2,108 件 ・ 関連度順
概要と使いどころ
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.
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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.
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Query DDInter drug-drug interactions via REST API (1.7M+ interactions, 2,400+ drugs). Search by drug name/ID for severity (major/moderate/minor), mechanisms, and clinical recommendations. No auth. For FDA labeling use dailymed-database; for pharmacogenomics use clinpgx-database.
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Look up EMDB cryo-EM density maps and fitted atomic models via the entry REST API + EBI Search WS. Fetch entry metadata (resolution, method, organism, sample), map download URLs, fitted PDB IDs, and citations. Keyword search via EBI Search. No auth. For atomic coordinates use pdb-database; for AlphaFold predictions use alphafold-database-access.
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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.
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Query the ZINC22 virtual compound library (CartBlanche API, billions of make-on-demand + purchasable molecules). Look up substances by ZINC ID, resolve a SMILES to its ZINC ID (exact match), inspect purchasability/catalogs, and assemble compound sets for docking. Property (MW/logP) filtering is done locally with RDKit. For bioactivity use chembl-database-bioactivity; for approved drugs use drugbank-database-access.
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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.
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Query bioRxiv/medRxiv preprints via REST API. Search by DOI, category, or date range; retrieve metadata (title, abstract, authors, category, DOI, version history) and PDFs. No auth. For peer-reviewed biomedical use pubmed-database; broader scholarly search use openalex-database.
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Query InterPro REST API for protein domain architecture, family classification, and member-DB integration. Search entries, retrieve a protein's domains, list family members, get taxonomic distribution, link to PDB. Unifies Pfam, PANTHER, PIRSF, PRINTS, PROSITE, SMART, CDD, NCBIfam. Use uniprot-protein-database for sequences; pdb-database for 3D structures.
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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.
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Parse HMDB (Human Metabolome Database) local XML for metabolite info, chemical properties, biological context, disease links, spectra, and cross-DB mapping. No REST API — uses ~6 GB XML download. Use drugbank-database-access for drugs; pubchem-compound-search for live lookups.
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Provides patterns to implement persistence layers with Spring Data JPA. Use when creating repositories, configuring entity relationships, writing queries (derived and `@Query`), setting up pagination, database auditing, transactions, UUID primary keys, multiple databases, and database indexing.
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Debug "API returns data that doesn't exist in database" when multiple Kubernetes clusters exist (production, staging, POC). Use when: (1) REST API returns records that direct database queries can't find, (2) Data counts match approximately but specific records don't overlap, (3) kubectl context points to a different cluster than the one serving the public domain, (4) ClickHouse/Postgres queries return stale or different data than the API, (5) "completely different datasets" despite same table names and schemas. Root cause: querying the wrong cluster's database.
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Design normalized database schemas with tables, relationships, indexes, and constraints for any application domain. Use when the user requests database schema design or provides relevant inputs for this workflow.
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Populate databases with realistic, reproducible test data for development, testing, and staging environments. Use when the user requests database seeding or provides relevant inputs for this workflow.
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Create, schedule, and verify database backups with support for full, incremental, and point-in-time recovery strategies. Use when the user requests database backup or provides relevant inputs for this workflow.
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Create, execute, and roll back versioned database schema migrations using tools like Alembic, Prisma Migrate, Flyway, and Knex. Use when the user requests database migration or provides relevant inputs for this workflow.
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Research and evaluate database lookup with current authoritative sources, provenance, and explicit evidence gaps. Use when the user asks for database lookup findings or verification.
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Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink). Use when navigating gene to protein/structure, sequence to publication, PubMed to GEO, BioProject to SRA runs, or discovering all link relationships for a record. Covers linkname semantics, cmd= variants, asymmetric link warnings, neighbor_history for >200 input IDs, and per-database link tables.
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Structure similarity search with Foldseek. Use this skill when: (1) Finding similar structures in PDB/AFDB databases, (2) Structural homology search, (3) Database queries by 3D structure, (4) Finding remote homologs not detected by sequence, (5) Clustering structures by similarity. For sequence similarity, use uniprot BLAST. For structure prediction, use chai or boltz.
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Think and work like an expert Database Systems Researcher. Use when a task calls for Database Systems Researcher judgment. Reasons from storage hierarchy, concurrency semantics, query-optimization theory, and declared workload models through TPC-C/H, YCSB, and JOB benchmarks, Jepsen/Elle correctness checkers, and perf/blktrace/fio profiling while treating cardinality-estimation plan regressions, tail-latency spikes under skew, unfair fsync-disabled speedups, and benchmark-trick wins as first-class failure modes.
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Expert at diagnosing and fixing performance bottlenecks across the stack. Covers Core Web Vitals, database optimization, caching strategies, bundle optimization, and performance monitoring. Knows when to measure vs optimize. Use when "slow page load, performance optimization, core web vitals, bundle size, lighthouse score, database slow, memory leak, optimize performance, speed up, reduce load time, performance, optimization, core-web-vitals, caching, profiling, bundle-size, database" mentioned.
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Expert knowledge for Drizzle ORM - the lightweight, type-safe SQL ORM for edge and serverlessUse when "drizzle, drizzle orm, drizzle-kit, drizzle schema, drizzle migration, drizzle relations, sql orm typescript, edge database, d1 database, orm, database, typescript, sql, edge, serverless, d1, postgres, mysql, sqlite" mentioned.
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World-class backend engineering - distributed systems, database architecture, API design, and the battle scars from scaling systems that handle millions of requestsUse when "backend, api, database, postgres, mysql, mongodb, redis, graphql, rest, authentication, authorization, caching, queue, background job, webhook, migration, transaction, n+1, rate limit, server, node.js, python, go, backend, api, database, architecture, performance, reliability, security" mentioned.
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