mining-pubmed-literature SKILL.md skillA
mining-pubmed-literature from maziyarpanahi/openmed is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add maziyarpanahi/openmed/mining-pubmed-literature@v1.0Pins v1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- maziyarpanahi/openmed
- Path
skills/mining-pubmed-literature/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
- Size
- 7,018 bytes
- Repository stars
- 5,784
- License
- Apache-2.0
Searches and fetches PubMed and PMC via NCBI E-utilities (ESearch then EFetch/ESummary) to gather biomedical evidence and build text corpora. Use when the user wants citations for a condition or drug, abstracts to summarize, MeSH-based searches, or a corpus of literature to run NER over. Trigger keywords: PubMed, PMC, NCBI, E-utilities, ESearch, EFetch, ESummary, MeSH, PMID, literature search, abstracts, evidence. Pairs adjacent to OpenMed: fetched abstracts feed openmed.analyze_text for…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Mining PubMed & PMC literature (NCBI E-utilities) Search **PubMed** (citations/abstracts) and **PMC** (full text) programmatically with **NCBI E-utilities** — the stable HTTP interface to Entrez. The core pattern is two steps: **ESearch** returns matching record IDs (PMIDs), then **EFetch** (or **ESummary**) downloads the records. The **Entrez History server** (`usehistory=y`) lets you chain the two without re-sending thousands of IDs. E-utilities are public. **No key is required**, but a free API key raises your limit from **3 to 10 requests/second** and is strongly recommended for batch work. ## When to use - OpenMed extracted a diagnosis, drug, or gene and you want supporting literature. - You need abstracts to summarize or to assemble a corpus for biomedical NER. - You want MeSH-anchored, reproducible searches (date ranges, article types). For ClinicalTrials.gov use `searching-clinicaltrials`; this skill is for the published literature. ## Quick start (real E-utilities calls) Base URL: `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/`. JSON for ESearch/ ESummary via `retmode=json`; EFetch returns text or XML (no JSON for PubMed). ```python import requests, time …
Read the whole file at its exact version.
How to install
mdr add maziyarpanahi/openmed/mining-pubmed-literature@sha256:eb93a7245f2d49b0The line at the top of this page pins the label v1.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_nrokhvulkan7ipgv)
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Versions
The registry has recorded 1 version of this file, committed on Jul 20, 2026.
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Source
maziyarpanahi/openmed · 5,784 stars · license Apache-2.0 · pushed 2026-11-07 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_nrokhvulkan7ipgv GET https://markdownregistry.com/api/v1/resolve?ref=maziyarpanahi/openmed/mining-pubmed-literature GET https://markdownregistry.com/api/v1/blob/eb93a7245f2d49b077535aed5bf185afd7b7e45f3e25884593b6aaf6fd276af3
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.