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affaan-m/pubmed-database

Flux de travail de recherche directs dans PubMed et les E-utilities du NCBI pour la littérature biomédicale, les requêtes MeSH, la recherche PMID, la récupération de citations et la surveillance de la littérature via API.

Qu'est-ce que pubmed-database ?

Cette compétence permet aux agents IA d'effectuer des recherches et de récupérer des informations à partir de la base de données PubMed du National Center for Biotechnology Information (NCBI) via les E-utilities. Elle prend en charge les requêtes MeSH (Medical Subject Headings), les recherches par identifiant PMID, la récupération de citations et la surveillance automatisée de la littérature biomédicale. Utile pour les chercheurs, les professionnels de la santé et les développeurs, elle s'intègre facilement dans les flux de travail automatisés basés sur des API. La compétence fonctionne sur les plateformes Claude Code, Cursor et Codex, offrant une interface en ligne de commande pour interroger PubMed sans nécessiter de clé API pour les appels de base, mais recommande une clé API NCBI pour des usages plus intensifs. Elle utilise les endpoints des E-utilities (esearch, efetch, esummary) pour obtenir des résultats précis et à jour.

Compatible avec~Claude Code~Codex CLI~Cursor
Part ofAgent Workflows
npx skills add https://github.com/affaan-m/everything-claude-code/tree/main/skills/pubmed-database

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Documentation

Que fait pubmed-database ?

Flux de travail de recherche directs dans PubMed et les E-utilities du NCBI pour la littérature biomédicale, les requêtes MeSH, la recherche PMID, la récupération de citations et la surveillance de la littérature via API.

Aperçu

Cette compétence fournit aux agents IA la capacité d'interroger directement PubMed et les E-utilities du NCBI pour récupérer des articles de littérature biomédicale, des informations sur les termes MeSH, des citations spécifiques par PMID, et de configurer une surveillance continue de la littérature via des appels API.

Utilisation

Recherche PubMed

pubmed search "CRISPR gene editing cancer" --max 20

Recherche MeSH

pubmed mesh "Diabetes Mellitus"

Recherche PMID

pubmed pmid 12345678

Récupération de citations

pubmed cite 12345678 23456789

Configuration

Aucune clé API n'est requise pour les usages de base. Pour une utilisation intensive, configurez une clé API NCBI :

export NCBI_API_KEY="votre_cle_api_ici"

Plateformes prises en charge

  • Claude Code
  • Cursor
  • Codex

Comment ça marche

La compétence utilise les endpoints des E-utilities du NCBI :

  • esearch – Recherche d'identifiants
  • efetch – Récupération de données complètes
  • esummary – Résumés de documents

Les résultats sont renvoyés en JSON formaté pour un traitement facile par les agents IA.

Individual skills in this repo

This repo contains 20 individual skills — each has its own dedicated page.

accessibility

Design, implement, and audit inclusive digital products using WCAG 2.2 Level AA. Use when building or auditing UI that must meet WCAG 2.2 Level AA, or when reviewing a change for keyboard, contrast, or screen-reader support.

affaan-m/claude-api

Anthropic Claude API patterns for Python and TypeScript. Covers Messages API, streaming, tool use, vision, extended thinking, batches, prompt caching, and Claude Agent SDK. Use when building applications with the Claude API or Anthropic SDKs.

affaan-m/everything-claude-code

End-to-end marketing campaign planning and execution. Covers audience research, positioning, campaign angle definition, landing page copy, email sequences, social posts, ad copy, short-form video scripts, and content calendars. Use as the orchestration layer for multi-channel product launches. Use when planning or executing a multi-channel product launch, or producing landing page, email, social, or ad copy.

affaan-m/everything-claude-code

Development conventions and patterns for everything-claude-code. JavaScript project with conventional commits.

affaan-m/everything-claude-code-conventions

Development conventions and patterns for everything-claude-code. JavaScript project with conventional commits.

affaan-m/frontend-design

Create distinctive, production-grade frontend interfaces with high design quality. Use when the user asks to build web components, pages, or applications and the visual direction matters as much as the code quality.

affaan-m/gget

gget CLI and Python workflow for quick genomic database queries, sequence lookup, BLAST-style searches, enrichment checks, and reproducible bioinformatics evidence logs.

affaan-m/literature-review

Systematic literature-review workflow for academic, biomedical, technical, and scientific topics, including search planning, source screening, synthesis, citation checks, and evidence logging.

affaan-m/motion-ui

Production-ready UI motion system for React/Next.js. Use when implementing animations, transitions, or motion patterns.

affaan-m/project-guidelines-example

Example project-specific skill template based on a real production application.

affaan-m/scholar-evaluation

Structured scholarly-work evaluation for papers, proposals, literature reviews, methods sections, evidence quality, citation support, and research-writing feedback.

affaan-m/uspto-database

USPTO patent and trademark data workflow for official record lookup, PatentSearch queries, TSDR checks, assignment data, and reproducible IP research logs.

agent-architecture-audit

Full-stack diagnostic for agent and LLM applications. Audits the 12-layer agent stack for wrapper regression, memory pollution, tool discipline failures, hidden repair loops, and rendering corruption. Produces severity-ranked findings with code-first fixes. Essential for developers building agent applications, autonomous loops, or any LLM-powered feature. Use when an agent or LLM feature misbehaves and the failing layer is unknown, or before shipping an agent stack.

agent-eval

Head-to-head comparison of coding agents (Claude Code, Aider, Codex, etc.) on custom tasks with pass rate, cost, time, and consistency metrics. Use when choosing between coding agents, or when a change to an agent setup needs measured pass rate, cost, and time rather than an impression.

agent-harness-construction

Design and optimize AI agent action spaces, tool definitions, and observation formatting for higher completion rates. Use when defining or revising an agent

agentic-engineering

Operate as an agentic engineer using eval-first execution, decomposition, and cost-aware model routing. Use when planning or executing engineering work that agents will carry out end to end.

agentic-os

Build persistent multi-agent operating systems on Claude Code. Covers kernel architecture, specialist agents, slash commands, file-based memory, scheduled automation, and state management without external databases. Use when building a persistent multi-agent system on Claude Code with its own memory, commands, and scheduling.

agent-introspection-debugging

Structured self-debugging workflow for AI agent failures using capture, diagnosis, contained recovery, and introspection reports. Use when an agent run fails and you need a reproducible diagnosis instead of a retry.

agent-payment-x402

Add x402 payment execution to AI agents with per-task budgets, spending controls, and non-custodial wallets. Supports Base through agentwallet-sdk and X Layer through OKX Payments / OKX Agent Payments Protocol. Use when an agent must pay for something itself and needs per-task budgets, spending controls, and a non-custodial wallet.

agent-self-evaluation

Use after completing any non-trivial task. The agent self-rates its output on 5 axes — accuracy, completeness, clarity, actionability, conciseness — with concrete evidence per criterion. Produces a structured 1-5 scorecard with specific improvement suggestions.

Skills associés

steipete/gemini

Gemini CLI one-shot prompts, summaries, generation, skills, hooks, MCP, or Gemma routing.

community

steipete/gh-issues

Fetch GitHub issues, select candidates, spawn background fix agents, open PRs, and optionally process PR review comments.

community

steipete/skill-creator

Create, edit, audit, tidy, validate, or restructure AgentSkills and SKILL.md files.

community

steipete/clawhub

Search, install, update, sync, or publish agent skills with the ClawHub CLI and registry.

community

steipete/coding-agent

Delegate coding work to Codex, Claude Code, or OpenCode as background workers; not simple edits or read-only code lookup.

community

steipete/mcporter

List, configure, authenticate, call, and inspect MCP servers/tools with mcporter over HTTP or stdio.

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