PubMed Search FAQ

Q: Can I search for papers by a specific author?

Yes. Name the author in your question, or add an [AU] field tag to your query. Author names should follow PubMed's "Last Initials" format, for example Doudna JA[AU]. You can also narrow by institution by naming it or adding an [AD] field tag.

Q: What is PubMed Search and how does it work on the platform?

PubMed Search queries the NCBI PubMed/MEDLINE database of 36+ million biomedical citations using the E-utilities API. On the platform, you type a natural language query in chat and the orchestrator translates it into a structured PubMed search. Results return in 3-30 seconds.

Q: Can I use Boolean operators and field tags?

Yes. PubMed supports AND, OR, NOT (uppercase) and field tags like [TI] for title, [AU] for author, [MH] for MeSH terms, and [DP] for date. You can mix natural language with PubMed syntax in the same query.

Does PubMed return citation counts? No — chain PMIDs into Semantic Scholar. Plus Boolean and field-tag syntax, the 100-article cap, and missing abstracts.

These answers cover how PubMed Search works on the platform — Boolean operators and field tags, why some results come back without an abstract, result limits, citation counts, entity extraction, author searches, and how current the data is.

Frequently asked questions

What is PubMed Search and how does it work on the platform?

PubMed Search queries the NCBI PubMed/MEDLINE database of over 36 million biomedical citations using the E-utilities API. On the platform, you type a natural language query in chat and the orchestrator translates it into a structured PubMed search. Results return in 3-30 seconds depending on query complexity. The tool handles API key management and rate limiting automatically.

Can I use Boolean operators and field tags?

Yes. PubMed supports AND, OR, NOT (must be uppercase) and field tags such as [TI] for title, [AU] for author, [MH] for MeSH terms, and [DP] for date published. You can mix natural language with PubMed syntax in the same query. For example: "checkpoint inhibitor"[TIAB] AND melanoma[MH] AND 2024[DP].

Why are abstracts missing from my results?

A plain PubMed search returns the abstract, MeSH terms, and author keywords for each article, alongside the title, authors, journal, and date. An abstract comes back empty only when PubMed itself holds no abstract text for that record, which is common for older and some non-English-language articles.

The exception is a search filtered by author, affiliation, date range, or article type: that filtered search returns metadata only, with no abstract or MeSH terms. If you need a filter and the abstracts together, ask Ivy to write the filter into the query as a field tag (for example Doudna JA[AU] or 2024[DP]) so it runs as a plain search.

How many results can I retrieve?

Up to 100 articles per query. The default is 20; ask for more or fewer (for example, "the top 50 papers"). The total field in the response tells you how many articles matched in PubMed overall, which may be much larger than your requested limit.

Does PubMed Search return citation counts?

No. PubMed does not natively provide citation counts in its API responses. For citation data, chain your results into Semantic Scholar by passing PMIDs. Semantic Scholar provides citation counts, influential citation identification, and citation network graphs.

How do I extract entities from PubMed results?

Ask the model directly in the same conversation — it reads the returned titles and abstracts and extracts genes, proteins, compounds, diseases, and their relationships as part of answering. There is no separate entity-extraction tool to call.

Can I search for papers by a specific author?

Yes. Name the author in your question, or add an [AU] field tag to your query. Author names should follow PubMed's "Last Initials" format, for example Doudna JA[AU]. You can also narrow by institution by naming it or adding an [AD] field tag.

How current is the PubMed data?

PubMed is updated daily with new citations from contributing journals. However, newly published articles may take days to weeks to be indexed depending on the journal's submission practices. MeSH term annotations can lag further behind initial indexing. For the most recent preprints and early-access content, consider supplementing PubMed searches with Europe PMC or bioRxiv.