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Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
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Query myvariant.info API for aggregated variant annotations from multiple databases (ClinVar, gnomAD, dbSNP, COSMIC, etc.) in a single request. Use when annotating variants with clinical and population data from multiple sources simultaneously.
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Process use when you need to archive historical database records to reduce primary database size. This skill automates moving old data to archive tables or cold storage (S3, Azure Blob, GCS). Trigger with phrases like "archive old database records", "implement data retention policy", "move historical data to cold storage", or "reduce database size with archival".
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Work with MongoDB (document database, BSON documents, aggregation pipelines, Atlas cloud) and PostgreSQL (relational database, SQL queries, psql CLI, pgAdmin). Use when designing database schemas, writing queries and aggregations, optimizing indexes for performance, performing database migrations, configuring replication and sharding, implementing backup and restore strategies, managing database users and permissions, analyzing query performance, or administering production databases.
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Builds professional search strategies for PubMed, Embase, Web of Science, and similar databases. Use when a user needs to construct a MeSH-based Boolean query, design a systematic review search, expand a concept with synonyms, apply study-type or date filters, or adapt a query across multiple databases. Also triggers when the user says "help me search for papers on X", "build a search strategy", "what are the MeSH terms for", or "I need a systematic review search string".
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Expert database administrator specializing in modern cloud databases, automation, and reliability engineering. Masters AWS/Azure/GCP database services, Infrastructure as Code, high availability, disaster recovery, performance optimization, and compliance. Handles multi-cloud strategies, container databases, and cost optimization. Use PROACTIVELY for database architecture, operations, or reliability engineering.
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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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Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests. Use when annotating variant lists from multiple databases simultaneously without managing per-source APIs, and when reproducibility-grade analyses require recording source data versions via _meta.
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Prioritizes rare-disease variants from trio/quad WES/WGS with de novo (DeNovoGear, Triodenovo), compound-heterozygous phasing (WhatsHap), mosaic VAF tiering, phenotype-driven ranking (Exomiser, Phen2Gene, AMELIE), ClinGen gene-disease validity gating, and ACMG SF v3.2 secondary findings reporting. Use when running diagnostic exome / genome pipelines, identifying candidate Mendelian disease genes, screening for incidental findings, or auditing VUS reclassification cycles. The ACMG/AMP classification framework (PVS1 decision tree, Pejaver PP3/BP4 calibration, Tavtigian point system) is in clinical-databases/acmg-classification.
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Resolves rsIDs, navigates RsMergeArch/SNPHistory merge chains, and converts between rsID, SPDI, HGVS, and VCF representations using the dbSNP Build 156 JSON architecture. Use when normalizing variant identifiers, joining variant databases by cluster ID, or tracking deprecated rsIDs through historical merges.
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Reads from, writes to, and manages relational databases using MATLAB Database Toolbox. Use when connecting to databases, reading data with sqlread or fetch, filtering with rowfilter, writing with sqlwrite, updating with sqlupdate, executing SQL statements, managing transactions with commit and rollback, mapping MATLAB classes to tables with ORM (Mappable, ormread, ormwrite, ormupdate), or performing any database operation from MATLAB. Triggers on: database, SQL, sqlread, sqlwrite, sqlupdate, fetch, execute, rowfilter, RowFilter, ORM, Mappable, ormread, ormwrite, ormupdate, orm2sql, transaction, commit, rollback, Database Toolbox, PostgreSQL, MySQL, SQLite, SQL Server, Oracle, database connection, database table, query database, insert data, update rows, delete rows, stored procedure, prepared statement, odbc, databaseConnectionOptions, datasource, data source, DSN, connection string, multithreaded, parallel.
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Provision Cloud SQL and Spanner databases. Configure high availability, backups, and security. Use when deploying managed databases on GCP.
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Provision and manage RDS databases. Configure backups, replication, and security. Use when deploying managed relational databases on AWS.
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AWS RDS relational database service for managed databases. Use when provisioning databases, configuring backups, managing replicas, troubleshooting connectivity, or optimizing performance.
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Expert blueprint for data-oriented design using Resource/RefCounted classes (item databases, character stats, reusable data structures). Covers typed arrays, serialization, nested resources, and resource caching. Use when implementing data systems OR inventory/stats/dialogue databases. Keywords Resource, RefCounted, ItemData, CharacterStats, database, serialization, @export, typed arrays.
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Expert blueprint for data-oriented design using Resource/RefCounted classes (item databases, character stats, reusable data structures). Covers typed arrays, serialization, nested resources, and resource caching. Use when implementing data systems OR inventory/stats/dialogue databases. Keywords Resource, RefCounted, ItemData, CharacterStats, database, serialization, @export, typed arrays.
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Use this skill AUTOMATICALLY before writing any Higgsfield prompt. Query the memory databases for relevant past failures and pre-apply known fixes before the user even hits generate. Triggers include: any request to write a Higgsfield prompt, any use of the higgsfield-prompt skill, any mention of generating a video or image on Higgsfield, any MCSLA prompt construction. This skill should run SILENTLY in the background — don't announce it, just apply what's known. If the databases are empty, skip silently and proceed with normal prompt generation.
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Relational database implementation across Python, Rust, Go, and TypeScript. Use when building CRUD applications, transactional systems, or structured data storage. Covers PostgreSQL (primary), MySQL, SQLite, ORMs (SQLAlchemy, Prisma, SeaORM, GORM), query builders (Drizzle, sqlc, SQLx), migrations, connection pooling, and serverless databases (Neon, PlanetScale, Turso).
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Execute read-only SQL queries against multiple PostgreSQL databases. Use when: (1) querying PostgreSQL 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.
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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.
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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.
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Work with MongoDB (document database, BSON documents, aggregation pipelines, Atlas cloud) and PostgreSQL (relational database, SQL queries, psql CLI, pgAdmin). Use when designing database schemas, writing queries and aggregations, optimizing indexes for performance, performing database migrations, configuring replication and sharding, implementing backup and restore strategies, managing database users and permissions, analyzing query performance, or administering production databases.
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Unified CLI/Python interface to 20+ genomic databases. Gene lookups (Ensembl search/info/seq), BLAST/BLAT, AlphaFold, Enrichr enrichment, OpenTargets disease/drug, CELLxGENE single-cell, cBioPortal/COSMIC cancer, ARCHS4 expression. Spans genomics, proteomics, disease. For batch/advanced BLAST use biopython; for multi-DB Python SDK use bioservices.
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Access and utilize open construction pricing databases. Match BIM elements to standardized work items, calculate costs using public unit price databases with 55,000+ work items.
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