Database Claude Skills
1 639 database skills from 232 authors. They work on schemas, queries and moving data between them. Half of them fit into 2 210 tokens or less — that is what one costs your context window when the agent loads it. 286 ship runnable scripts rather than instructions alone. 7 of them cannot work without an MCP server, most often rube. We also found 387 copies of these same skills sitting in other people's repositories — counted once here, not 387 times.
1 639 unique 232 authors 5 updated this month 163 from vendors
KEGG REST API (academic only). Pathways, genes, compounds, enzymes, diseases, drugs via 7 ops (info/list/find/get/conv/link/ddi). ID conversion (NCBI/UniProt/PubChem). Use bioservices for multi-DB Python.
Query Metabolomics Workbench REST API (4,200+ NIH studies) for metabolite ID, study discovery, RefMet standardization, m/z precursor searches, and gene/protein annotations. Quirks: compound input_item rejects `name` (use pubchem_cid/kegg_id/inchi_key/etc.); free-text → compound is a two-step refmet/match→refmet/name flow; moverz endpoint returns TSV text, not JSON. Use hmdb-database for local XML; pubchem-compound-search for general compound lookup.
Monarch Initiative knowledge graph REST API for disease-gene-phenotype associations and cross-species orthology. MONDO disease-to-gene/phenotype, HP phenotype profiles, cross-species comparisons. Use for rare disease gene prioritization and phenotype-based candidate ranking. For GWAS use gwas-database; for clinical pathogenicity use clinvar-database.
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure metadata, pull strain-level means (raw or LS-mean adjusted) and per-animal values, find measures by MP/VT ontology terms, and resolve strain nomenclature or gene coordinates. Use for QTL support, cross-strain comparison, mouse model selection, and ontology-driven phenotype discovery. Use monarch-database for disease-gene-phenotype knowledge graphs; ensembl-database for mouse genome annotations.
Query OpenAlex REST API for 250M+ scholarly works, authors, institutions, journals, concepts. Search by keyword, author, DOI, ORCID, or ID; filter by year, OA, citations, field; retrieve citations, references, author disambiguation. Free, no auth. For PubMed use pubmed-database; preprints use biorxiv-database.
Query Open Targets GraphQL API for target-disease associations, evidence, drug links, safety. Search targets by gene, diseases by EFO ID; scores from 20+ sources, drug mechanisms, tractability. For ChEMBL use chembl-database-bioactivity; for trials use clinicaltrials-database-search.
Query RCSB PDB (200K+ structures) via the public REST + GraphQL APIs with plain `requests` (no SDK). Search by text, attribute, sequence, or 3D structure similarity (Search API); retrieve metadata via GraphQL (Data API); download PDB/mmCIF from files.rcsb.org. For AlphaFold predictions use alphafold-database-access; for protein sequences only use uniprot-protein-database.
Search the PRIDE Archive v3 REST API for proteomics datasets: discover projects by keyword + faceted filters (organism, instrument, disease, software), fetch project metadata, list and download RAW/PEAK/RESULT/FASTA files (with FTP/Aspera URLs), look up which projects mention a UniProt accession, and find similar projects. PRIDE v3 no longer exposes peptide/PSM-level identification endpoints — for spectrum-level data download the project's RESULT files. Use uniprot-protein-database for protein sequences; interpro-database for domain architecture.
Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download annotations filtered by taxon, evidence code, aspect. Use for GO resolution, ontology traversal, annotation retrieval before enrichment. Use gseapy-gene-enrichment for enrichment; uniprot-protein-database for proteins.
Query Reactome pathways via REST: pathway queries, entity lookup, keyword search, gene list enrichment, hierarchy, cross-refs. Content + Analysis services. Python wrapper: reactome2py. For KEGG use kegg-database; for PPIs use string-database-ppi.
Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks, footprints, motifs, eQTLs, chromatin state). Scores range 1a (strongest) to 7 (none). Use for GWAS hit prioritization, regulatory variant annotation, cis-regulatory discovery. Use clinvar-database for pathogenicity; gwas-database for trait associations.
Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by species, peaks filtered by biotype (promoter, enhancer), and BED files for a TF-cell type pair. Use for TF co-occupancy, regulatory annotation, and TF binding atlases. Use jaspar-database for PWM motifs; encode-database for ENCODE tracks.
Query STRING REST API for PPIs (59M proteins, 20B interactions, 5000+ species). Retrieve networks, run GO/KEGG enrichment, find partners, test PPI significance, visualize networks, analyze homology. For chemical interactions use chembl-database-bioactivity; pathways use kegg-database.
Cross-reference compound IDs across 20+ databases (ChEMBL, DrugBank, PubChem, ChEBI, PDB, SureChEMBL, HMDB, DrugCentral, BindingDB) via UniChem REST API. Resolve InChIKeys to source IDs, translate between source-specific IDs, find structurally related compounds by connectivity. POST with a JSON body for all cross-reference queries; only /sources is GET. No auth required.
Access USPTO patent data via PatentsView REST API and Google Patents Public Data (BigQuery). Search by inventor, assignee, CPC, or keywords; download metadata and claims; analyze portfolios; track tech trends. For IP landscape analysis, competitor monitoring, prior art search, and tech forecasting in life sciences and biotech.
Query ZINC15/ZINC22 virtual compound libraries (1.4B compounds, 750M purchasable). Search lead/fragment/drug-like compounds by MW, logP, reactivity, or SMILES similarity; download 3D sets for docking. For bioactivity use chembl-database-bioactivity; for approved drugs use drugbank-database-access.
>- Provision instant temporary Postgres databases via Claimable Postgres by Neon (neon.new) with no login, signup, or credit card. Supports REST API, CLI, and SDK. Use when users ask for a quick Postgres environment, a throwaway DATABASE_URL for prototyping/tests, or "just give me a DB now". Triggers "no credit card database", "instant DATABASE_URL", "npx neon-new", "neon.new", "neon.new API", "claimable postgres API".
PostgreSQL-specific code review assistant focusing on PostgreSQL best practices, anti-patterns, and unique quality standards. Covers JSONB operations, array usage, custom types, schema design, function optimization, and PostgreSQL-exclusive security features like Row Level Security (RLS).
Work with MongoDB databases using best practices. Use when designing schemas, writing queries, building aggregation pipelines, or optimizing performance. Triggers on MongoDB, Mongoose, NoSQL, aggregation pipeline, document database, MongoDB Atlas.
Execute read-only SQL queries against multiple Microsoft SQL Server databases. Use when: (1) querying MSSQL/SQL Server databases, (2) exploring database schemas/tables, (3) running SELECT queries for data analysis, (4) checking database contents. Supports multiple database connections with descriptions for intelligent auto-selection. Blocks all write operations (INSERT, UPDATE, DELETE, DROP, etc.) for safety.
Execute read-only SQL queries against multiple MySQL databases. Use when: (1) querying MySQL databases, (2) exploring database schemas/tables, (3) running SELECT queries for data analysis, (4) checking database contents. Supports multiple database connections with descriptions for intelligent auto-selection. Blocks all write operations (INSERT, UPDATE, DELETE, DROP, etc.) for safety.
PostgreSQL-specific development assistant focusing on unique PostgreSQL features, advanced data types, and PostgreSQL-exclusive capabilities. Covers JSONB operations, array types, custom types, range/geometric types, full-text search, window functions, and PostgreSQL extensions ecosystem.
Design a PostgreSQL-specific schema. Covers best-practices, data types, indexing, constraints, performance patterns, and advanced features
Universal SQL performance optimization assistant for comprehensive query tuning, indexing strategies, and database performance analysis across all SQL databases (MySQL, PostgreSQL, SQL Server, Oracle). Provides execution plan analysis, pagination optimization, batch operations, and performance monitoring guidance.
Deploy applications on Railway platform. Use when deploying containerized apps, setting up databases, configuring private networking, or managing Railway projects. Triggers on Railway, railway.app, deploy container, Railway database.
SQLAlchemy and database patterns for Python. Triggers on: sqlalchemy, database, orm, migration, alembic, async database, connection pool, repository pattern, unit of work.
PostgreSQL database documentation - SQL queries, database design, administration, performance tuning, and advanced features. Use when working with PostgreSQL databases, writing SQL, or managing database systems.
TimescaleDB - PostgreSQL extension for high-performance time-series and event data analytics, hypertables, continuous aggregates, compression, and real-time analytics
PROACTIVELY query the code graph database to understand relationships and impact of changes. Use this skill WHEN READING any file to understand context, when searching for files, when exploring the codebase, or when you need to understand what depends on a component. This is your primary tool for understanding code structure and avoiding breaking changes.
Implement caching strategies using @delon/cache. Use this skill when adding memory cache, LocalStorage cache, SessionStorage cache, or cache interceptors for HTTP requests. Supports TTL-based expiration, cache invalidation, cache grouping, and persistent storage. Optimizes performance by reducing redundant API calls and database queries.
SQL query optimization and database performance specialist. Use when optimizing slow queries, fixing N+1 problems, designing indexes, implementing caching, or improving database performance. Works with PostgreSQL, MySQL, and other databases.
Comprehensive backend development skill for building scalable backend systems using NodeJS, Express, Go, Python, Postgres, GraphQL, REST APIs. Includes API scaffolding, database optimization, security implementation, and performance tuning. Use when designing APIs, optimizing database queries, implementing business logic, handling authentication/authorization, or reviewing backend code.
Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.
Efficient database search tool for bioRxiv preprint server. Use this skill when searching for life sciences preprints by keywords, authors, date ranges, or categories, retrieving paper metadata, downloading PDFs, or conducting literature reviews.
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct REST control, use individual database skills (uniprot-database, kegg-database).
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
Query NCBI ClinVar for variant clinical significance. Search by gene/position, interpret pathogenicity classifications, access via E-utilities API or FTP, annotate VCFs, for genomic medicine.
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic research.
Query openFDA API for drugs, devices, adverse events, recalls, regulatory submissions (510k, PMA), substance identification (UNII), for FDA regulatory data analysis and safety research.
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
Access NCBI GEO for gene expression/genomics data. Search/download microarray and RNA-seq datasets (GSE, GSM, GPL), retrieve SOFT/Matrix files, for transcriptomics and expression analysis.
Systematic database and table profiling for DBX Studio. Use when a user wants to understand their data, explore schema structure, or profile a dataset.
Systematic database and table profiling for DBX Studio. Use when a user wants to understand their data, explore schema structure, or profile a dataset.
Expert SQL query generation for DBX Studio. Use when writing, optimizing, or debugging SQL queries against user database connections.
Expert SQL query generation for DBX Studio. Use when writing, optimizing, or debugging SQL queries against user database connections.
Create reversible, focused database migrations with proper naming, version control practices, and zero-downtime deployment considerations. Use this skill when creating or editing migration files in database/migrations/, when writing schema changes (creating/modifying tables, columns, indexes, foreign keys), when implementing migration rollback methods, when managing database version control, when adding or modifying indexes on large tables, or when separating schema changes from data migrations for safer deployments.
Define and configure database models with proper naming, relationships, timestamps, data types, constraints, and validation. Use this skill when creating or editing model files in app/Models/, Eloquent model classes, model relationships (hasMany, belongsTo, etc.), database table structures, model attributes and casts, model factories, or seeders. Use when working on model validation logic, database constraints, foreign key relationships, indexes, scopes, accessors, mutators, or any ORM-related model configuration.