parse_pmcid
Retrieves open-access articles from Europe PMC by PMCID and parses full text and supplements into a structured map, enabling batch assessment without a local file.
Instructions
CONVENIENCE / BATCH entry point: retrieve an open-access article from
Europe PMC by PMCID and parse it. Reach for this in the corpus/batch case
(no file in hand) or to auto-fetch an open-access paper's supplement; for a
single manuscript you were given, use parse_manuscript instead. Fetches JATS
main text plus (if available) PMC-hosted supplementary files, merged into
one source-tagged SectionMap. supplement_status is 'retrieved' when a
supplement was obtained, else 'not_retrieved' (a supplement may still exist
on the publisher site; absence of retrieval is not proof of absence).
Raises if no open-access full text is available. Returns the same summary
as parse_manuscript, including the text hash for assess_manuscript.
An APA-style citation is auto-built from the article's JATS metadata and
displayed on every rendered checklist; pass citation= to override it (e.g.
when the auto-built reference is incomplete).
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| pmcid | Yes | ||
| citation | No | ||
| include_supplements | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| source | No | ||
| n_pages | No | ||
| citation | No | ||
| sections | No | ||
| warnings | No | ||
| documents | No | ||
| full_text | No | ||
| text_sha256 | No | ||
| manuscript_id | No | ||
| extractor_version | No | ||
| supplement_status | No | ||
| flow_diagram_detected | No | ||
| protocol_table_detected | No |