC content, translation
"dna_tools": os.path.join(current_dir, "data", "dna_tools.json"),
# Drug Synergy - Bliss, HSA, ZIP synergy models (local computation)
"drug_synergy": os.path.join(current_dir, "data", "drug_synergy_tools.json"),
# Dose-Response Analysis - 4PL curve fitting and IC50 calculation (local)
"dose_response": os.path.join(current_dir, "data", "dose_response_tools.json"),
# Survival Analysis - Kaplan-Meier, log-rank test, Cox regression (local)
"survival": os.path.join(current_dir, "data", "survival_tools.json"),
# ChemCompute - Local computational chemistry tools (RDKit SA Score)
"chem_compute": os.path.join(current_dir, "data", "chem_compute_tools.json"),
# L1000FWD - L1000 Fireworks Connectivity Map signature search
"l1000fwd": os.path.join(current_dir, "data", "l1000fwd_tools.json"),
# Cell Painting - IDR high-content microscopy screens, plates, and well-level data
"cellpainting": os.path.join(current_dir, "data", "cellpainting_tools.json"),
}
# Auto-load any user-provided tools from ~/.tooluniverse/user_tools/
user_tools_dir = os.path.expanduser("~/.tooluniverse/data/user_tools")
if os.path.exists(user_tools_dir):
for filename in os.listdir(user_tools_dir):
if filename.endswith(".json"):
key = f"user_{filename.replace('.json', '')}"
default_tool_files[key] = os.path.join(user_tools_dir, filename)
def _get_hook_config_file_path():
"""
Get the path to the hook configuration file.
This function uses the same logic as HookManager._get_config_file_path()
to ensure consistent path resolution across different installation scenarios.
Returns
Path: Path to the hook_config.json file
"""
try:
import importlib.resources as pkg_resources
except ImportError:
import importlib_resources as pkg_resources
try:
data_files = pkg_resources.files("tooluniverse.template")
return data_files / "hook_config.json"
except Exception:
return Path(__file__).parent / "template" / "hook_config.json"
[docs]
def get_default_hook_config():
"""
Get default hook configuration from hook_config.json.
This function loads the default hook configuration from the hook_config.json
template file, providing a single source of truth for default hook settings.
If the file cannot be loaded, it falls back to a minimal configuration.
Returns
dict: Default hook configuration with basic settings
"""
try:
config_file = _get_hook_config_file_path()
content = (
config_file.read_text(encoding="utf-8")
if hasattr(config_file, "read_text")
else Path(config_file).read_text(encoding="utf-8")
)
return json.loads(content)
except Exception:
# Fallback to minimal configuration if file cannot be loaded
# This ensures the system continues to work even if the config file
# is missing or corrupted
return {
"global_settings": {
"default_timeout": 30,
"max_hook_depth": 3,
"enable_hook_caching": True,
"hook_execution_order": "priority_desc",
},
"exclude_tools": [
"Tool_RAG",
"ToolFinderEmbedding",
"ToolFinderLLM",
],
"hook_type_defaults": {
"SummarizationHook": {
"default_output_length_threshold": 5000,
"default_chunk_size": 32000,
"default_focus_areas": "key_findings_and_results",
"default_max_summary_length": 3000,
},
"FileSaveHook": {
"default_temp_dir": None,
"default_file_prefix": "tool_output",
"default_include_metadata": True,
"default_auto_cleanup": False,
"default_cleanup_age_hours": 24,
},
},
"hooks": [
{
"name": "default_summarization_hook",
"type": "SummarizationHook",
"enabled": True,
"priority": 1,
"conditions": {
"output_length": {"operator": ">", "threshold": 5000}
},
"hook_config": {
"composer_tool": "OutputSummarizationComposer",
"chunk_size": 32000,
"focus_areas": "key_findings_and_results",
"max_summary_length": 3000,
},
}
],
"tool_specific_hooks": {},
"category_hooks": {},
}
