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This is a 20-year-old male patient, resident in the urban area of Medellín, student, who consulted for a spot on the right palm, asymptomatic, of two months of evolution, without previous treatment, with a single hyperpigmented macule, dark grey, without desquamation, measuring 2 cm x 1 cm, on physical examination. At ... | [
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We present the case of an 11-year-old boy from Gambia who consulted for macroscopic haematuria predominantly at the end of micturition and dysuria of one year's duration; with no history of fever. On taking the medical history, the patient reported a recent trip to his country of origin and several baths in lakes in th... | [
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A 59-year-old woman from China. No relevant medical history. She presented with fever and emesis of 10 days evolution. Last trip to China 1 year ago. No other epidemiological or exposure data of interest.
Laboratory alteration of the liver profile (Bilirubin 2.6 mg/dL and hypertransaminasemia). Isolation of Klebsiella ... | [
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47-year-old male, resident of Cariari in Pococí de Limón. Carrier of type 2 diabetes mellitus, hypertension and chronic liver disease with Child Pugh B clinical stage, secondary to hepatitis B virus infection, with portal hypertension, oesophageal varices and hypersplenism.
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This is a male newborn with a perinatal history of euthecological delivery, gestational age 40 weeks, Apgar 9/9 stitches, Apgar 9/9 stitches. 2 weeks, Apgar 9/9 points and a weight of 3640 grams, who was discharged from the puerperium service at 72 hours of life and at 12 days of age is received in the Neonatology serv... | [
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Anamnesis
No family history of note.
Personal history: no known drug allergies. No toxic habits.
Dyslipidaemia. Stage V chronic kidney disease secondary to juvenile polycystic kidney disease. He started renal replacement therapy in 1991. First kidney transplant from a related living donor (mother) on 16/4/1991, and st... | [
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A 67-year-old man was admitted with fever, cough, nasal congestion, sore throat and diarrhoea, 20 months after an uncomplicated heart transplant. He was not hypoxic.
A chest CT scan showed peripheral, multifocal, bilateral ground-glass opacities. The white blood cell count was 4720/ml, with a lymphocyte count of 1040/... | [
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A 54-year-old male smoker with a history of obesity, dyslipidaemia, ischaemic heart disease and intermittent claudication. He underwent vascular surgery and underwent right ilio-femoral bypass, with placement of a dacron vascular prosthesis due to critical stenosis of the iliac artery. In the immediate postoperative pe... | [
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A 42 year old male traveller from Catalonia who made a 6 month trip (first half of 2001) to South America. He started his trip in the south of Argentina, then in Chile and Bolivia, ending with a month and a half in the Peruvian Amazon, specifically in Iquitos. He came to the clinic with a three-week history of symptoms... | [
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Child aged 6 weeks (March 2014).
Reason for consultation: presence of nasal mucus and cough since 3 weeks of life. During the last week there were more intense coughing spells at night, accompanied by peribuccal cyanosis on some occasions. Afebrile. No other symptoms reported.
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We present the case of a 45-year-old man who presented to the emergency department with progressive dyspnoea for approximately two weeks accompanied by palpitations. He worked in a florist's shop and reported no past history of interest. He denied recent travel or exposure to environmental toxic agents. Physical examin... | [
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End of preview. Expand in Data Studio
LivingNER: Named entity recognition, normalization & classification of species, pathogens and food
Dataset Summary
The LivingNER Gold Standard corpus is a collection of 2000 clinical case reports covering a broad range of medical specialities, i.e. infectious diseases (including Covid-19 cases), cardiology, neurology, oncology, dentistry, pediatrics, endocrinology, primary care, allergology, radiology, psychiatry, ophthalmology, urology, internal medicine, emergency and intensive care medicine, tropical medicine, and dermatology annotated with species [SPECIES] (including living organisms and microorganisms) and infectious diseases [ENFERMEDAD] mentions. Species mentions include many pathogens and infectious agents, but also food, allergens, pets or other species, taxonomic groups and organisms of clinical relevance.
The LivingNER corpus has also annotations of mentions of humans (tag HUMAN), including the patients itself, family members, healhcare professionals or other persons mentioned in the case reports. Thus it can be useful to extract family history information of patients or information about the social and healthcare personal environment and interactions.
All mentions have been exhaustively manually mapped by experts to their corresponding (NCBI Taxonomy)[https://www.ncbi.nlm.nih.gov/taxonomy] identifiers.
It was used for the (LivingNER)[https://temu.bsc.es/livingner/] Shared Task on pathogens and living beings detection and normalization in Spanish medical documents, which was celebrated as part of IberLEF 2022.
Usage
from datasets import load_dataset
# Load the dataset
dataset = load_dataset('path/to/dataset', '{lang}')
# Access splits
train_data = dataset['train']
test_data = dataset['test']
Labels
The following entity types are annotated in this dataset: ['O', 'B-HUMAN', 'I-HUMAN', 'B-SPECIES', 'I-SPECIES']
Citation Information
@article{amiranda2022nlp,
title={Mention detection, normalization \& classification of species, pathogens, humans and food in clinical documents: Overview of LivingNER shared task and resources},
author={Miranda-Escalada, Antonio and Farr{\'e}-Maduell, Eul{`a}lia and Lima-L{\'o}pez, Salvador and Estrada, Darryl and Gasc{\'o}, Luis and Krallinger, Martin},
journal = {Procesamiento del Lenguaje Natural}, year={2022}
}
@dataset{miranda_escalada_2022_7684093,
author = {Miranda-Escalada, Antonio and
Farré-Maduell, Eulàlia and
Lima-López, Salvador and
González Gacio, Gloria and
Krallinger, Martin},
title = {LivingNER corpus: Named entity recognition,
normalization \& classification of species,
pathogens and food
},
month = jun,
year = 2022,
publisher = {Zenodo},
version = {6.3.1},
doi = {10.5281/zenodo.7684093},
url = {https://doi.org/10.5281/zenodo.7684093},
}
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