We describe a corpus of consumer health questions annotated with named entities. The corpus consists of 1548 de-identified questions about diseases and drugs, written in English. We defined 15 broad categories of biomedical named entities for annotation. A pilot annotation phase in which a small portion of the corpus was double-annotated by four annotators was followed by a main phase in which double annotation was carried out by six annotators, and a reconciliation phase in which all annotations were reconciled by an expert. We conducted the annotation in two modes, manual and assisted, to assess the effect of automatic pre-annotation and calculated inter-annotator agreement. We obtained moderate inter-annotator agreement; assisted annotation yielded slightly better agreement and fewer missed annotations than manual annotation. Due to complex nature of biomedical entities, we paid particular attention to nested entities for which we obtained slightly lower inter-annotator agreement, confirming that annotating nested entities is somewhat more challenging. To our knowledge, the corpus is the first of its kind for consumer health text and is publicly available.
@InProceedings{KILICOGLU16.727,
author = {Halil Kilicoglu and Asma Ben Abacha and Yassine Mrabet and Kirk Roberts and Laritza Rodriguez and Sonya Shooshan and Dina Demner-Fushman}, title = {Annotating Named Entities in Consumer Health Questions}, booktitle = {Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016)}, year = {2016}, month = {may}, date = {23-28}, location = {Portorož, Slovenia}, editor = {Nicoletta Calzolari (Conference Chair) and Khalid Choukri and Thierry Declerck and Sara Goggi and Marko Grobelnik and Bente Maegaard and Joseph Mariani and Helene Mazo and Asuncion Moreno and Jan Odijk and Stelios Piperidis}, publisher = {European Language Resources Association (ELRA)}, address = {Paris, France}, isbn = {978-2-9517408-9-1}, language = {english} }
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