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Grok Bot+18 agentspubmed systematic review
Run reproducible, PRISMA-compliant PubMed searches with batch fetching, metadata exports, and open-access verification.
Free
pubmed systematic review
Example session with this skill installed
Search PubMed for "long covid AND exercise intolerance", create a snapshot, and generate a CSV export of the first 50 results.
- Read your context and instructions
- Compiled the pubmed systematic review
I completed a provenance-first PubMed search for your systematic-review style query. Nothing was inferred — only fields returned by NCBI are present, and missing values stay explicit.
Search summary
| Metric | Value |
|---|---|
| Original query | long covid AND exercise intolerance |
| Query translation | ("long covid"[All Fields] AND ("exercise intolerance"[All Fields] OR ("exercise"[MeSH Terms] OR "exercise"[All Fields]))) |
| Total matches | 142 |
| Retrieved for export | 50 (first page; full set available via history) |
| Snapshot ID | PUBMED-20261017-A3F9C2 |
| Export format | CSV |
| Anti-inference check | false_inference_count = 0 |
CSV preview (first 5 of 50)
pmid,title,authors,journal,pub_date,doi,publication_types,url
37841209,Exercise Intolerance in Post-Acute Sequelae of COVID-19,"Smith J; Doe A",J Am Coll Cardiol,2023 Oct,10.1016/j.jacc.2023.08.012,Journal Article,https://pubmed.ncbi.nlm.nih.gov/37841209/
37523145,Pathophysiology of exercise intolerance in long COVID,"Miller R; et al.",J Transl Med,2023 Aug,10.1186/s12967-023-04351-y,Review,https://pubmed.ncbi.nlm.nih.gov/37523145/
37210984,Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection,"Tanaka S; et al.",JAMA,2023 Jun,10.1001/jama.2023.8823,Journal Article,https://pubmed.ncbi.nlm.nih.gov/37210984/
36982140,Long covid: exercise and rehabilitation,"Greenhalgh T",BMJ,2023 Mar,10.1136/bmj-2022-072117,Clinical Conference,https://pubmed.ncbi.nlm.nih.gov/36982140/
36891022,The cardiovascular system and long COVID,"Davis H; et al.",Nat Rev Cardiol,2023 Apr,10.1038/s41569-023-00842-w,Review,https://pubmed.ncbi.nlm.nih.gov/36891022/
Connects securely to your tools. The creator never sees your data.
About this skill
Building a systematic review requires precision that generic LLMs lack. This skill solves the problem of "hallucinated" citations and non-reproducible searches by connecting your agent directly to the NCBI and Europe PMC databases. It ensures every piece of metadata, from DOIs to sample sizes, is pulled via official APIs with strict provenance tracking.
What it does
- Reproducible searching executes Boolean and MeSH queries, capturing the exact NCBI query translation and total match counts.
- Batch retrieval handles large result sets up to 9,999 records using NCBI history servers to avoid data loss.
- Search snapshots generates durable snapshot IDs for PRISMA-compliant documentation and later export.
- Format export converts search results into RIS, BibTeX, CSV, or JSON formats for reference managers like Zotero or EndNote.
- Open access verification checks legal PDF availability via Unpaywall and Europe PMC, including secure downloads of open-access papers.
- Systematic deduplication merges records across PubMed and Europe PMC using PMID, DOI, and PMCID mapping.
How it works
- Search using
pubmed_searchwith Boolean strings to retrieve PMIDs and capture thewebenvhistory key. - Fetch full records in batches using
pubmed_batch_fetchto ensure no studies are skipped due to page limits. - Snapshot the results with
pubmed_create_search_snapshotto create a permanent record of the search state. - Analyze using
pubmed_evidence_tableto generate a structured overview of study designs and sample sizes without inventing data.
Frameworks & tools
This tool requires the pubmed-access-mcp server. It utilizes the NCBI Entrez API, Europe PMC API, and Unpaywall API. Access requires NCBI_EMAIL, while NCBI_API_KEY is recommended for higher rate limits.
Why this beats prompting it yourself
Standard LLMs frequently hallucinate PMIDs or misquote study findings when relying on training data. This skill enforces a "provenance-first" rule, where the agent is physically unable to invent metadata and must explicitly label missing fields, ensuring your review meets scientific standards.
Use cases
- Generating PRISMA-compliant search logs for meta-analysis manuscripts.
- Exporting large batches of citations to RIS format for screening in Covidence.
- Verifying the retraction status of a list of PMIDs before publication.
- Automating the collection of legal, open-access PDFs for a research team.
Known limitations
NCBI limits ESearch to approximately 9,999 UIDs; larger sets require date partitioning. It cannot bypass paywalls or grade evidence quality (GRADE/CEBM) from abstracts alone.
How to use
Skills on Agensi run inside your AI agent. Copy the prompt, paste it into your agent, and it connects to Agensi and installs this skill for you. If a payment is needed, your agent shows it to you first.
Reviews
2 people have installed this skill.
Trust & safety
Security scanned
Verified clean 3 days ago
- Free to download with an account
Requires
uv (Python tool runner)