PubMed
The PubMed block searches the PubMed biomedical literature database from inside your workflows — find articles, fetch details and abstracts, follow citations, search clinical trials, and look up MeSH terms.
Research Automation: Build literature-monitoring agents that search PubMed on a schedule, summarize new abstracts with an AI block, and deliver a digest to your team.
Key Features
- Article Search: Query PubMed with keywords, authors, journals, and date ranges
- Full Details: Fetch article metadata, abstracts, and citation lists by PMID
- Discovery: Find related articles and clinical trials
- MeSH Terms: Look up Medical Subject Headings for precise queries
- Works Without a Key: An API key is optional — add one only for higher rate limits
Operations
| Operation | Description |
|---|---|
| Search Articles | Search PubMed with a query, with max results, sort order, and date range |
| Get Article Details | Fetch metadata for an article by PMID |
| Get Citations | Fetch the citation data for an article (returned as XML) |
| Get Related Articles | Find articles related to a PMID |
| Get Abstract | Fetch an article's abstract text |
| Search Clinical Trials | Search clinical-trial literature |
| Get MeSH Terms | Look up MeSH terms for a topic |
| Get Author Articles | List articles by an author, optionally filtered by journal |
Configuration
| Parameter | Type | Required | Description |
|---|---|---|---|
| Credentials | Select | Yes | Your saved PubMed connection (the API key inside it can be empty) |
| Action | Select | Yes | One of the operations above |
| Query | Text | For searches | Search terms — supports {{variables}} and PubMed query syntax |
| PMID | Text | For article ops | The PubMed ID of the article |
| Max Results | Text | No | Maximum number of results to return |
| Sort By | Text | No | Sort order for search results |
| Date Range | Text | No | Restrict results to a publication date range |
| Author / Journal | Text | For author search | Author name and optional journal filter |
| MeSH Term | Text | For MeSH lookup | The term to look up |
Connecting PubMed
PubMed's E-utilities API is free and works without a key, but NCBI enforces stricter rate limits for anonymous use.
- In Indite, add the PubMed block and click Connect new.
- Either save the connection with an empty key, or paste an API Key for higher limits.
- To get a key: sign in at ncbi.nlm.nih.gov (opens in a new tab), open Account Settings, and create an API Key under "API Key Management".
Without a key NCBI allows about 3 requests per second; with a key, about 10. If your workflow loops over many articles, add the key.
Output
The block returns the PubMed API response for the operation. Search operations return result lists with PMIDs; Get Abstract returns { "abstract": "..." } and Get Citations returns { "xml": "..." }. Reference fields in later blocks with {{<blockId>.<field>}}.
Example: weekly literature digest
- Schedule Trigger — every Friday at 07:00.
- PubMed → Search Articles — query
"GLP-1 receptor agonist" AND obesity, max results 10, sorted by most recent. - For Each result → PubMed → Get Abstract with the article's PMID.
- AI Summarizer — condense the abstracts into key findings.
- Send Email — deliver the digest to the research team.