Medical Information Extraction

A dataset of relationships between medical terms in PubMed articles, for relation extraction and related natural language processing tasks.

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About this data

This dataset contains 3,984 medical sentences extracted from PubMed abstracts and relationships between discrete medical terms were annotated. This dataset focuses primarily on “treat” and “cause” relationships, with 1,043 sentences containing treatment relations and 1,787 containing causal ones.

Human-in-the-loop annotators were given two different terms (such as “Lewy Body Dementia” and “Well-formed Visual Hallucinations”) and were asked to mark the relationship between those terms (in this case “Lewy Body Dementia causes Well-Formed Visual Hallucinations).

This corpus has been referenced in the following papers:

  • Anca Dumitrache, Lora Aroyo, Chris Welty: CrowdTruth Measures for Language Ambiguity: The Case of Medical Relation Extraction. LD4IE at ISWC 2015.
  • Anca Dumitrache, Lora Aroyo, Chris Welty: Achieving Expert-Level Annotation Quality with CrowdTruth: The Case of Medical Relation Extraction. BDM2I at ISWC 2015.
View Instructions and Job Design

Below, you’ll find a link to the Figure Eight job used to annotate relationships between medical terms. The “Duplicate Job” button above will take you to a template that follows this exact workflow.

Preview Job

Raw Data

The input data for this job are sentences from medical publications, medical relations, and a pair of key terms from that sentence.

relationsentenceterm1term2                      
causesMarch Hemoglobinuria MARCH HEMOGLOBINURIA a disorder that somewhat resembles MICROANGIOPATHIC HEMOLYSIS usually occurs in young persons after prolonged marching or running or playing on bongo drums.MICROANGIOPATHIC HEMOLYSISMARCH HEMOGLOBINURIA
causesFluctuations in cognition, parkinsonian symptoms, WELL FORMED VISUAL HALLUCINATIONS and relative preservation of short term memory suggest LEWY BODY DEMENTIA rather than Alzheimer's disease (see Table 213 5.WELL FORMED VISUAL HALLUCINATIONSLEWY BODY DEMENTIA
causesAnd for GLAUCOMATOUS PAINFUL BLIND EYE and some cases of GLAUCOMA Cyclocryotherapy for ciliary body ablation could be considered to be performed.[28] [edit] Veterinary implant TR BioSurgical has commercialized a new implant specifically for veterinary medicine, called TR ClarifEYE.GLAUCOMATOUS PAINFUL BLIND EYEGLAUCOMA
causesAccording to an expert review, POSTOPERATIVE HYPERTENSION occurs in up to 50% of patients after PHEOCHROMOCYTOMA RESECTION ( 29.POSTOPERATIVE HYPERTENSIONPHEOCHROMOCYTOMA RESECTION
causesNerve injury and reduced sensory input more often cause NEUROPATHIC PAIN than cure it, and augmenting sensory input often lessens NEURALGIANEUROPATHIC PAINNEURALGIA
causesMarch Hemoglobinuria MARCH HEMOGLOBINURIA a disorder that somewhat resembles MICROANGIOPATHIC HEMOLYSIS usually occurs in young persons after prolonged marching or running or playing on bongo drums.MICROANGIOPATHIC HEMOLYSISMARCH HEMOGLOBINURIA
causesFluctuations in cognition, parkinsonian symptoms, WELL FORMED VISUAL HALLUCINATIONS and relative preservation of short term memory suggest LEWY BODY DEMENTIA rather than Alzheimer's disease (see Table 213 5.WELL FORMED VISUAL HALLUCINATIONSLEWY BODY DEMENTIA
causesAnd for GLAUCOMATOUS PAINFUL BLIND EYE and some cases of GLAUCOMA Cyclocryotherapy for ciliary body ablation could be considered to be performed.[28] [edit] Veterinary implant TR BioSurgical has commercialized a new implant specifically for veterinary medicine, called TR ClarifEYE.GLAUCOMATOUS PAINFUL BLIND EYEGLAUCOMA
causesAccording to an expert review, POSTOPERATIVE HYPERTENSION occurs in up to 50% of patients after PHEOCHROMOCYTOMA RESECTION ( 29.POSTOPERATIVE HYPERTENSIONPHEOCHROMOCYTOMA RESECTION
causesFluctuations in cognition, parkinsonian symptoms, WELL FORMED VISUAL HALLUCINATIONS and relative preservation of short term memory suggest LEWY BODY DEMENTIA rather than Alzheimer's disease (see Table 213 5.WELL FORMED VISUAL HALLUCINATIONSLEWY BODY DEMENTIA
Download Options
test.csv | 1.9 MB
train.csv | 5.7 MB
validation.csv | 1.8 MB