「query」の検索結果

Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes. Use when fetching UniProtKB entries, navigating the JSON schema, choosing between UniProtKB/UniRef/UniParc/Proteomes resources, deciding stream vs search endpoint for batch retrieval, running ID-mapping jobs with the async pattern, handling isoform suffixes, or filtering reviewed Swiss-Prot vs auto-annotated TrEMBL. Encodes the legacy URL migration (2022), the new JSON schema layout, and bulk-pull patterns.

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Query the Ensembl REST API for gene/transcript/protein lookup, sequence retrieval, comparative genomics (Compara), variant effect prediction (VEP), regulatory features, and cross-species ortholog/paralog calls. Use when pulling Ensembl-native data (Ensembl Gene IDs, version-pinned releases, archive endpoints for reproducibility), gene/transcript/exon structure with stable IDs, or VEP for variant annotation. Encodes the 15 req/sec rate limit, archive (e110.rest.ensembl.org) for reproducibility, Ensembl divisions (vertebrates / plants / fungi / metazoa / bacteria), and the symbol-vs-ID stability problem.

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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 UpSet plots to visualize set intersections beyond 4 sets (where Venn fails) using ComplexUpset (modern, ggplot2-grammar) or the unmaintained UpSetR, with explicit cardinality vs degree sorting, attribute panels, and query highlighting. Use when comparing overlap across many gene sets, peak sets, variant lists, or any set membership matrix where Venn diagrams become illegible.

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Project gene annotations across genomes using TOGA (Kirilenko 2023 whole-genome-alignment chain-based projection with intactness classification), CESAR 2.0 (Sharma & Hiller 2017 codon-aware exon projection), LiftOff (Shumate & Salzberg 2020 reference-based annotation transfer), Liftover (UCSC), GeMoMa (Keilwagen 2019 evidence-based projection), and Comparative Annotation Toolkit (CAT). Use when transferring annotations from a well-annotated reference to query genome(s), classifying gene-loss vs gene-intact across many genomes at scale, building Zoonomia-style comparative annotations across hundreds of mammals or birds (Kirilenko 2023), detecting pseudogenization, projecting alternative isoforms, or selecting between WGA-anchored (TOGA) vs ortholog-based (LiftOff) annotation transfer strategies.

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Performs molecular similarity searching using Tanimoto, Tversky, Dice, and cosine coefficients on bit/count fingerprints with explicit choice rules for symmetric vs asymmetric measures, scaffold-hopping vs lead-optimization regimes, activity-cliff diagnosis, and large-library nearest-neighbor methods (BulkTanimoto, Annoy MHFP6, USRCAT). Use when ranking compounds by structural resemblance to a query, clustering libraries, finding analogs, or diagnosing activity cliffs.

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WheatOmics 平台（wheatomics.sdau.edu.cn）数据查询技能。当用户需要查询小麦/麦族基因信息、表达谱、共表达、蛋白互作、同源与共线性、序列获取、BLAST、GO/KEGG 富集、变异数据、文献检索或引物设计时使用。

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Provides Spring Data Neo4j integration patterns for Spring Boot applications. Use when you need to work with a graph database, Neo4j nodes and relationships, Cypher queries, or Spring Data Neo4j. Creates node entities with @Node annotation, defines relationships with @Relationship, writes Cypher queries using @Query, configures imperative and reactive Neo4j repositories, implements graph traversal patterns, and sets up testing with embedded databases.

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Hunt for adversary techniques in telemetry you are authorized to query. Hypothesis-driven, evidence-first, no live offensive operations.

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Provides expert knowledge for building Next.js 15+ applications with the App Router, TypeScript, Server Components, Server Actions, and TanStack Query.

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JPA/Hibernate patterns for entity design, relationships, query optimization, transactions, auditing, indexing, pagination, and pooling in Spring Boot.

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Audits Hibernate database interactions to prevent N+1 query problems in JVM apps.

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Query and interpret security logs you are authorized to read. Build detections and investigations without leaking PII.

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Use when generating JPA entities, repositories, queries, or anything touching the persistence layer. Covers entity conventions, N+1 prevention, projections, and query patterns.

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Django ORM patterns for multi-tenant POS projects: efficient queries, bulk operations, transactions, and multi-schema upload paths. Trigger: When writing queryset logic, model saves, or DB-touching service code.

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Revisa cambios de performance de queries ClickHouse y Postgres (vambe-datascience, CRM, réplicas) contra los errores y aprendizajes de la ronda

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Access the Firebase Emulator Suite (Firestore, Auth, Functions, Hub) via REST and Admin SDK without trial-and-error. Use this skill whenever you read/write/query/clear Firestore Emulator data, create test users or obtain ID tokens from the Auth Emulator, verify Functions triggers, seed/export emulator data, or hit unexpected 403/404 from an emulator endpoint. Consult it BEFORE curling any emulator port — it encodes the auth header and host-resolution rules that otherwise cause retries.

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Query PostgreSQL with pg and navigate Openrind Shell's primary FUSE or compatibility workspace; /db is custom-agent-only.

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Enable, record, query, summarize, or verify the opt-in PWDEV Flow semantic audit trail. Use when the user asks what Flow actions occurred, wants audit integrity checked, or needs a portable JSONL record of workflow gates and artifacts.

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Use when the user asks for the state of pwdev-feat plans — 'status do feat', 'quais planos estão pendentes', 'show feature status' — listing pending, complete, with-caveats, failed and resumable plans plus codebase-context health. Read-only. Do NOT use to execute (feat-exec) or query the audit trail (feat-audit).

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Consultas, inspeção de schema e mutações seguras (DML/DDL com dry-run) no PostgreSQL via MCP (@soarescbm/postgres-mcp). Use quando o usuário disser "postgres", "postgresql", "banco de dados", "tabela", "query", "SELECT", "índice", "schema", "constraint", "foreign key", "coluna", "DDL", "insert", "update", "delete", "criar tabela", ou pedir para consultar/alterar dados de um banco Postgres.

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Diagnóstico e tuning de PostgreSQL — EXPLAIN ANALYZE, índice, VACUUM, bloat, lock, replicação, WAL, PITR e particionamento. Use quando o usuário disser "postgres", "query lenta", "índice", "EXPLAIN", "vacuum", "lock", "deadlock", "replicação", "conexões", "banco lento".

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Use when the user wants to query the local pwdev audit trail — 'ver auditoria', 'relatório de auditoria', 'audit stats', 'exportar auditoria em PDF' — summary, events, decisions, artifacts, statistics, a Markdown/PDF export or a custom read-only SELECT. Do NOT use to enable the audit (feat-init) or for plan status (feat-status).

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Roslyn-powered semantic query CLI for C# solutions. Use when you need to find references, callers, implementations, dependencies, members, or trace call chains in a C# codebase — replaces multi-round grep/read cycles with single precise queries.

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