pubmed-database SKILL.md skillA
pubmed-database from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/pubmed-database@git:20260528.99f3f73Pins git:20260528.99f3f73 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/scientific-writing/pubmed-database/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260528.99f3f73, committed May 28, 2026
- Size
- 17,749 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Programmatic PubMed access via NCBI E-utilities REST API. Covers Boolean/MeSH queries, field-tagged search, endpoints (ESearch, EFetch, ESummary, EPost, ELink), history server for batches, citation matching, systematic review strategies. Use for biomedical literature search or automated pipelines.
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
# PubMed Database ## Overview PubMed is the U.S. National Library of Medicine's database providing free access to 36M+ biomedical citations from MEDLINE and life sciences journals. This skill covers programmatic access via the E-utilities REST API and advanced search query construction using Boolean operators, MeSH terms, and field tags. ## When to Use - Searching biomedical literature with structured Boolean/MeSH queries - Building automated literature monitoring or extraction pipelines - Conducting systematic literature reviews or meta-analyses - Retrieving article metadata, abstracts, or citation information by PMID/DOI - Finding related articles or exploring citation networks programmatically - Batch processing large sets of PubMed records - For Python-native PubMed access, prefer BioPython (`Bio.Entrez`) — this skill covers direct REST API usage - For broader academic search (non-biomedical), use OpenAlex or Semantic Scholar APIs ## Prerequisites ```bash pip install requests # HTTP client for E-utilities API # Optional: pip install biopython — Bio.Entrez wrapper (higher-level API) ``` **API Rate Limits**: - Without API key: **3 requests/second** …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/pubmed-database@sha256:5707187b2f003726The line at the top of this page pins the label git:20260528.99f3f73, 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_vmpcyt76esmcs75u)
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Versions
The registry has recorded 1 version of this file, committed on May 28, 2026.
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (17749 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_vmpcyt76esmcs75u GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/pubmed-database GET https://markdownregistry.com/api/v1/blob/5707187b2f003726f64daa1f57c9ae07eaac3c8370a5fd61a0be111b8b38a065
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
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.