Results for “database”

Expert database optimizer specializing in modern performance tuning, query optimization, and scalable architectures. Masters advanced indexing, N+1 resolution, multi-tier caching, partitioning strategies, and cloud database optimization. Handles complex query analysis, migration strategies, and performance monitoring. Use PROACTIVELY for database optimization, performance issues, or scalability challenges.

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Designs database schemas, indexing strategies, query optimization, and migration patterns for SQL and NoSQL databases. Use when designing tables, optimizing queries, fixing N+1 problems, planning migrations, or when asked about database performance, normalization, ORMs, or data modeling.

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Query protein-protein and gene interaction databases (STRING, BioGRID, IntAct, SIGNOR, Reactome, HuRI, HuMAP, OmniPath, ConsensusPathDB, DIP). Use when building PPI networks, choosing between physical vs functional vs genetic interactions, signed/directed vs undirected, high-throughput vs curated, picking confidence thresholds, aggregating across resources, or navigating license constraints. Encodes the database decision matrix, STRING v12 channel semantics, OmniPath as meta-database, SIGNOR for signed signaling, and per-resource rate limits.

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Build local BLAST databases and run searches using NCBI BLAST+ command-line tools. Use when running >50 queries, building custom databases with -parse_seqids and -taxid, downloading prebuilt NCBI databases via update_blastdb.pl, choosing -task variants (megablast/dc-megablast/blastn/blastn-short), tuning soft/hard masking, scaling threads, or extracting hits with blastdbcmd. Encodes BLAST v5 vs v4 database format, taxonomy filtering, makeblastdb pitfalls.

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Use DuckDB from MATLAB via Database Toolbox (R2026a+) as a non-math operations engine on large tabular files (CSV/Parquet/JSON) and as a zero-config embedded database. Use when connecting to DuckDB, querying CSV, Parquet, and JSON files directly with SQL, reducing or profiling large data before MATLAB analysis, creating portable development databases, or installing DuckDB extensions. Triggers on: DuckDB, duckdb(), large CSV/Parquet/JSON, file too large for readtable, filter/aggregate at source, deduplicate, reduce before analysis, profile large file, persistent file import, analytical engine, SQL on CSV, SQL on Parquet, SQL on JSON, query CSV with SQL, query Parquet with SQL, run SQL on files, SQL queries on files, query files directly, SQL without database, in-process SQL.

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[Deprecated] This is the required documentation for agents operating on the CloudBase Relational Database through MCP. It defines the canonical SQL management flow with `queryMysqlDatabase`, `manageMysqlDatabase`, `queryPermissions`, and `managePermissions`, including destroy flow, async status checks, safe query execution, schema initialization, and permission updates. MySQL provisioning is no longer available through MCP; new environments should use PostgreSQL — see postgresql-development skill instead.

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Generate database seed scripts with realistic sample data. Reads Drizzle schemas or SQL migrations, respects foreign key ordering, produces idempotent TypeScript or SQL seed files. Handles D1 batch limits, unique constraints, and domain-appropriate data. Use when populating dev/demo/test databases. Triggers: 'seed database', 'seed data', 'sample data', 'populate database', 'db seed', 'test data', 'demo data', 'generate fixtures'.

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This skill should be used when the user asks to "optimize SQL queries", "explore database schemas", "generate migration SQL", "analyze query performance", or "document database structure".

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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.

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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.

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SQLAlchemy and database patterns for Python. Triggers on: sqlalchemy, database, orm, migration, alembic, async database, connection pool, repository pattern, unit of work.

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Create and manage database migrations with reversible changes, proper naming conventions, and zero-downtime deployment strategies. Use this skill when creating database migration files, modifying schema, adding or removing tables/columns, managing indexes, or handling data migrations. Apply when working with migration files (e.g., db/migrate/, migrations/, alembic/, sequelize migrations), schema changes, database versioning, rollback implementations, or when you need to ensure backwards compatibility during deployments. Use for any task involving database structure changes, index creation, constraint modifications, or data transformation scripts.

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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).

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Query COSMIC for cancer somatic mutations, gene census, mutational signatures, drug resistance variants. REST API v3.1 supports gene/sample/variant queries; free registration. For germline use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.

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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.

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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.

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Query openFDA REST API for adverse events (FAERS), labeling, product info, recalls, enforcement. Search by drug name, ingredient, MedDRA, or NDC. 1k req/day no key; 120k with free key. For trials use clinicaltrials-database-search; for structures use drugbank-database-access or chembl-database-bioactivity.

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Designs relational and document database schemas from requirements or an existing app - tables and collections, keys, relationships, constraints, indexes driven by real query patterns, ERDs, and reversible migration scripts - with PostgreSQL (including Supabase) as the default and MySQL, SQLite, and MongoDB supported. Use when the user wants to model data for a new app or feature, review or fix an existing schema, choose keys or indexes, plan multi-tenancy, normalize or denormalize, or write CREATE TABLE statements or migrations, even if they just describe their app and ask "how should I store this". For moving data between database providers, use database-migrator.

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Validate database integrity, test migrations forward and backward, verify schema constraints, manage seed data, detect migration drift, and identify query performance issues. Covers PostgreSQL, MySQL, MongoDB with Prisma, TypeORM, Drizzle, and SQLAlchemy, plus Testcontainers test databases. Use when: "database test," "migration test," "migration rollback," "rollback test," "data integrity," "SQL test," "schema validation," "seed data," "query performance," "Testcontainers." Not for: synthetic data generation/masking at scale — use test-data-management; Docker/IaC test-environment provisioning — use test-environments; SQL injection — use security-testing. Related: test-data-management, test-environments, security-testing, ci-cd-integration.

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Sets up automated database backup, restore, and disaster recovery procedures for PostgreSQL, MySQL, MongoDB, and Redis. Use when you need to implement backup schedules, point-in-time recovery, cross-region replication, backup verification, or disaster recovery runbooks. Trigger words: database backup, pg_dump, mysqldump, mongodump, disaster recovery, point-in-time recovery, WAL archiving, backup rotation, restore database, RTO, RPO, backup verification.

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Build database-powered applications with Baserow, the open-source no-code database. Use when a user asks to create spreadsheet databases, build API-connected workflows, manage relational data, or self-host Baserow as an Airtable alternative.

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Expert patterns for Neon serverless Postgres, branching, connection pooling, and Prisma/Drizzle integrationUse when "neon database, serverless postgres, database branching, neon postgres, postgres serverless, connection pooling, preview environments, database per preview, neon, postgres, serverless, database, branching, prisma, drizzle, connection-pooling" mentioned.

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Firebase gives you a complete backend in minutes - auth, database, storage, functions, hosting. But the ease of setup hides real complexity. Security rules are your last line of defense, and they're often wrong. Firestore queries are limited, and you learn this after you've designed your data model. This skill covers Firebase Authentication, Firestore, Realtime Database, Cloud Functions, Cloud Storage, and Firebase Hosting. Key insight: Firebase is optimized for read-heavy, denormalized data. If you're thinking relationally, you're thinking wrong. 2025 lesson: Firestore pricing can surprise you. Reads are cheap until they're not. A poorly designed listener can cost more than a dedicated database. Plan your data model for your query patterns, not your data relationships. Use when "firebase, firestore, firebase auth, cloud functions, firebase storage, realtime database, firebase hosting, firebase emulator, security rules, firebase admin, firebase, firestore, cloud-functions, serverless, backend, realtime, authentication, google-cloud" mentioned.

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Expert at evolving database schemas safely. Covers migration strategies, zero-downtime deployments, rollback planning, and data transformation. Knows how to change production schemas without breaking running applications. Use when "database migration, schema change, add column, alter table, drizzle migrate, prisma migrate, zero downtime migration, rollback migration, database, migrations, schema, drizzle, prisma, postgresql, zero-downtime" mentioned.

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