pubmed-database
Direct PubMed and NCBI E-utilities search workflows for biomedical literature
by affaan-mFree
Description
pubmed-database is an agent skill from the ECC collection by affaan-m, listed on skills.sh. It runs direct searches of PubMed and NCBI E-utilities for biomedical literature, for cases where a general web search is not enough. It covers building queries with MeSH terms, field tags, dates and article types, looking up PMIDs, abstracts and publication metadata, retrieving related citations, and running repeatable search strings for systematic-review passes. It also covers calling the NCBI E-utilities from Python, shell or another HTTP client. The query method is to start from the research question, split it into concepts, and combine those concepts with Boolean operators. The skill applies when someone is searching MEDLINE or life-science literature, preparing a systematic review search, or needs a precise record for a paper. A skill is a SKILL.md file of instructions that an AI agent loads when a task calls for it. It is free and open source, and the skills.sh listing shows a Snyk warning, with Gen Agent Trust Hub and Socket passing.…
Highlights
- MeSH, field tag and date queries
- PMID, abstract and metadata lookup
- Related citation retrieval
- Repeatable search strings for reviews
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pubmed-database FAQ
What does the pubmed-database skill do?
It runs PubMed and NCBI E-utilities searches for biomedical literature, building MeSH and Boolean queries and retrieving PMIDs and abstracts.
When is it better than web search?
When the task needs MEDLINE or life-science literature specifically, the skill says.
Can I use it from code?
Yes. It covers E-utilities from Python, shell or another HTTP client.
How do I install it?
Run: npx skills add https://github.com/affaan-m/ecc --skill pubmed-database
Is it free?
Yes. It is free and open source. PubMed is a free NCBI service.
Are there security warnings?
The skills.sh listing shows Snyk with a warning, while Gen Agent Trust Hub and Socket pass.
What are the best pubmed-database alternatives?
Popular alternatives to pubmed-database include arxiv-search, webapp-testing and content-research-writer. See all pubmed-database alternatives