Databases Skills

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

> CHARLS (China Health and Retirement Longitudinal Study) database-specific knowledge for reproducing published papers. Use when reproducing or analyzing papers that use CHARLS data, including variable mapping from harmonized to raw questionnaire items, cognitive function scoring (episodic memory, mental status, TICS), CESD-10 depression screening, social isolation index construction, and chronic disease coding. Also use for any CHARLS data cleaning, variable construction, or cohort selection task.

Search ChEMBL bioactive molecules database with natural language queries. Find compounds and assay data with Valyu semantic search.

Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.

Gene set enrichment analysis with correct geneset format handling. Critical guidance for loading pathway databases and running enrichment in OmicVerse.

Provide comprehensive clinical interpretation of somatic mutations in cancer. Given a gene symbol + variant (e.g., EGFR L858R, BRAF V600E) and optional cancer type, performs multi-database analysis covering clinical evidence (CIViC), mutation prevalence (cBioPortal), therapeutic associations (OpenTargets, ChEMBL, FDA), resistance mechanisms, clinical trials, prognostic impact, and pathway context. Generates an evidence-graded markdown report with actionable recommendations for precision oncology. Use when oncologists, molecular tumor boards, or researchers ask about treatment options for specific cancer mutations, resistance mechanisms, or clinical trial matching.

Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open Targets Genetics, ClinVar). Retrieves variant annotations, GWAS trait associations, fine-mapping evidence, locus-to-gene predictions, and clinical significance. Use when asked to interpret a SNP by rsID, find disease associations for a variant, assess clinical significance, or answer questions like "What diseases is rs429358 associated with?" or "Interpret rs7903146".

Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate metabolites (HMDB IDs, chemical properties, pathways), retrieve metabolomics study information from MetaboLights (MTBLS*) or Metabolomics Workbench (ST*), search for studies by keywords or disease, or generate comprehensive metabolomics research reports.

Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes structural data. No API key required for core functionality (STRING). Use when analyzing protein networks, discovering interaction partners, identifying functional modules, or studying protein complexes.

Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. Creates detailed reports with sequence metadata, cross-database references, and download options. Use when users need nucleotide sequences, protein sequences, genome data, or mention GenBank, RefSeq, EMBL accessions.

Comprehensive systems biology and pathway analysis using multiple pathway databases (Reactome, KEGG, WikiPathways, Pathway Commons, BioModels). Performs pathway enrichment, protein-pathway mapping, keyword searches, and systems-level analysis. Use when analyzing gene sets, exploring biological pathways, or investigating systems-level biology.

| Skills for querying and downloading data from genomic, transcriptomic, 3D-genome, and cancer-genomics databases. Covers programmatic access to public repositories, gene annotation, sequence retrieval, processed functional-genomics tracks, Hi-C / Micro-C contact matrices, TCGA-style cohorts, and large-scale single-cell data.

> pathways, ChEMBL/ChEBI/PubChem, BLAST, cross-database ID mapping, GO annotations, PPI. For deep single-DB queries use dedicated tools (gget for Ensembl, pubchempy for PubChem); bioservices excels at cross-database workflows.

Cancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use dgidb-database.

Query PubChem (110M+ compounds) directly via the PUG-REST/JSON API with plain `requests` — no SDK install required. Search by name/CID/SMILES/InChIKey/formula, retrieve properties (MW, XLogP, TPSA, H-bond counts), do similarity/substructure searches with async ListKey polling, fetch synonyms, descriptions, assay summaries, and download SDF/PNG. For local cheminformatics use rdkit; for bioactivity-centric workflows use chembl-database-bioactivity.

Query UniProt REST API: search by gene/protein name, fetch FASTA, map IDs (Ensembl, PDB, RefSeq), access Swiss-Prot annotations. Use bioservices for multi-DB access; alphafold-database for structures.

Log all chat messages to a SQLite database for searchable history and audit. Use when: (1) Building chat history, (2) Auditing conversations, (3) Searching past messages, or (4) User asks to log chats.

Query SQLite, PostgreSQL, and MySQL databases and export results to CSV/JSON. Use when: (1) Extracting data for reports, (2) Database backup and migration, (3) Data analysis workflows, or (4) Automated database queries.

Log all file changes (write, edit, delete) to a SQLite database for debugging and audit. Use when: (1) Tracking code changes, (2) Debugging issues, (3) Auditing file modifications, or (4) The user asks to track file changes.

>- Distributed traces, spans, service dependencies, and request flow analysis. Use when investigating span-level details, failures, performance bottlenecks, or trace correlation. "distributed trace", "span details", "HTTP status codes in traces", "database query spans", "messaging spans", "gRPC calls", "Lambda cold starts", "trace ID lookup", "exception analysis", "correlate logs and traces", "request attributes". Do NOT use for explaining existing queries, product documentation or configuration questions, service-level RED metrics (use dt-obs-services), log searching (use dt-obs-logs), or problem analysis (use dt-obs-problems).

> Odoo 17 development reference for Python models and ORM (search, domain, read_group, compute fields), XML/CSV data and views, OWL/JS client code, QWeb reports, security (ACL, record rules, groups), cron and server actions, migrations and module upgrades, tests, i18n, and performance. Use this skill whenever work involves Odoo 17 or custom addons—even if the user only pastes a traceback, mentions addons/ or __manifest__.py, describes form/tree/kanban/XML errors, HTTP controllers, or business rules on models—including building features, fixing bugs, refactoring, or reviewing addon code.

> Odoo 16 development reference for Python models and ORM (search, domain, read_group, compute fields), XML/CSV data and views, OWL/JS client code, QWeb reports, security (ACL, record rules, groups), cron and server actions, migrations and module upgrades, tests, i18n, and performance. Use this skill whenever work involves Odoo 16 or custom addons—even if the user only pastes a traceback, mentions addons/ or __manifest__.py, describes form/tree/kanban/XML errors, HTTP controllers, or business rules on models—including building features, fixing bugs, refactoring, or reviewing addon code.

> Odoo 18 development reference for Python models and ORM (search, domain, read_group, compute fields), XML/CSV data and views, OWL/JS client code, QWeb reports, security (ACL, record rules, groups), cron and server actions, migrations and module upgrades, tests, i18n, and performance. Use this skill whenever work involves Odoo 18 or custom addons—even if the user only pastes a traceback, mentions addons/ or __manifest__.py, describes form/list/kanban/XML errors, HTTP controllers, or business rules on models—including building features, fixing bugs, refactoring, or reviewing addon code.

Everything about the data layer — pick one of six ready-to-run backend templates (TanStack Start + Drizzle + better-auth, Hono + Drizzle + better-auth, Hono + Prisma + better-auth, Hono + Drizzle + Auth.js/NextAuth, FastAPI + SQLAlchemy + JWT, Supabase) and wire the frontend to it through the Repository + AuthProvider seams; scaffold a CRUD resource (Postgres table + server fns + query hooks + DataTable page + create/edit dialog + sidebar entry); bind or swap one resource's data source (Drizzle / REST / GraphQL / in-memory); or re-point the whole app's data + auth at a different backend. Use when adding a data entity or pointing the app at a backend other than the default Postgres + better-auth.

Delegates dbt and warehouse work to altimate-code, a specialized CLI agent with 100+ purpose-built data tools. USE THIS SKILL FIRST whenever the task mentions or implies: warehouse access (Snowflake, BigQuery, Redshift, Databricks, Postgres, MySQL, DuckDB), column-level lineage, downstream-impact analysis, dbt builds against a real warehouse, cross-database migration or validation, query cost attribution, schema diff, data parity checking, PII detection from sampled rows, incremental/SCD2/backfill verification, FinOps reporting, model documentation generation, query optimization, anomaly detection, dev-vs-prod diffing, or when the user says "altimate", "altimate-code", or "the data agent". Strongly preferred over Read/Write/Edit whenever the task touches live data, lineage, or warehouse state — consult before doing the work yourself.

| (1) Task mentions "fix", "error", "broken", "failing", "debug", "wrong", or "not working" (2) Compilation Error, Database Error, or test failures occur (3) Model produces incorrect output or unexpected results (4) Need to troubleshoot why a dbt command failed Reads full error, checks upstream first, runs dbt build (not just compile) to verify fix.

| (1) User provides a Snowflake query_id (UUID format) to analyze or optimize (2) Task mentions "slow query", "optimize", "query history", or "query profile" with a query ID (3) Analyzing query performance metrics - bytes scanned, spillage, partition pruning (4) User references a previously run query that needs optimization Fetches query profile, identifies bottlenecks, returns optimized SQL with expected improvements.

| (1) User provides or pastes a SQL query and asks to optimize, tune, or improve it (2) Task mentions "slow query", "make faster", "improve performance", "optimize SQL", or "query tuning" (3) Reviewing SQL for performance anti-patterns (function on filter column, implicit joins, etc.) (4) User asks why a query is slow or how to speed it up

Agent-callable Notion tools for searching pages and databases, reading and creating pages, querying data sources, appending content, and managing schemas. Use when the user mentions Notion or wants to find, read, create, or edit Notion content, even if they don't name Notion explicitly.

Fix bugs and broken behavior when there is enough evidence to act on a repair path. Use for errors, crashes, incorrect results, API failures (500, 404, 403), CORS problems, database exceptions, broken rendering, duplicated or wrong data, off-by-one mistakes, timezone/date bugs, broken forms, config-caused runtime failures, and regressions. Trigger when the user wants the bug repaired and the conversation already contains a clear failing area, a reproducible failing test, a concrete error path, or a prior diagnosis to implement. Do NOT use for new features, pure explanation, architecture discussion, broad research, or bug reports where the main need is figuring out why the behavior happens — use diagnose for that.

Database migration patterns and schema versioning

>- Build, fix, audit, and migrate Drift persistence in Dart CLI, server-side, and non-Flutter desktop apps. Use when adding SQLite with migrations, resolving build_runner or drift_dev failures, or validating Dart database code with code generation, analysis, tests, and migration checks.

Implement, fix, review, migrate, test, or debug Drift persistence in Flutter apps using SQLite, drift_flutter, type-safe Dart queries, generated tables, StreamBuilder or Riverpod StreamProvider UI, write operations, transactions, schema migrations, web assets, isolate sharing, and local database testing. Use when a Flutter task mentions drift, local database storage, SQLite, reactive database streams, CRUD, schemaVersion, build_runner, drift_dev make-migrations, migration tests, or Flutter-specific database setup across mobile, web, or desktop.

Build a safe recommendation plan for PlanetScale Postgres Database Traffic Control budgets and rules without applying them.

Collect read-only evidence about PlanetScale org, database, branches, webhooks, backups, roles, Insights, recommendations, and traffic configuration.

Use PlanetScale Insights and SQLCommenter-style query tags to attribute database load, identify risky queries, and prepare safe Traffic Control or schema recommendations.

Review PlanetScale Postgres for Traffic Control, query tags, roles, pg_strict, backups/PITR, private connectivity, webhooks, branches, and safe agent operation.

Review a PlanetScale Vitess database for safe migrations, deploy requests, schema recommendations, Insights, webhooks, and operational safety.

Enforce explicit approval gates for any PlanetScale, database, repository, credential, network, or automation mutation.

Search, query, and manage Weaviate vector database collections. Use for semantic search, hybrid search, keyword search, natural language queries with AI-generated answers, collection management, data exploration, filtered fetching, data imports from PDF/CSV/JSON/JSONL files, create example data and collection creation.

Diagnoses and fixes slow Neo4j Cypher queries by reading execution plans, identifying bad operators (AllNodesScan, CartesianProduct, Eager, NodeByLabelScan), and prescribing fixes (indexes, hints, query rewrites, runtime selection). Use when a query is slow, when EXPLAIN or PROFILE output needs interpretation, when dbHits or pageCacheHitRatio are poor, when cardinality estimation diverges from actuals, or when deciding between slotted/pipelined/parallel runtimes. Covers USING INDEX / USING SCAN / USING JOIN hints, db.stats.retrieve, SHOW QUERIES, SHOW TRANSACTIONS, TERMINATE TRANSACTION. Does NOT write new Cypher from scratch — use neo4j-cypher-skill. Does NOT cover GDS algorithm tuning — use neo4j-gds-skill. Does NOT cover index/constraint creation syntax details — use neo4j-cypher-skill references/indexes.md.

Programmatic security management in Neo4j — RBAC/ABAC, user lifecycle (CREATE/ALTER/DROP USER), role lifecycle (CREATE/GRANT ROLE/DROP ROLE), privilege grants and denies (GRANT/DENY/REVOKE on graph, database, DBMS), property-level access control, sub-graph access control, SHOW PRIVILEGES inspection, and auth provider config reference (LDAP, OIDC/SSO). Use when an agent needs to manage users, roles, or privileges programmatically via Cypher on the system database. Does NOT handle Cypher query writing — use neo4j-cypher-skill. Does NOT handle cluster ops or backups — use neo4j-cli-tools-skill. Property-level security and ABAC require Enterprise Edition.

Controls interactive terminal sessions for running long-lived processes, servers, REPLs, debuggers, and TUI programs without blocking. Use when you need to run dev servers (npm run dev), debuggers (pdb, gdb), REPLs (python, node), databases (psql, mysql), SSH sessions, or editors (vim, nano) — any interactive or blocking program.

This skill should be used when the user asks to "design system architecture", "evaluate microservices vs monolith", "create architecture diagrams", "analyze dependencies", "choose a database", "plan for scalability", "make technical decisions", or "review system design". Use for architecture decision records (ADRs), tech stack evaluation, system design reviews, dependency analysis, and generating architecture diagrams in Mermaid, PlantUML, or ASCII format.

Redis observability guidance — which metrics to monitor (memory, connections, hit ratio, ops/sec, rejected connections), which built-in commands to reach for during incident triage (SLOWLOG, INFO, MEMORY DOCTOR, CLIENT LIST, FT.PROFILE), and when to use the Redis Insight GUI. Use when setting up monitoring or alerts for a Redis instance, diagnosing a performance regression, profiling a slow FT.SEARCH query, or wiring Redis metrics into Prometheus, Datadog, or similar.

Redis Search guidance covering FT.CREATE schema design, field type selection (TEXT, TAG, NUMERIC, GEO, GEOSHAPE, VECTOR, JSON path), DIALECT 2 query syntax, FT.SEARCH / FT.AGGREGATE / FT.HYBRID command selection, vector similarity with HNSW or FLAT, hybrid retrieval combining lexical and vector ranking, RAG pipelines, zero-downtime index updates via aliases, and debugging with FT.PROFILE and FT.EXPLAIN. Use when defining a search index on Hash or JSON documents, writing FT.SEARCH queries with filters, sorting, aggregation, or vector KNN, tuning HNSW parameters, building a RAG retrieval pipeline, or troubleshooting slow or empty search results.

Redis client and connection guidance covering connection pooling, multiplexing, pipelining, client-side caching with RESP3, avoiding slow commands (KEYS, SMEMBERS, HGETALL), and tuning socket timeouts. Use when configuring a Redis client (redis-py, Jedis, Lettuce, NRedisStack), batching commands for throughput, eliminating per-request connection creation, iterating large keyspaces with SCAN, enabling client-side caching for read-heavy workloads, or setting connect and read timeouts.

Redis security guidance covering authentication (requirepass and ACL users), TLS, ACL-based least-privilege access control, restricting network exposure via bind and protected-mode, firewall rules, and disabling dangerous commands. Use when deploying Redis to production, defining ACL users for an application, configuring TLS connections, locking down a Redis instance behind a firewall, or auditing a Redis deployment for security hardening.