claude-scientific-skills/docs/scientific-databases.md

Scientific Databases

• AlphaFold DB - AI-predicted protein structure database with 200M+ predictions, confidence metrics (pLDDT, PAE), and Google Cloud bulk access
• ChEMBL - Bioactive molecule database with drug-like properties (2M+ compounds, 19M+ activities, 13K+ targets)
• ClinPGx - Clinical pharmacogenomics database (successor to PharmGKB) providing gene-drug interactions, CPIC clinical guidelines, allele functions, drug labels, and pharmacogenomic annotations for precision medicine and personalized pharmacotherapy (consolidates PharmGKB, CPIC, and PharmCAT resources)
• ClinVar - NCBI's public archive of genomic variants and their clinical significance with standardized classifications (pathogenic, benign, VUS), E-utilities API access, and bulk FTP downloads for variant interpretation and precision medicine research
• ClinicalTrials.gov - Comprehensive registry of clinical studies conducted worldwide (maintained by U.S. National Library of Medicine) with API v2 access for searching trials by condition, intervention, location, sponsor, study status, and phase; retrieve detailed trial information including eligibility criteria, outcomes, contacts, and locations; export to CSV/JSON formats for analysis (public API, no authentication required, ~50 req/min rate limit)
• COSMIC - Catalogue of Somatic Mutations in Cancer, the world's largest database of somatic cancer mutations (millions of mutations across thousands of cancer types, Cancer Gene Census, mutational signatures, structural variants, and drug resistance data)
• ENA (European Nucleotide Archive) - Comprehensive public repository for nucleotide sequence data and metadata with REST APIs for accessing sequences, assemblies, samples, studies, and reads; supports advanced search, taxonomy lookups, and bulk downloads via FTP/Aspera (rate limit: 50 req/sec)
• Ensembl - Genome browser and bioinformatics database providing genomic annotations, sequences, variants, and comparative genomics data for 250+ vertebrate species (Release 115, 2025) with comprehensive REST API for gene lookups, sequence retrieval, variant effect prediction (VEP), ortholog finding, assembly mapping (GRCh37/GRCh38), and region analysis
• FDA Databases - Comprehensive access to all FDA (Food and Drug Administration) regulatory databases through openFDA API covering drugs (adverse events, labeling, NDC, recalls, approvals, shortages), medical devices (adverse events, 510k clearances, PMA, UDI, classifications), foods (recalls, adverse events, allergen tracking), animal/veterinary medicines (species-specific adverse events), and substances (UNII/CAS lookup, chemical structures, molecular data) for drug safety research, pharmacovigilance, regulatory compliance, and scientific analysis
• GEO (Gene Expression Omnibus) - High-throughput gene expression and functional genomics data repository (264K+ studies, 8M+ samples) with microarray, RNA-seq, and expression profile access
• GWAS Catalog - NHGRI-EBI catalog of published genome-wide association studies with curated SNP-trait associations (thousands of studies, genome-wide significant associations p≤5×10⁻⁸), full summary statistics, REST API access for variant/trait/gene queries, and FTP downloads for genetic epidemiology and precision medicine research
• HMDB (Human Metabolome Database) - Comprehensive metabolomics resource with 220K+ metabolite entries, detailed chemical/biological data, concentration ranges, disease associations, pathways, and spectral data for metabolite identification and biomarker discovery
• KEGG - Kyoto Encyclopedia of Genes and Genomes for biological pathway analysis, gene-to-pathway mapping, compound searches, and molecular interaction networks (pathway enrichment, metabolic pathways, gene annotations, drug-drug interactions, ID conversion)
• Metabolomics Workbench - NIH Common Fund metabolomics data repository with 4,200+ processed studies, standardized nomenclature (RefMet), mass spectrometry searches, and comprehensive REST API for accessing metabolite structures, study metadata, experimental results, and gene/protein-metabolite associations
• Open Targets - Comprehensive therapeutic target identification and validation platform integrating genetics, omics, and chemical data (200M+ evidence strings, target-disease associations with scoring, tractability assessments, safety liabilities, known drugs from ChEMBL, GraphQL API) for drug target discovery, prioritization, evidence evaluation, drug repurposing, competitive intelligence, and mechanism research
• NCBI Gene - Work with NCBI Gene database to search, retrieve, and analyze gene information including nomenclature, sequences, variations, phenotypes, and pathways using E-utilities and Datasets API
• Protein Data Bank (PDB) - Access 3D structural data of proteins, nucleic acids, and biological macromolecules (200K+ structures) with search, retrieval, and analysis capabilities
• PubChem - Access chemical compound data from the world's largest free chemical database (110M+ compounds, 270M+ bioactivities)
• PubMed - Access to PubMed literature database with advanced search capabilities
• Reactome - Curated pathway database for biological processes and molecular interactions (2,825+ human pathways, 16K+ reactions, 11K+ proteins) with pathway enrichment analysis, expression data analysis, and species comparison using Content Service and Analysis Service APIs
• STRING - Protein-protein interaction network database (5000+ genomes, 59.3M proteins, 20B+ interactions) with functional enrichment analysis, interaction partner discovery, and network visualization from experimental data, computational prediction, and text-mining
• UniProt - Universal Protein Resource for protein sequences, annotations, and functional information (UniProtKB/Swiss-Prot reviewed entries, TrEMBL unreviewed entries) with REST API access for search, retrieval, ID mapping, and batch operations across 200+ databases
• USPTO - United States Patent and Trademark Office data access including patent searches, trademark lookups, patent examination history (PEDS), office actions, assignments, citations, and litigation records; supports PatentSearch API (ElasticSearch-based patent search), TSDR (Trademark Status & Document Retrieval), Patent/Trademark Assignment APIs, and additional specialized APIs for comprehensive IP analysis
• ZINC - Free database of commercially-available compounds for virtual screening and drug discovery (230M+ purchasable compounds in ready-to-dock 3D formats)