Biogod/PMC-ClinicalLogs-1K

PMC Clinical Logs 1K

A free, open sample of PMC Clinical Logs: 1,000 time-ordered clinical logs of PubMed Central case reports with 5,848 original figures, previewable on the Hub. No access request is needed.

Cases	1,000 (also in the full release, is_showcase = true)
Original figures	5,848, embedded in data/images/*.parquet
Source licenses	All CC BY, CC BY-SA or CC0; commercial use allowed with attribution
Clinical validation	None yet: logs are model-generated and not checked by physicians
Reproducible revision	tag v1.0.1-20261104

The full release has 150,272 cases and 480,791 figures and needs approval: PMC-ClinicalLogs.

Original figures from CC BY articles in the 1K sample, centre-cropped to squares. Sources, captions and licenses: assets/gallery.json.

What a clinical log is

Each case report is rewritten as an ordered list of events: context, observations, reasoning, actions and results. Every event cites the source text it comes from. Where the article states it, an event also records when it happened and when the information became available. Each event is marked as reported at the time, reconstructed from the text, or a retrospective interpretation. This lets you cut a case at any point and see only what was known by then.

One case, three views. Left: numbered paragraphs of the article (shortened with …). Middle: 9 of the case's 13 events, with links to the paragraphs they cite, the uses links of one reasoning event and the original figure panels; a cut before the MRI hides the later events. Right: the MRI result event as stored. Case: Manjaly et al., "An Unusual Cause of Pseudomedian Nerve Palsy" (2011), PMC3420447, CC BY 3.0; panels are crops of its Fig. 1.

How the sample was chosen

Cases were drawn to vary publication year (2004–2026), number of events and number of figures. Every case has all its figures available and an open license. Cases used by the maintainers for evaluation or as fixed references were excluded. The sample is not representative of all case reports and is not a held-out test set. Selection details: provenance/showcase-selection.json.

Fields

cases config (data/cases/*.parquet), one row per case:

Field	Content
case_id, pmcid, title, publication_year, source_url	Identity and link to the article
license_id, license_url, license_text	The source article's license and its statement
clinical_log_json	The full log as a JSON string (schema clinical-log/1.4): participants, events, source_notes
clinical_log_text	The same log as readable text
source_json	JSON string: article text split into segments, figure captions and metadata (schema clinical-source/1.0)
event_count, media_count, source_media_count	Events; figures released; figures in the article
has_multisubject_events	The case involves more than one person (for example mother and infant)
clinical_review_status	Always model_generated_not_physician_gold in this release

Main event fields in clinical_log_json: kind (context, observation, reasoning, action, result), phase, text, occurred, available, basis (reported, reconstructed, retrospective), actor, status, links between events (result_of, response_to, uses, after, revises), patient_state.facts, and sources (segment id, character span and the quoted text).

images config, one row per figure: case_id, pmcid, media_id, figure_id, caption, source_url, license_id, license_url, sha256, bytes, image. Join to cases on case_id.

Loading

from datasets import load_dataset

cases = load_dataset("Biogod/PMC-ClinicalLogs-1K", "cases", split="train", revision="v1.0.1-20261104")
images = load_dataset("Biogod/PMC-ClinicalLogs-1K", "images", split="train", revision="v1.0.1-20261104")

One case with its original images, checksums verified:

hf download Biogod/PMC-ClinicalLogs-1K read_case.py --repo-type dataset --local-dir .
uv run --with huggingface_hub --with pyarrow read_case.py --pmcid PMC10001472 --output ./PMC10001472

Licenses

Every record keeps the license of its source article (license_id, license_url, license_text); this collection grants no further rights. Cite this collection and the source articles you use.

Limitations

• Not clinically validated. A single language model wrote the logs from each article. Automated checks confirm structure, source quotes and file integrity, not clinical correctness. Event order and times can be wrong, and errors in the original articles are kept.
• Multiple subjects. Check cases with has_multisubject_events = true against the source before treating facts as belonging to one patient.
• Privacy. The source case reports are already published. This release adds no further de-identification: dates, ages, places and occupations appear as the article states them. Do not try to identify patients.
• Coverage. Case reports over-represent rare and unusual presentations; they are not a sample of routine care.

Release checks and counts: provenance/export-summary.json. Built from the maintainers' snapshot full-20260928-v1.

Citation

@misc{pmc_clinical_logs_2026,
  title  = {PMC Clinical Logs},
  author = {Ji, Jiahao and Yu, Jintai and Yuan, Zhiyuan},
  year   = {2026},
  howpublished = {\url{https://huggingface.co/datasets/Biogod/PMC-ClinicalLogs}},
  note   = {Revision v1.0.1-20261104}
}