Finding Mentions of Abbreviations and Their Definitions in Spanish Clinical Cases: The BARR2 Shared Task Evaluation Results

A common characteristic of content generated by healthcare professionals, regardless the actual clinical discipline or language, is the widespread and frequent use of abbreviations, acronyms, telegraphic phrases and shorthand notes. Despite the well-known issues related to the ambiguity and misinterpretation of abbreviations, their use in practice is required to simplify and enable communication-avoiding repetition of long complex specialized medical terminologies. Moreover, clinical texts typically do not provide explicit abbreviation definitions. Thus the performance of clinical natural language processing and text mining systems is significantly affected by the previous recognition and definition resolution of medical abbreviations. To promote the development of such key components, we have organized the second Biomedical Abbreviation Recognition and Resolution (BARR2) track. The overall aim of this effort was to evaluate strategies for detecting automatically mentions of abbreviations in running text, as well as returning their corresponding definition given the corresponding context from Spanish clinical case studies. For this track, we constructed the Spanish clinical case corpus (SPACCC). This collection was exhaustively annotated by hand by domain experts with abbreviation mentions together with their corresponding definitions, resulting in the BARR2 corpus. A total of 5 teams submitted 26 runs for the two BARR2 subtasks: (a) the detection of explicit occurrences of abbreviation-definition pairs and (b) the resolution of abbreviations regardless whether their definition is mentioned within the actual document. Here we summarize the BARR2 track setting, the obtained results and the methodologies used by participating systems. The BARR2 task summary, resources and evaluation tool for testing systems beyond this campaign are available at: http://temu.bsc.es/BARR2.