'databases' 검색 결과

Plan literature searches for six review types, from systematic to rapid reviews. Develop database-specific search queries, selection criteria, citation tracking, and search records, while comparing approaches for coverage, reproducibility, and available time.

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• Choose a review method for a research question
• Build search queries for multiple databases
• Map a research field and identify gaps

Draft and check a systematic literature review using PRISMA 2020, a reporting guideline for transparent reviews. Organize methods and findings into a Word manuscript, create a study selection flow diagram, and format references in APA 7th Edition style.

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• Drafting a first systematic literature review
• Turning a protocol or extraction sheet into a manuscript
• Creating a PRISMA study selection flow diagram

Direct REST API access to UniProt. Protein searches, FASTA retrieval, ID mapping, Swiss-Prot/TrEMBL. For broader biological evidence lookup across databases, use bio-database-evidence. Use this for direct HTTP/REST work or UniProt-specific control.

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Analyze git repositories to build a security ownership topology (people-to-file), compute bus factor and sensitive-code ownership, and export CSV/JSON for graph databases and visualization. Trigger only when the user explicitly wants a security-oriented ownership or bus-factor analysis grounded in git history (for example: orphaned sensitive code, security maintainers, CODEOWNERS reality checks for risk, sensitive hotspots, or ownership clusters). Do not trigger for general maintainer lists or non-security ownership questions.

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Implement efficient similarity search with vector databases. Use when building semantic search, implementing nearest neighbor queries, or optimizing retrieval performance.

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Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

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Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files. Use when working with geographic data for spatial analysis, geometric operations, coordinate transformations, spatial joins, overlay operations, choropleth mapping, or any task involving reading/writing/analyzing vector geographic data. Supports PostGIS databases, interactive maps, and integration with matplotlib/folium/cartopy. Use for tasks like buffer analysis, spatial joins between datasets, dissolving boundaries, clipping data, calculating areas/distances, reprojecting coordinate systems, creating maps, or converting between spatial file formats.

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Generate multiple sequence alignments (MSAs) for protein sequences using the ColabFold MSA-Search NIM. Use for homolog search, UniRef30/ColabFold env searches, A3M or FASTA alignments, paired MSA search for complexes, PDB70 structural templates, hosted NVIDIA API calls, or local Docker deployment. For local deployment, download the databases in parallel with aria2c and launch via NIM_MODEL_NAME (the recommended default fast path, ~14 min vs over 80 min for the built-in downloader); a plain docker run uses the slow built-in downloader.

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Automate Notion tasks via Rube MCP (Composio): pages, databases, blocks, comments, users. Always search tools first for current schemas.

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Identify domains, families, and sites in proteins; find all proteins in a family or sharing a domain; explore species distribution for a domain; annotate genomes with protein families and GO terms. InterPro combines 14 databases (e.g., Pfam, CDD) into one searchable resource. InterPro-N significantly expands annotation and sequence coverage with deep learning. Includes domain architecture (IDA) search.

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Retrieve protein and nucleotide sequences from NCBI databases using E-utilities. Supports direct accession lookup, CDS translation, gene+organism search, locus lookup, PubMed-linked sequences, patent protein extraction, and organism+length fallback search. Use when you need to fetch biological sequences by accession, gene name, locus tag, PubMed ID, or patent number.

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Performs 3D structural searches of proteins against various databases (PDB, AlphaFold, CATH, MGnify, etc.) using the Foldseek API. Use ONLY when the user provides a physical 3D coordinate file (.cif, .mmcif, or .pdb) and wants to find structurally similar proteins. Do NOT use if the user only provides a protein sequence, gene name, or UniProt ID.

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Search PubMed for scientific literature, including published clinical trials. Fetch abstracts and full text. Link published research to biological databases (gene, protein, nucleotide, PubChem) to discover associations between papers and specific compounds or genes. Verify medical spelling, match raw citations, and cache result sets for bulk processing. Interfaces NCBI E-utilities and PMC BioC APIs.

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Azure Storage Services including Blob Storage, File Shares, Queue Storage, Table Storage, and Data Lake. Answers questions about storage access tiers (hot, cool, cold, archive), when to use each tier, and tier comparison. Provides object storage, SMB file shares, async messaging, NoSQL key-value, and big data analytics. Includes lifecycle management. USE FOR: blob storage, file shares, queue storage, table storage, data lake, upload files, download blobs, storage accounts, access tiers, storage tiers, hot cool cold archive, storage tier comparison, when to use storage tiers, lifecycle management, Azure Storage concepts. DO NOT USE FOR: SQL databases, Cosmos DB (use azure-prepare), messaging with Event Hubs or Service Bus (use azure-messaging).

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Azure Resource Manager SDK for Cosmos DB in .NET. Use for MANAGEMENT PLANE operations: creating/managing Cosmos DB accounts, databases, containers, throughput settings, and RBAC via Azure Resource Manager. NOT for data plane operations (CRUD on documents) - use Microsoft.Azure.Cosmos for that. Triggers: "Cosmos DB account", "create Cosmos account", "manage Cosmos resources", "ARM Cosmos", "CosmosDBAccountResource", "provision Cosmos DB".

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Azure Resource Manager SDK for Azure SQL in .NET. Use for MANAGEMENT PLANE operations: creating/managing SQL servers, databases, elastic pools, firewall rules, and failover groups via Azure Resource Manager. NOT for data plane operations (executing queries) - use Microsoft.Data.SqlClient for that. Triggers: "SQL server", "create SQL database", "manage SQL resources", "ARM SQL", "SqlServerResource", "provision Azure SQL", "elastic pool", "firewall rule".

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Azure PostgreSQL Flexible Server SDK for .NET. Database management for PostgreSQL Flexible Server deployments. Use for creating servers, databases, firewall rules, configurations, backups, and high availability. Triggers: "PostgreSQL", "PostgreSqlFlexibleServer", "PostgreSQL Flexible Server", "Azure Database for PostgreSQL", "PostgreSQL database management", "PostgreSQL firewall", "PostgreSQL backup", "Postgres".

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Azure MySQL Flexible Server SDK for .NET. Database management for MySQL Flexible Server deployments. Use for creating servers, databases, firewall rules, configurations, backups, and high availability. Triggers: "MySQL", "MySqlFlexibleServer", "MySQL Flexible Server", "Azure Database for MySQL", "MySQL database management", "MySQL firewall", "MySQL backup".

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Manage MongoDB Atlas Organizations as Azure ARM resources using Azure.ResourceManager.MongoDBAtlas SDK. Use when creating, updating, listing, or deleting MongoDB Atlas organizations through Azure Marketplace integration. This SDK manages the Azure-side organization resource, not Atlas clusters/databases directly.

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Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (DADA2, IDTAXA) and exact matching approaches. Use when assigning taxonomy to ASVs after DADA2 amplicon processing.

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Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.

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Calculate tumor mutational burden from panel or WES data with proper normalization and clinical thresholds. Use when assessing immunotherapy eligibility or characterizing tumor immunogenicity.

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Call HLA alleles from NGS data using OptiType, HLA-HD, or arcasHLA for immunogenomics applications. Use when determining HLA genotype for transplant matching, neoantigen prediction, or pharmacogenomic screening.

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Calculate polygenic risk scores using PRSice-2, LDpred2, or PRS-CS from GWAS summary statistics. Use when predicting disease risk from genome-wide genetic variants.

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