PubMed Articles Search

PubMed articles scraper returns bibliographic records and available abstracts from NCBI. PubMed API results include identifiers, authors, journal details, publication dates, indexing terms, and source links.

Input example

{
  "pmids": [
    "31452104"
  ],
  "maxItems": 2
}

The input keys and allowed values follow .actor/input_schema.json.

Output fields

Field	Type	Example or excerpt from sample
source	string	"NCBI PubMed E-utilities"
pmid	string	"31452104"
url	string	"https://pubmed.ncbi.nlm.nih.gov/31452104/"
title	string	"Molegro Virtual Docker for Docking."
abstract	string or null	"Molegro Virtual Docker is a protein-ligand docking simulation program that allows us…
abstractSections	array	[]
authors	array	[{"name": "Gabriela Bitencourt-Ferreira", "lastName": "Bitencourt-Ferreira", "foreNam…
journal	string	"Methods in molecular biology (Clifton, N.J.)"
journalAbbreviation	string	"Methods Mol Biol"
issn	string	"1940-6029"
publicationDate	string	"2019"
publicationYear	integer	2019
volume	string	"2053"
issue	string or null	"8"
pages	string	"149-167"
doi	string	"10.1007/978-1-4939-9752-7_10"
doiUrl	string	"https://doi.org/10.1007/978-1-4939-9752-7_10"
pmcId	string or null	null
meshTerms	array	[]
meshHeadings	array	[]
keywords	array	[]
languages	array	["eng"]
publicationTypes	array	["Journal Article", "Research Support, Non-U.S. Gov't"]
status	string	"ok"
errors	array	[]
retrievedAt	string	"2026-10-05T13:50:30.094Z"

Output example

Trimmed from sample_output.json; omitted fields remain available in the dataset.

{
  "source": "NCBI PubMed E-utilities",
  "pmid": "31452104",
  "url": "https://pubmed.ncbi.nlm.nih.gov/31452104/",
  "title": "Molegro Virtual Docker for Docking.",
  "abstract": "Molegro Virtual Docker is a protein-ligand docking simulation program that allows us to carry out docking simulations in a fully integrated computational package. MVD has been successfully applied to hundreds of different proteins, with docking performance similar to other docking programs such as AutoDock4 and AutoDock Vina. The program MVD has four search algorithms and four native scoring functions. Considering that we may have water molecules or not in the docking simulations, we have a total of 32 docking protocols. The integration of the programs SAnDReS ( https://github.com/azevedolab/sandres ) and MVD opens the possibility to carry out a detailed statistical analysis of docking results, which adds to the native capabilities of the program MVD. In this chapter, we describe a tutorial to carry out docking simulations with MVD and how to perform a statistical analysis of the docking results with the program SAnDReS. To illustrate the integration of both programs, we describe the redocking simulation focused the cyclin-dependent kinase 2 in complex with a competitive inhibitor.",
  "abstractSections": [
    {
      "label": null,
      "category": null,
      "text": "Molegro Virtual Docker is a protein-ligand docking simulation program that allows us to carry out docking simulations in a fully integrated computational package. MVD has been successfully applied to hundreds of different proteins, with docking performance similar to other docking programs such as AutoDock4 and AutoDock Vina. The program MVD has four search algorithms and four native scoring functions. Considering that we may have water molecules or not in the docking simulations, we have a total of 32 docking protocols. The integration of the programs SAnDReS ( https://github.com/azevedolab/sandres ) and MVD opens the possibility to carry out a detailed statistical analysis of docking results, which adds to the native capabilities of the program MVD. In this chapter, we describe a tutorial to carry out docking simulations with MVD and how to perform a statistical analysis of the docking results with the program SAnDReS. To illustrate the integration of both programs, we describe the redocking simulation focused the cyclin-dependent kinase 2 in complex with a competitive inhibitor."
    }
  ],
  "authors": [
    {
      "name": "Gabriela Bitencourt-Ferreira",
      "lastName": "Bitencourt-Ferreira",
      "foreName": "Gabriela",
      "initials": "G",
      "suffix": null,
      "affiliations": [
        "Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil."
      ],
      "orcid": null
    },
    {
      "name": "Walter Filgueira de Azevedo Jr",
      "lastName": "de Azevedo",
      "foreName": "Walter Filgueira",
      "initials": "WF",
      "suffix": "Jr",
      "affiliations": [
        "Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil. walter@azevedolab.net."
      ],
      "orcid": null
    }
  ],
  "status": "ok"
}

Limits and failure behavior

• ESearch exposes the first 10,000 matching PubMed records. Narrow broad searches with date ranges or field tags; this actor does not bypass that limit.
• NCBI permits 3 requests/second without an API key and 10 with a key by default. One limiter covers this run's search, summary, fetch and retries; separate runs or other clients sharing an IP/key also count toward NCBI's limit. See NCBI usage guidelines.
• Article requests use batches of 50 and at most the configured number of active batches. They have a 30-second HTTP timeout and four attempts with backoff. Transient responses honor Retry-After; a cooldown over 300 seconds returns a diagnostic so the run can be retried later.
• Missing PMID records, malformed items and failed article enrichment produce per-item diagnostics. When EFetch fails but a summary has a title, the record is partial. An unavailable search fails the run clearly and preserves any rows already saved.
• Empty searches succeed with no rows. Invalid global settings fail before querying NCBI. maxItems and the Apify event budget limit output.
• Abstracts, DOI, affiliations, ORCID and MeSH can be absent in the source. Missing abstracts do not indicate a failure. The actor does not download full text or infer unpublished metadata.
• Bibliographic content and abstracts can carry publisher copyright. Review NCBI and publisher reuse terms for your use case. No login or proxy configuration is needed by this implementation.

FAQ

What are the output limits? maxItems caps output. ESearch exposes the first 10,000 matching records; narrow broad searches with date filters.

Do I need a proxy or login? Public NCBI E-utilities need no login or proxy. An API key is optional; a contact email is recommended for production use.

How is this priced? Proposed pay per event: $0.002 for each usable article row, including partial records with a title. Error-only rows are uncharged. These are proposals in PRICING.md; the owner must configure Store billing.

How are rate limits handled? The shared limiter follows NCBI defaults of 3 requests per second without a key or 10 with a key; retries honor Retry-After.

How fresh is the data? PubMed records can be updated and abstracts may be absent. retrievedAt marks collection time. This actor does not fetch full text, assess clinical validity, or provide medical advice; check publisher reuse terms.

Use with AI agents / MCP

After the actor is published, connect your agent to the Apify MCP server with an Apify API token. Use call-actor with the published actor identifier and the JSON input shown above. Read the returned dataset with get-dataset-items; the run response itself contains status and storage IDs, not the result rows. Alternatively, use the Apify API to start a run and read its default dataset. Keep the actor input bounded with maxItems, and inspect source links and any error fields before using results in an answer.