Cadec: A corpus of adverse drug event annotations

[Display omitted] •Introduction of CADEC an annotated corpus of consumer reviews in pharmacovigilance.•A review and comparison of available relevant resources.•Challenges and lessons from the process of creating such resources. CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus o...

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Published in:	Journal of biomedical informatics Vol. 55; pp. 73 - 81
Main Authors:	Karimi, Sarvnaz, Metke-Jimenez, Alejandro, Kemp, Madonna, Wang, Chen
Format:	Journal Article
Language:	English
Published:	United States Elsevier Inc 01.06.2015
Subjects:	Adverse drug reaction Adverse Drug Reaction Reporting Systems - organization & administration Annotated corpus Annotations Consumer Health Information - organization & administration Consumer reviews Data Mining - methods Datasets as Topic - statistics & numerical data Digital media Drug safety Drug-Related Side Effects and Adverse Reactions - classification Drug-Related Side Effects and Adverse Reactions - epidemiology Drugs Grammars Guidelines Guidelines as Topic Humans Information extraction Information retrieval Machine Learning MedDRA Medical forum Natural Language Processing SNOMED CT Social media Social Media - classification Social Media - organization & administration Social networks Terminology as Topic Texts Vocabulary, Controlled SNOMED CT Consumer reviews MedDRA Social media Medical forum Annotated corpus Information extraction Adverse drug reaction Drug safety
ISSN:	1532-0464, 1532-0480
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Abstract	[Display omitted] •Introduction of CADEC an annotated corpus of consumer reviews in pharmacovigilance.•A review and comparison of available relevant resources.•Challenges and lessons from the process of creating such resources. CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au.1The data can be used for research purposes only, under the CSIRO data licence.1
AbstractList	CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au. 1 CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au.(1). [Display omitted] •Introduction of CADEC an annotated corpus of consumer reviews in pharmacovigilance.•A review and comparison of available relevant resources.•Challenges and lessons from the process of creating such resources. CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au.1The data can be used for research purposes only, under the CSIRO data licence.1
Author	Karimi, Sarvnaz Wang, Chen Metke-Jimenez, Alejandro Kemp, Madonna
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Keywords	SNOMED CT Consumer reviews MedDRA Social media Medical forum Annotated corpus Information extraction Adverse drug reaction Drug safety
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Snippet	[Display omitted] •Introduction of CADEC an annotated corpus of consumer reviews in pharmacovigilance.•A review and comparison of available relevant... CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is...
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SubjectTerms	Adverse drug reaction Adverse Drug Reaction Reporting Systems - organization & administration Annotated corpus Annotations Consumer Health Information - organization & administration Consumer reviews Data Mining - methods Datasets as Topic - statistics & numerical data Digital media Drug safety Drug-Related Side Effects and Adverse Reactions - classification Drug-Related Side Effects and Adverse Reactions - epidemiology Drugs Grammars Guidelines Guidelines as Topic Humans Information extraction Information retrieval Machine Learning MedDRA Medical forum Natural Language Processing SNOMED CT Social media Social Media - classification Social Media - organization & administration Social networks Terminology as Topic Texts Vocabulary, Controlled
Title	Cadec: A corpus of adverse drug event annotations
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