Add support for OpenAlex

docs/scientific-skills.md

@@ -17,6 +17,7 @@
 - **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, comprehensive database resource integrating genomic, chemical, and systemic functional information. Provides pathway databases (KEGG PATHWAY with 500+ reference pathways, metabolic pathways, signaling pathways, disease pathways), genome databases (KEGG GENES with gene catalogs from 5,000+ organisms), chemical databases (KEGG COMPOUND, KEGG DRUG, KEGG GLYCAN), and disease/drug databases (KEGG DISEASE, KEGG DRUG). Features pathway enrichment analysis, gene-to-pathway mapping, compound searches, molecular interaction networks, ortholog identification (KO - KEGG Orthology), ID conversion across databases, and visualization tools. Supports REST API access, KEGG Mapper for pathway mapping, and integration with bioinformatics tools. Use cases: pathway enrichment analysis, metabolic pathway reconstruction, drug target identification, comparative genomics, systems biology, and functional annotation of genes
 - **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
+- **OpenAlex** - Comprehensive open catalog of 240M+ scholarly works, authors, institutions, topics, sources, publishers, and funders. Provides complete bibliometric database for academic literature search, citation analysis, research trend tracking, author publication discovery, institution research output analysis, and open access paper identification. Features REST API with no authentication required (100k requests/day, 10 req/sec with email), advanced filtering (publication year, citations, open access status, topics, authors, institutions), aggregation/grouping capabilities, random sampling for research studies, batch ID lookups (DOI, ORCID, ROR, ISSN), and comprehensive metadata (titles, abstracts, citations, authorships, topics, funding). Supports literature reviews, bibliometric analysis, research output evaluation, citation network analysis, and academic database queries across all scientific domains
 - **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** - Comprehensive gene-specific database from NCBI providing curated information about genes from 500+ organisms. Contains gene nomenclature (official symbols, aliases, full names), genomic locations (chromosomal positions, exons, introns), sequences (genomic, mRNA, protein), gene function and phenotypes, pathways and interactions, orthologs and paralogs, variation data (SNPs, mutations), expression data, and cross-references to 200+ external databases (UniProt, Ensembl, HGNC, OMIM, Reactome). Supports programmatic access via E-utilities API (Entrez Programming Utilities) and NCBI Datasets API, bulk downloads, and web interface. Enables gene annotation, comparative genomics, variant interpretation, pathway analysis, and integration with other NCBI resources (PubMed, dbSNP, ClinVar). Use cases: gene information retrieval, variant annotation, functional genomics, disease gene discovery, and bioinformatics workflows
 - **Protein Data Bank (PDB)** - Worldwide repository for 3D structural data of proteins, nucleic acids, and biological macromolecules. Contains 200K+ experimentally determined structures from X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy. Provides comprehensive structure information including atomic coordinates, experimental data, structure quality metrics, ligand binding sites, protein-protein interfaces, and metadata (authors, methods, citations). Features advanced search capabilities (by sequence, structure similarity, ligand, organism, resolution), REST API and FTP access, structure visualization tools, and integration with analysis software. Supports structure comparison, homology modeling, drug design, structural biology research, and educational use. Maintained by wwPDB consortium (RCSB PDB, PDBe, PDBj, BMRB). Use cases: structural biology research, drug discovery, protein engineering, molecular modeling, and structural bioinformatics