Datasets:
pmcid large_stringlengths 9 11 | title large_stringlengths 7 305 | journal large_stringclasses 811
values | publication_date large_stringlengths 10 12 | article_link large_stringlengths 52 54 | license large_stringclasses 273
values | abstract large_stringlengths 0 4.17k | body_text large_stringlengths 0 51.8k | sections listlengths 0 42 | abstract_section large_stringclasses 70
values | background large_stringlengths 0 18.6k | case_presentation large_stringlengths 0 20.6k | investigations large_stringclasses 468
values | management large_stringclasses 918
values | outcome large_stringclasses 162
values | discussion large_stringlengths 0 23.9k | conclusion large_stringlengths 0 14.1k | references large_stringclasses 1
value | other large_stringlengths 0 49.7k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PMC10000501 | Multisystem Inflammatory Syndrome in Adults Associated with Recent Infection with COVID-19 | Diagnostics | 2023-03-04 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10000501/ | Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( | Multisystem inflammatory syndrome in adults (MIS-A) is an uncommon but severe and still understudied post-infectious complication of COVID-19. Clinically, the disease manifests itself most often 2–6 weeks after overcoming the infection. Young and middle-aged patients are especially affected. The clinical picture of the... | Multisystem inflammatory syndrome was first described as a nosological entity in 2020, initially mainly in a group of pediatric patients (as MIS-C). Later, the first cases of this disease also began to appear in a group of adult patients (MIS-A). In adults, the clinical course is extremely variable, with primarily febr... | [
{
"section_type": "background",
"heading": "1. Introduction",
"text": "Multisystem inflammatory syndrome was first described as a nosological entity in 2020, initially mainly in a group of pediatric patients (as MIS-C). Later, the first cases of this disease also began to appear in a group of adult pati... | Multisystem inflammatory syndrome was first described as a nosological entity in 2020, initially mainly in a group of pediatric patients (as MIS-C). Later, the first cases of this disease also began to appear in a group of adult patients (MIS-A). In adults, the clinical course is extremely variable, with primarily febr... | A 22-year-old patient, who was not treated for anything prior to testing, was examined at the outpatient department of the infectious disease clinic for fever lasting 3 days with a maximum temperature of up to 40.2 °C, as well as myalgia, arthralgia, headache, a dry cough with dyspnea, and vomiting. The patient reporte... | Multisystem inflammatory syndrome represents a potentially life-threatening complication upon infection with COVID-19, the pathophysiology of which is not yet fully understood. The syndrome was first described in April 2020 in a group of children whose clinical symptoms resembled Kawasaki disease. Later, similar cases ... | Multisystem inflammatory syndrome in adults represents a severe complication of COVID-19, whose pathophysiology has not yet been clarified. It likely arises from the dysregulated immune response of the host caused by the SARS-CoV-2 virus. It most often occurs in the postacute period of infection, and the clinical manif... | ||||||
PMC10003745 | Body Stalk Anomaly Complicated by Ectopia Cordis: First-Trimester Diagnosis of Two Cases Using 2- and 3-Dimensional Sonography | Journal of Clinical Medicine | 2023-02-27 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10003745/ | Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( | Introduction: Body stalk anomaly is a severe defect of the abdominal wall, characterized by the evisceration of abdominal organs and, in more severe cases, thoracic organs as well. The most serious condition in a body stalk anomaly may be complicated by ectopia cordis, an abnormal location of the heart outside the thor... | Body stalk anomaly is a congenital abnormality of the abdominal wall, depending on the evisceration of abdominal organs and, in more complicated clinical cases, thoracic organs. This anomaly is usually characterized also by kyphoscoliosis and by a defect of the umbilical cord, which is usually short or not present . Th... | [
{
"section_type": "background",
"heading": "1. Introduction",
"text": "Body stalk anomaly is a congenital abnormality of the abdominal wall, depending on the evisceration of abdominal organs and, in more complicated clinical cases, thoracic organs. This anomaly is usually characterized also by kyphoscol... | Body stalk anomaly is a congenital abnormality of the abdominal wall, depending on the evisceration of abdominal organs and, in more complicated clinical cases, thoracic organs. This anomaly is usually characterized also by kyphoscoliosis and by a defect of the umbilical cord, which is usually short or not present . Th... | A 25-year-old woman was referred for an ultrasound scan at 9 weeks of gestation.
There was no relevant medical history, and she was taking no medication. There were no teratogenic risk factors in the clinical history of the woman. It was her second pregnancy, and her first pregnancy was uneventful. The ultrasound scan... | In our scientific work, we described our experience with two cases of prenatal diagnosis of a body stalk anomaly complicated by ectopia cordis during a routine sonographic screening for chromosomic abnormalities in the first trimester. A body stalk anomaly is defined as a pathological congenital condition of multiple a... | Body stalk anomaly is a congenital pathological condition with uncertain etiopathogenesis, uncertain pathophysiology, and an uncertain incidence rate. In the scientific literature, most of the reported clinical cases described an early diagnosis performed between 10 and 14 weeks of gestation; in our first case report, ... | ||||||
PMC10006300 | Primary intramuscular and intermuscular Echinococcal disease of the iliopsoas and sartorius muscles: A case report | Radiology Case Reports | 2023-05-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10006300/ | This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). | Hydatid disease is a parasitic infection caused by the Echinococcus tapeworm. Classically, Echinococcal lesions are slowly growing cystic masses with daughter cysts. The most common sites of disease are the liver in 75% of cases and lungs in 15% of cases. This report covers a case of a patient from Southeast Europe wit... | Hydatid disease is a parasitic disease caused by the Echinococcus tapeworm. The most common species are Echinococcus granulosis and Echinococcus multilocularis, where they are endemic to South America, Central Europe, the Mediterranean, Central Asia, Western China, and East Africa . Classically, hydatid lesions are slo... | [
{
"section_type": "background",
"heading": "Introduction",
"text": "Hydatid disease is a parasitic disease caused by the Echinococcus tapeworm. The most common species are Echinococcus granulosis and Echinococcus multilocularis, where they are endemic to South America, Central Europe, the Mediterranean,... | Hydatid disease is a parasitic disease caused by the Echinococcus tapeworm. The most common species are Echinococcus granulosis and Echinococcus multilocularis, where they are endemic to South America, Central Europe, the Mediterranean, Central Asia, Western China, and East Africa . Classically, hydatid lesions are slo... | A 60-year-old male with a history of poliomyelitis as a child and residual right-sided weakness presented initially to his primary care physician for left lower quadrant abdominal pain, a left groin painful mass, and left lower extremity swelling. The patient grew up in Montenegro and moved to the United States as a te... | Hydatid disease is a parasitic infection caused by ingestion of the Echinococcus tapeworm larva. The most common species are Echinococcus granulosus, which causes cystic hydatid disease, and E multilocularis, which causes alveolar hydatid disease. The definitive host is usually a dog where the adult worm lives in the p... | Informed consent was obtained from the subject described in this report. | ||||||
PMC10006302 | Hydrosalpinx with adnexal torsion in an adult patient–A case report | Radiology Case Reports | 2023-05-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10006302/ | This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). | Adnexal torsion is a common gynecological emergency and a significant cause of acute pelvic pain in women. Hydrosalpinx-induced torsion of the adnexa is a rare situation and requires prompt and accurate management. Twenty-three years old nulliparous woman admitted in our structure for acute pelvic pain. The ultrasound ... | Adnexal torsion usually involves both the ovary and fallopian tube, but can involve only one of them in some cases .
Hydrosalpinx is a rare predisposing factor of adnexal or isolated fallopian tube torsion. Infection causes damage to the endosalpinx, resulting in a distal occlusion of the tube and accumulation of the ... | [
{
"section_type": "background",
"heading": "Introduction",
"text": "Adnexal torsion usually involves both the ovary and fallopian tube, but can involve only one of them in some cases .\n\nHydrosalpinx is a rare predisposing factor of adnexal or isolated fallopian tube torsion. Infection causes damage to... | Adnexal torsion usually involves both the ovary and fallopian tube, but can involve only one of them in some cases .
Hydrosalpinx is a rare predisposing factor of adnexal or isolated fallopian tube torsion. Infection causes damage to the endosalpinx, resulting in a distal occlusion of the tube and accumulation of the ... | Twenty-three years old nulliparous woman, without history of illness or drug use, admitted to the Gynecology Emergency Department for sudden-onset, intense, acute pelvic pain, which had started 2 hours before the admission.
Firstly, anamnesis revealed that the patient had similar but much less severe episodes in the p... | Hydrosalpinx occurs following a complete distal occlusion due to tubal damage and adhesions caused by various conditions of the fimbriated end of the tube .
In adults, the most common cause of hydrosalpinx is pelvic inflammatory disease.
Hydrosalpinx is one of the predisposing factors of adnexal torsion. Any increase... | Hydrosalpinx-induced adnexal torsion is a rare gynecological emergency. Clinical presentation is nonspecific and is often difficult to distinguish from other acute abdominal conditions.
Early diagnosis is important for preventing necrosis of the twisted adnexa. Multiplanar MR imaging may be used to help differentiate ... | ZE is the corresponding author, she participated in the organization and writing of the article and studying the cases with YC. Professor NE, MH, BA and YL supervised working and validated the figures. YB and FM contributed in clinical examination, surgical treatment and follow up of the patient. Professor and chief of... | |||||
PMC10006724 | Pancreatic involvement in Erdheim-Chester disease: Rare presentation of a rare disease | Radiology Case Reports | 2023-05-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10006724/ | "This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/b(...TRUNCATED) | "Erdheim-Chester disease (ECD) as a rare non-Langerhans histiocytosis has various clinical manifesta(...TRUNCATED) | "Erdheim-Chester disease (ECD) is a rare, potentially fatal systemic myeloid neoplastic disease, fir(...TRUNCATED) | [{"section_type":"background","heading":"Introduction","text":"Erdheim-Chester disease (ECD) is a ra(...TRUNCATED) | "Erdheim-Chester disease (ECD) is a rare, potentially fatal systemic myeloid neoplastic disease, fir(...TRUNCATED) | "A 73-year-old lady was evaluated at our hospital because of a recently detected infiltrative middle(...TRUNCATED) | "The etiology of ECD still remains unclear. It is classified as a neoplastic disease due to recently(...TRUNCATED) | "Erdheim-Chester has been known as a disease of long bones and retroperitoneum, However, it potentia(...TRUNCATED) | "Bone pain, most commonly around the knees and ankles is the most frequent presenting manifestation (...TRUNCATED) | |||||
PMC10008222 | Kaposi sarcoma at the base of the tongue in a renal transplant patient | BMJ Case Reports | 2023-01-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10008222/ | "This is an open access article distributed in accordance with the Creative Commons Attribution Non (...TRUNCATED) | "Oral Kaposi Sarcoma (OKS) commonly occurs in patients with AIDS. The incidence of Kaposi sarcoma (K(...TRUNCATED) | "Kaposi sarcoma (KS) is an angioproliferative disease that is rare in the general population. The in(...TRUNCATED) | [{"section_type":"background","heading":"Background","text":"Kaposi sarcoma (KS) is an angioprolifer(...TRUNCATED) | "Kaposi sarcoma (KS) is an angioproliferative disease that is rare in the general population. The in(...TRUNCATED) | "A man in his early 40s was admitted to the hospital after reporting a lump in his throat for the pr(...TRUNCATED) | "Blood analysis including complete blood count and blood chemistry was done. In addition, the follow(...TRUNCATED) | "Treatment with the calcineurin inhibitor was stopped, and the patient started with an mTOR (mammali(...TRUNCATED) | "Clinically, KS strongly resembles certain vascular lesions, including haemangiomas, lymphangiomas, (...TRUNCATED) | "Two months following radiotherapy, the tracheostomy was removed. A fibreoptic examination revealed (...TRUNCATED) | ||||
PMC10009334 | "Acute cervicitis resembling gastric-type mucinous adenocarcinoma that was definitively diagnosed by(...TRUNCATED) | Radiology Case Reports | 2023-05-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10009334/ | "This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/b(...TRUNCATED) | "Although imaging studies are not typically performed for clinical diagnosis of cervicitis, in this (...TRUNCATED) | "Uterine cervicitis, known as the initial manifestation of sexually transmitted diseases (STDs), is (...TRUNCATED) | [{"section_type":"background","heading":"Introduction","text":"Uterine cervicitis, known as the init(...TRUNCATED) | "Uterine cervicitis, known as the initial manifestation of sexually transmitted diseases (STDs), is (...TRUNCATED) | "The patient, a 30-year-old woman (gravida [G] 2, para [P] 2), was referred to a gynecologist with a(...TRUNCATED) | "Uterine cervical infection is defined as invasion of cervical tissue by a microorganism or virus wi(...TRUNCATED) | |||||||
PMC10009337 | Solitary juvenile xanthogranuloma in the parotid gland | Radiology Case Reports | 2023-05-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10009337/ | "This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/b(...TRUNCATED) | "Juvenile xanthogranuloma (JX) is a non-Langerhans cell histiocytosis. Although precipitating factor(...TRUNCATED) | "Juvenile xanthogranuloma (JX) is the most common non-Langerhans cell histiocytosis and occurs in in(...TRUNCATED) | [{"section_type":"background","heading":"Introduction","text":"Juvenile xanthogranuloma (JX) is the (...TRUNCATED) | "Juvenile xanthogranuloma (JX) is the most common non-Langerhans cell histiocytosis and occurs in in(...TRUNCATED) | "An otherwise healthy 1 month old girl presented with a firm, palpable mass located anterior-inferio(...TRUNCATED) | "JX is an uncommon lesion caused by proliferation of histiocytes, of the non-Langerhans type. It is (...TRUNCATED) | "The authors declare and confirm that written, informed consent for publication of our patients’ c(...TRUNCATED) | ||||||
PMC10010120 | "A Rare Case of COVID-19-Induced Acute Exacerbation of Oral Dermatitis Herpetiformis in a Geriatric (...TRUNCATED) | International Medical Case Reports Journal | 2023-03-09 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10010120/ | "This work is published and licensed by Dove Medical Press Limited. The full terms of this license a(...TRUNCATED) | "Introduction Dermatitis herpetiformis (DH) is an autoimmune vesiculobullous disease associated with(...TRUNCATED) | "Dermatitis herpetiformis (DH) is an autoimmune vesiculobullous disease that was first proposed by L(...TRUNCATED) | [{"section_type":"background","heading":"Introduction","text":"Dermatitis herpetiformis (DH) is an a(...TRUNCATED) | "Dermatitis herpetiformis (DH) is an autoimmune vesiculobullous disease that was first proposed by L(...TRUNCATED) | "A 74-year-old woman was referred from the Department of Dermatology and Venereology to the Departme(...TRUNCATED) | "Dermatitis herpetiformis (DH) is a mucocutaneous manifestation of celiac disease (CD), in which the(...TRUNCATED) | "In this case report, COVID-19 infection can trigger an acute exacerbation of dermatitis herpetiform(...TRUNCATED) | ||||||
PMC10010791 | Autoimmune Enteropathy: A Rare Cause of Chronic Diarrhea in an Adult Patient | ACG Case Reports Journal | 2023-03-01 | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10010791/ | This is an open access article distributed under the terms of the | "ABSTRACT Autoimmune enteropathy is a rare cause of malabsorption usually associated with circulatin(...TRUNCATED) | "Autoimmune enteropathy (AIE) is a rare cause of intractable diarrhea associated with villous atroph(...TRUNCATED) | [{"section_type":"background","heading":"INTRODUCTION","text":"Autoimmune enteropathy (AIE) is a rar(...TRUNCATED) | "Autoimmune enteropathy (AIE) is a rare cause of intractable diarrhea associated with villous atroph(...TRUNCATED) | "A 73-year-old woman with type 2 diabetes under metformin was admitted to the emergency department w(...TRUNCATED) | "AIE is a rare disorder characterized by intractable diarrhea and small intestine mucosal atrophy re(...TRUNCATED) | "Author contributions: AC Carvalho drafted the manuscript, performed a review of the literature, and(...TRUNCATED) |
End of preview. Expand in Data Studio
PubMed Case Reports
A collection of 13,989 full-text case reports from the PubMed Central (PMC) Open Access subset, spanning 2005–2025. Each article includes structured metadata, abstract, full body text, and section-level annotations. This dataset is designed for medical NLP, clinical reasoning, and biomedical text mining.
Dataset Description
Summary
This dataset comprises case reports published in peer-reviewed medical journals, sourced from the PMC Open Access Subset. Case reports are detailed accounts of individual patient encounters — including presentation, diagnosis, treatment, and outcome — making them a rich resource for clinical reasoning research.
Each row corresponds to one article with:
- Bibliographic metadata (title, journal, publication date, PMCID, license)
- Structured abstract and full body text
- Section-level breakdown of the body text with normalised section types (background, case presentation, investigations, management, outcome, discussion, etc.)
Supported Tasks
| Task | Description |
|---|---|
| Clinical text generation | Pre-train or fine-tune language models on medical case report text |
| Abstractive QA / summarisation | Generate summaries of clinical encounters from full text |
| Section classification | Classify paragraphs by clinical section type |
| Information extraction | Extract medical entities, relations, and treatment-outcome pairs |
| Clinical reasoning evaluation | Use as a knowledge source for retrieval-augmented generation (RAG) pipelines |
Languages
All articles are in English.
Dataset Structure
Data Fields
| Field | Type | Description |
|---|---|---|
pmcid |
string |
PubMed Central identifier (e.g., PMC1234567) |
title |
string |
Article title |
journal |
string |
Journal name |
publication_date |
string |
Publication date in YYYY-MM-DD format |
article_link |
string |
URL to the article on PubMed Central |
license |
string |
License text or URL |
abstract |
string |
Article abstract (may be empty for some entries) |
body_text |
string |
Full body text, concatenated from all sections |
sections |
list[dict] |
Section-level breakdown (see below) |
background |
string |
Concatenated text of all background‑type sections |
case_presentation |
string |
Concatenated text of all case_presentation‑type sections |
discussion |
string |
Concatenated text of all discussion‑type sections |
conclusion |
string |
Concatenated text of all conclusion‑type sections |
investigations |
string |
Concatenated text of all investigations‑type sections |
management |
string |
Concatenated text of all management‑type sections |
outcome |
string |
Concatenated text of all outcome‑type sections |
other |
string |
Concatenated text of all other‑type sections (declarations, ethics, supplementary, etc.) |
references |
string |
Concatenated text of all references‑type sections |
Each element in the sections list is a dictionary with:
| Sub-field | Type | Description |
|---|---|---|
section_type |
string |
Normalised section type (one of: abstract, background, case_presentation, investigations, management, outcome, discussion, conclusion, references, other) |
heading |
string |
Original section heading (e.g., "Case Presentation", "Discussion") |
text |
string |
Section body text |
In addition to the nested sections list, each section type is also available as a top-level string column (e.g. background, case_presentation, discussion) containing the concatenated text of all sections of that type, making it easy to access specific clinical sections without iterating over lists.
Data Splits
The dataset contains a single split:
| Split | Size |
|---|---|
train |
13,989 |
Data Instance Example
{
"pmcid": "PMC10000501",
"title": "Multisystem Inflammatory Syndrome in Adults Associated with Recent Infection with COVID-19",
"journal": "Diagnostics",
"publication_date": "2023-03-04",
"article_link": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10000501/",
"license": "© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license",
"abstract": "Multisystem inflammatory syndrome in adults (MIS-A) is a rare but severe complication of coronavirus disease 2019 (COVID-19)...",
"body_text": "Background\\n\\nMultisystem inflammatory syndrome in adults (MIS-A) is a rare but severe complication...",
"sections": [
{"section_type": "background", "heading": "1. Introduction", "text": "Multisystem inflammatory syndrome in adults (MIS-A) is a rare..."},
{"section_type": "case_presentation", "heading": "2. Case Report", "text": "A 34-year-old male with no significant past medical history..."},
{"section_type": "discussion", "heading": "3. Discussion", "text": "MIS-A is a newly recognized entity that presents with..."},
{"section_type": "conclusion", "heading": "4. Conclusions", "text": "This case highlights the importance of considering MIS-A..."}
],
"background": "Multisystem inflammatory syndrome in adults (MIS-A) is a rare...",
"case_presentation": "A 34-year-old male with no significant past medical history...",
"discussion": "MIS-A is a newly recognized entity that presents with...",
"conclusion": "This case highlights the importance of considering MIS-A...",
"investigations": "",
"management": "",
"outcome": "",
"other": "",
"references": ""
}
Dataset Statistics
Overview
| Metric | Value |
|---|---|
| Total articles | 13,989 |
| Unique PMCIDs | 13,989 |
| Unique journals | 811 |
| Year range | 2005–2025 |
| Total characters (abstract + body) | ~171 M |
| Total words (abstract + body) | ~25 M |
Per-Column Statistics
| Column | Non-empty | Mean chars | Mean words | Min chars | Max chars |
|---|---|---|---|---|---|
title |
13,989 | 92 | 13 | 7 | 305 |
abstract |
13,527 | 1,038 | 148 | 0 | 4,171 |
body_text |
13,988 | 11,174 | 1,635 | 0 | 51,830 |
sections |
13,988 | 6.0 sec/row | — | 0 | 42 |
background |
13,215 (94.5%) | 1,248 | 184 | 0 | 18,594 |
case_presentation |
11,557 (82.6%) | 3,082 | 452 | 0 | 20,614 |
discussion |
12,940 (92.5%) | 4,350 | 637 | 0 | 23,891 |
conclusion |
8,227 (58.8%) | 356 | 52 | 0 | 14,062 |
investigations |
468 (3.3%) | 64 | 9 | 0 | 9,375 |
management |
918 (6.6%) | 75 | 11 | 0 | 8,123 |
outcome |
161 (1.2%) | 7 | 1 | 0 | 5,412 |
other |
9,311 (66.6%) | 1,982 | 289 | 0 | 49,658 |
references |
0 (0.0%) | 0 | 0 | 0 | 0 |
Note: Section-type columns (background, case_presentation, etc.) contain empty strings when no section of that type is present in an article. The "Non-empty" column shows how many rows have content for each field.
Publication Years
| Year Range | Articles |
|---|---|
| 2005–2010 | 418 |
| 2011–2015 | 2,498 |
| 2016–2020 | 4,167 |
| 2021–2025 | 7,205 |
The collection skews toward recent publications, with the majority (51%) from 2021–2025.
Top Journals
| Articles | Journal |
|---|---|
| 1,136 | Journal of Medical Case Reports |
| 1,057 | Clinical Case Reports |
| 959 | International Journal of Surgery Case Reports |
| 886 | Radiology Case Reports |
| 403 | Journal of Surgical Case Reports |
| 345 | JAAD Case Reports |
| 299 | SAGE Open Medical Case Reports |
| 294 | Journal of Orthopaedic Case Reports |
| 263 | Case Reports in Medicine |
| 228 | European Heart Journal: Case Reports |
| 204 | American Journal of Ophthalmology Case Reports |
| 190 | Case Reports in Dentistry |
License Distribution (Top 10)
| Count | License |
|---|---|
| 2,412 | CC BY-NC-ND 4.0 |
| 2,227 | Creative Commons Attribution License |
| 1,321 | Terms of CC Attribution license |
| 907 | CC BY 4.0 |
| 774 | CC BY-NC 4.0 |
| 703 | CC BY 3.0 |
| 609 | CC BY-NC-SA 4.0 |
| 567 | CC BY-NC-ND 3.0 |
| 420 | CC BY-SA 4.0 |
| 386 | CC BY 2.0 |
Section Types
Sections are normalised into the following categories:
| Section Type | Coverage | Description |
|---|---|---|
background |
94.5% | Introduction, background |
case_presentation |
82.6% | Case report, clinical history, patient presentation |
discussion |
92.5% | Discussion, differential diagnosis |
conclusion |
58.8% | Conclusion |
other |
66.6% | Declarations, ethics, supplementary, etc. |
management |
6.6% | Treatment, therapeutic intervention |
investigations |
3.3% | Diagnostic workup, lab findings, imaging |
outcome |
1.2% | Follow-up, outcome |
references |
<0.1% | References |
abstract¹ |
— | Article abstract (stored as top-level abstract column) |
¹ abstract section types from the body are not duplicated as a separate column since the article's structured abstract is already available as the top-level abstract field.
Dataset Creation
Source Data
The raw XML files were downloaded from the PMC Open Access Subset via the PMC Cloud Service S3 bucket (pmc-oa-opendata).
Curation Process
- Discovery: Case report PMCIDs were discovered by querying PubMed with the
Case Reports[pt]filter, segmented by year to stay within the 10K-result cap. - Download: Full-text XML was downloaded in parallel using async HTTP (aiohttp) from the PMC Cloud Service S3 bucket.
- Parsing: Each XML file was parsed to extract:
- Article metadata (title, journal, publication date, license, abstract)
- Section-aware body text with normalised section type labels
- Text cleaning (citation markers, figure references, whitespace normalisation)
- Format: The parsed data was saved as a Parquet file.
Curation Rationale
Clinical case reports are a uniquely valuable genre of medical literature. Unlike randomised trials or systematic reviews, case reports provide fine-grained, narrative descriptions of individual patient journeys — from initial presentation through diagnosis, treatment, and follow-up. This makes them especially suited for:
- Evaluating clinical reasoning capabilities of language models
- Building retrieval-augmented generation systems for rare conditions
- Training models to understand the structure of clinical narratives
Usage
Loading the Dataset
from datasets import load_dataset
# Load the full dataset
ds = load_dataset("awinml/pubmed_case_reports", split="train")
# Access a single example
example = ds[0]
print(example["title"])
print(example["abstract"])
# Iterate in streaming mode (low memory)
ds_stream = load_dataset("awinml/pubmed_case_reports", split="train", streaming=True)
for i, row in enumerate(ds_stream):
if i >= 10:
break
print(row["pmcid"], row["title"][:80])
Working with Sections
The dataset provides two ways to access section text:
1. Via the sections list (full detail with original headings):
from datasets import load_dataset
ds = load_dataset("awinml/pubmed_case_reports", split="train")
for row in ds:
sections = row["sections"]
presentation = [s for s in sections if s["section_type"] == "case_presentation"]
if presentation:
print(f"PMCID: {row['pmcid']}")
print(f"Heading: {presentation[0]['heading']}")
print(f"Text: {presentation[0]['text'][:200]}...")
break
2. Via direct section columns (simpler, concatenated across all sections of that type):
from datasets import load_dataset
ds = load_dataset("awinml/pubmed_case_reports", split="train")
for row in ds:
if row["case_presentation"]:
print(f"PMCID: {row['pmcid']}")
print(f"Case presentation: {row['case_presentation'][:200]}...")
break
3. Section length analysis with pandas:
from datasets import load_dataset
import pandas as pd
ds = load_dataset("awinml/pubmed_case_reports", split="train")
df = ds.to_pandas()
# Which sections are most common?
for col in ["background", "case_presentation", "discussion", "conclusion"]:
pct = (df[col].str.len() > 0).mean() * 100
print(f"{col}: {pct:.1f}% of articles have this section")
# Average discussion length
df[df["discussion"] != ""]["discussion"].str.len().describe()
Converting to Pandas
import pandas as pd
from datasets import load_dataset
ds = load_dataset("awinml/pubmed_case_reports", split="train")
df = ds.to_pandas()
# Journal distribution
print(df["journal"].value_counts().head(10))
# Average body text length by year
df["year"] = pd.to_datetime(df["publication_date"]).dt.year
print(df.groupby("year")["body_text"].apply(lambda x: x.str.len().mean()))
Retrieval-Augmented Generation
from datasets import load_dataset
from sentence_transformers import SentenceTransformer
# Load and chunk for RAG
ds = load_dataset("awinml/pubmed_case_reports", split="train", streaming=True)
# Build a simple in-memory index from body texts
corpus = []
pmcids = []
for i, row in enumerate(ds):
if i >= 1000:
break
corpus.append(row["body_text"][:2000]) # first 2000 chars
pmcids.append(row["pmcid"])
model = SentenceTransformer("all-MiniLM-L6-v2")
embeddings = model.encode(corpus, show_progress_bar=True)
Limitations & Considerations
- Case reports are inherently anecdotal: They describe individual patient experiences and should not be treated as population-level evidence.
- Publication bias: Journals are more likely to publish rare or novel cases, so the dataset may overrepresent unusual presentations.
- Temporal skew: The collection is weighted toward recent publications (51% from 2021–2025).
- No structured outcome labels: The dataset does not include standardised diagnostic or treatment outcome labels — this is a raw text corpus.
- License variability: Articles carry different Creative Commons licenses. Users should verify license compatibility for their specific use case (see the
licensefield per row). - No PHI redaction guarantee: While the source articles are published in open-access journals, individual case reports may contain identifiable patient information. Users should exercise appropriate caution.
Citation
If you use this dataset, please cite it as:
@misc{awinml_pubmed_case_reports_2025,
author = {Ashwin Mathur},
title = {PubMed Case Reports: A Dataset of Full-Text Clinical Case Reports from PMC},
year = {2025},
publisher = {Hugging Face},
journal = {Hugging Face Datasets},
howpublished = {\\url{https://huggingface.co/datasets/awinml/pubmed_case_reports}}
}
License
The dataset itself is released under CC BY 4.0. Individual articles carry their own licenses as specified in the license field and may have additional restrictions.
Contact
For questions or feedback, open an issue on the dataset repository.
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