PMC (PubMed Central)

PMC is a full-text archive of biomedical and life sciences articles. It is separate from PubMed -- PubMed has citations/abstracts, PMC has full text. Not all PubMed articles are in PMC, and vice versa.

E-utilities for PMC

Base URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/

Same E-utilities as PubMed, but with db=pmc.

eSearch -- Search PMC

GET /esearch.fcgi?db=pmc&term={query}&retmode=json

Same parameters as PubMed eSearch. PubMed and PMC ESearch are both limited to the first 10,000 matching IDs; partition larger searches or use an appropriate bulk workflow. Returns PMC UIDs (numeric, e.g., 13033346). You need to prepend "PMC" to get a PMCID (e.g., PMC13033346).

eFetch -- Get Full Text XML

GET /efetch.fcgi?db=pmc&id={pmcid}&retmode=xml

Example:

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id=7029759&retmode=xml

The XML uses JATS (Journal Article Tag Suite) format:

• <front> -- journal metadata, article metadata, author info
• <body> -- full article text with <sec> sections, <p> paragraphs, <fig> figures
• <back> -- <ref-list> with all references

Pass numeric IDs only (not "PMC7029759", just "7029759").

Hazard: eFetch returns metadata-only XML for non-OA articles, with HTTP 200

This is the most dangerous failure in this skill, because nothing about the response says it failed. When the publisher does not permit XML redistribution, eFetch returns a **well-formed <pmc-articleset>** containing <front> metadata, **no <body>**, and the reason as an XML comment -- which every standard parser discards. Verified 2026-07-27 on PMCID 1500000:

HTTP/1.1 200 OK

<pmc-articleset><article article-type="obituary" ...>
  <!--The publisher of this article does not allow downloading of the full text in XML form.-->
  <front>...</front>
</article></pmc-articleset>

An agent that fetches this, parses it, and reports "retrieved full text" has retrieved only the title, journal, and author list. An article being readable on the PMC website does not establish that its XML is available through this API. The absence of a body is a retrieval limitation, not evidence about the article contents.

**Always confirm <body> exists before claiming you have full text.** Two ways, in order of preference:

1. **Use scripts/jats_to_text.py**, which exits non-zero with no <body> element when the article is metadata-only and surfaces the publisher-restriction comment instead of dropping it.
2. Fall back to Europe PMC (references/europepmc.md), whose fullTextXML endpoint returns a clean 404 for the same article rather than a 200 with no body -- an honest failure is easier to handle than a plausible one.

If full text is unavailable, say so explicitly and offer the abstract (PubMed eFetch) or an OA copy elsewhere (Unpaywall, CORE) rather than presenting <front> metadata as the article.

Retired OA Web Service

The PMC OA Web Service (oa.fcgi) was retired on 2026-08-25. Do not use it as an availability preflight, retraction check, or source of FTP package links. The old OA-package FTP workflow is no longer the supported retrieval path. For a targeted paper, fetch via E-utilities, BioC, or Europe PMC and validate that the response actually contains article text. For bulk access consult PMC Article Datasets and the PMC Cloud Service.

Use the article's current license for reuse decisions. For retractions inspect PubMed/publisher notices and Crossref update relationships; a missing OA copy says nothing about retraction status.

BioC API -- Structured Full Text

An alternative way to get full text in a structured passage format.

Base URL

https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/

Endpoint

GET /BioC_{format}/{id}/{encoding}

Example:

https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC7029759/unicode

Response structure (JSON): a list of BioC collections. Read [0].documents, not a top-level documents object.

[{
  "source": "PMC",
  "documents": [{
    "id": "PMC7029759",
    "infons": {"license": "...", "doi": "..."},
    "passages": [
      {
        "offset": 0,
        "infons": {"section_type": "TITLE"},
        "text": "Article title..."
      },
      {
        "offset": 42,
        "infons": {"section_type": "ABSTRACT"},
        "text": "Abstract text..."
      },
      {
        "offset": 500,
        "infons": {"section_type": "INTRO"},
        "text": "Introduction text..."
      }
    ]
  }]
}]

Section types: TITLE, ABSTRACT, INTRO, METHODS, RESULTS, DISCUSS, CONCL, REF, SUPPL, FIG, TABLE

Coverage: PMC Open Access and eligible Author Manuscript articles; not all PMC records. Do not use the count in the 2019 BioC paper as a current coverage total.

PMC ID Converter API

Converts between PMID, PMCID, DOI, and Manuscript ID.

Base URL

https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/

Parameters

Example:

https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/?ids=PMC7029759&format=json

Response:

{
  "status": "ok",
  "records": [{
    "pmcid": "PMC7029759",
    "pmid": "32117569",
    "doi": "10.12688/f1000research.22211.2"
  }]
}

The JSON pmid may be numeric; normalize identifiers to strings before joining across APIs. Inspect per-record errors/availability as well as top-level status. Only returns related identifiers for articles that are in PMC. If an article is in PubMed but not PMC, no PMCID will be returned.

Rate Limits

Include tool and email parameters on E-utility requests. Large batch jobs should run outside peak hours (Mon-Fri 5AM-9PM ET).

Official sources reviewed 2026-09-30

• https://pmc.ncbi.nlm.nih.gov/tools/developers/
• https://pmc.ncbi.nlm.nih.gov/tools/oa-service/
• https://pmc.ncbi.nlm.nih.gov/tools/id-converter-api/
• https://www.ncbi.nlm.nih.gov/research/bionlp/APIs/BioC-PMC/
• https://pmc.ncbi.nlm.nih.gov/tools/textmining/