# 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. 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 ``` | rettype | retmode | Returns | |---------|---------|---------| | *(omit)* | `xml` | JATS XML -- full text **only for open-access articles**; metadata only otherwise, with no error. See the hazard below before using this. | | `medline` | `text` | MEDLINE format | **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: - `` -- journal metadata, article metadata, author info - `` -- full article text with `` sections, `

` paragraphs, `` figures - `` -- `` 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 ``** containing `` metadata, **no ``**, and the reason as an XML *comment* -- which every standard parser discards. Verified 2026-07-27 on PMCID 1500000: ``` HTTP/1.1 200 OK

...

``` An agent that fetches this, parses it, and reports "retrieved full text" has retrieved only the title, journal, and author list. **This is the common case, not an edge case:** full text via eFetch is limited to roughly the 3M-article PMC Open Access Subset, while PMC holds ~10M — so most PMCIDs you hand to eFetch come back without a body. **Always confirm `` exists before claiming you have full text.** Three ways, in order of preference: 1. **Check availability first** with the PMC OA Web Service (below). It tells you whether a package exists before you spend the fetch. 2. **Use `scripts/jats_to_text.py`**, which exits non-zero with `no element` when the article is metadata-only and surfaces the publisher-restriction comment instead of dropping it. 3. **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 `` metadata as the article. ## PMC OA Web Service -- is full text actually available? Not the same thing as the ID Converter: this answers "does a downloadable full-text package exist for this PMCID", which is exactly what the eFetch hazard above requires you to know in advance. ``` GET https://www.ncbi.nlm.nih.gov/pmc/utils/oa/oa.fcgi?id={pmcid} ``` Returns XML (no JSON option). Verified 2026-07-27: ```xml ``` Distinguish the two failure codes -- they mean different things and both arrive with **HTTP 200**: | Response | Meaning | |---|---| | `` with a `` and `` | In the OA Subset; full text is retrievable | | `` | The article exists but is **not** in the OA Subset -- eFetch will return metadata only. This is the case to route to Europe PMC or Unpaywall. | | `` | No such PMCID. A bad identifier, not a coverage gap -- re-check the format or convert via the ID Converter. | Per-record attributes worth reading: | Attribute | Why it matters | |---|---| | `license` | The actual reuse terms (`CC BY`, `CC BY-NC`, ...). Report these when you quote or redistribute text. | | `retracted` | `"no"` or `"yes"`. Summarizing a retracted paper as current evidence is a correctness failure, not a formatting one -- check it before quoting. | | `citation` | Human-readable citation string, handy for provenance. | `format` values are `tgz` (article XML plus figures) and sometimes `pdf`. **The `href` is an FTP URL, and swapping the scheme to HTTPS does not work** -- `https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_package/...` returns 404 (verified 2026-07-27). Use the FTP URL as given, or get the same XML over HTTPS from eFetch / Europe PMC `fullTextXML` once this service has confirmed the article is in the subset. ## 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} ``` | Parameter | Values | |-----------|--------| | `format` | `json` or `xml` | | `id` | PMID (e.g., `17299597`) or PMCID (e.g., `PMC7029759`) | | `encoding` | `unicode` or `ascii` | **Example:** ``` https://www.ncbi.nlm.nih.gov/research/bionlp/RESTful/pmcoa.cgi/BioC_json/PMC7029759/unicode ``` **Response structure (JSON):** ```json { "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:** ~3 million articles from the PMC Open Access Subset. ## 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 | Parameter | Required | Description | |-----------|----------|-------------| | `ids` | Yes | Up to 200 comma-separated IDs | | `idtype` | No | `pmcid`, `pmid`, `mid`, `doi` (default: auto-detect) | | `format` | No | `json`, `xml`, `csv` (default: xml) | | `tool` | Recommended | Your application name | | `email` | Recommended | Your contact email | **Example:** ``` https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/?ids=PMC7029759&format=json ``` **Response:** ```json { "status": "ok", "records": [{ "pmcid": "PMC7029759", "pmid": "32117569", "doi": "10.12688/f1000research.22211.2" }] } ``` Only returns results for articles that are in PMC. If an article is in PubMed but not PMC, no PMCID will be returned. ## Rate Limits | Service | Limit | |---------|-------| | E-utilities (`db=pmc`) | 3/sec without key, 10/sec with key | | BioC API | Follow general NCBI policy (3/sec without key) | | ID Converter | Follow general NCBI policy | Include `tool` and `email` parameters on E-utility requests. Large batch jobs should run outside peak hours (Mon-Fri 5AM-9PM ET).