A survey on annotation tools for the biomedical literature

Abstract

New approaches to biomedical text mining crucially depend on the existence of comprehensive annotated corpora. Such corpora, commonly called gold standards, are important for learning patterns or models during the training phase, for evaluating and comparing the performance of algorithms and also for better understanding the information sought for by means of examples. Gold standards depend on human understanding and manual annotation of natural language text. This process is very time-consuming and expensive because it requires high intellectual effort from domain experts. Accordingly, the lack of gold standards is considered as one of the main bottlenecks for developing novel text mining methods.This situation led the development of tools that support humans in annotating texts. Such tools should be intuitive to use, should support a range of different input formats, should include visualization of annotated texts and should generate an easy-to-parse output format. Today, a range of tools which implement some of these functionalities are available. In this survey, we present a comprehensive survey of tools for supporting annotation of biomedical texts. Altogether, we considered almost 30 tools,13 of which were selected for an in-depth comparison. The comparison was performed using predefined criteria and was accompanied by hands-on experiences whenever possible.Our survey shows that current tools can supportmany of the tasks in biomedical text annotation in a satisfying manner, but also that no tool can be considered as a true comprehensive solution. © The Author 2012. Published by Oxford University Press.