Agent skill · research science · affaan-m
pubmed-database
Direct PubMed and NCBI E-utilities search workflows for biomedical literature, MeSH queries, PMID lookup, citation retrieval, and API-backed literature monitoring. Use when a task needs biomedical literature from PubMed rather than general web search.
Why this skill is useful
Provides specific commands and workflows for interacting with the PubMed API that the AI wouldn't reliably generate on its own.
What it needs
Requires ncbi account access. About 3k tokens when loaded. Last updated 2026-08-06. 238,342 stars on the source repository.
What this skill does
PubMed Database Use this skill when a task needs biomedical literature from PubMed rather than general web search. When to Use Searching MEDLINE or life-sciences literature. Building PubMed queries with MeSH terms, field tags, dates, or article types. Looking up PMIDs, abstracts, publication metadata, or related citations. Running systematic-review search passes that need repeatable search strings. Using NCBI E-utilities directly from Python, shell, or another HTTP client. Query Construction Start with the research question, split it into concepts, then combine concepts with Boolean operators. Useful PubMed field tags: [ti]: title [ab]: abstract [tiab]: title or abstract [au]: author [ta]: journal title abbreviation [mh]: MeSH term [majr]: major MeSH topic [pt]: publication type [dp]: date of publication [la]: language Examples: MeSH and Subheadings Prefer MeSH when the concept has a stable controlled-vocabulary term. Combine MeSH with title/abstract terms when the topic is new or terminology varies. Correct subheading syntax puts the subheading before the field tag: Use [majr] only when the topic must be central to the paper. It can improve precision but may miss relevant work. Filters Publication types: clinical trial[pt] meta-analysis[pt] randomized controlled trial[pt] review[pt] systematic review[pt] guideline[pt] Date filters: Availability filters: E-utilities Workflow NCBI E-utilities supports repeatable API workflows: 1. esearch.fcgi: search and return PMIDs. 2. esummary.fcgi: return lightweight article metadata. 3. efetch.fcgi: fetch abstracts or full records in XML, MEDLINE, or text. 4. elink.fcgi: find related articles and linked resources. Use an email and API key for production scripts. Store API keys in environment variables, never in committed files or command history. For batches, prefer NCBI history server parameters (usehistory=y, WebEnv, querykey) instead of passing very long PMID lists through URLs. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills affaan-m/scientific-db-pubmed-database--16a009