Abstract
Fully automated text mining (TM) systems promote efficient literature searching, retrieval, and review but are not sufficient to produce ready-to-consume curated documents. These systems are not meant to replace biocurators, but instead to assist them in one or more literature curation steps. To do so, the user interface is an important aspect that needs to be considered for tool adoption. The BioCreative Interactive task (IAT) is a track designed for exploring user-system interactions, promoting development of useful TM tools, and providing a communication channel between the biocuration and the TM communities. In BioCreative V, the IAT track followed a format similar to previous interactive tracks, where the utility and usability of TM tools, as well as the generation of use cases, have been the focal points. The proposed curation tasks are user-centric and formally evaluated by biocurators. In BioCreative V IAT, seven TM systems and 43 biocurators participated. Two levels of user participation were offered to broaden curator involvement and obtain more feedback on usability aspects. The full level participation involved training on the system, curation of a set of documents with and without TM assistance, tracking of time-on-task, and completion of a user survey. The partial level participation was designed to focus on usability aspects of the interface and not the performance per se. In this case, biocurators navigated the system by performing pre-designed tasks and then were asked whether they were able to achieve the task and the level of difficulty in completing the task. In this manuscript, we describe the development of the interactive task, from planning to execution and discuss major findings for the systems tested.Database URL: http://www.biocreative.org
Highlights
BioCreative: Critical Assessment of Information Extraction in Biology is an international community-wide effort that evaluates text mining (TM) and information extraction (IE) systems applied to the biomedical domain [1,2,3,4,5]
Using the concept annotations of the expert who voluntarily curated all of the 124 documents in the data set, we evaluated the performance of the Argo workflow, which formed the basis of the TM support provided to the biocurators
The tool does not seem to speed up curation of BEL statements significantly when compare to non-TM assisted, but this could be due to the learning curve for the BEL language and the interface, and the low number of documents that were annotated
Summary
BioCreative: Critical Assessment of Information Extraction in Biology is an international community-wide effort that evaluates text mining (TM) and information extraction (IE) systems applied to the biomedical domain [1,2,3,4,5]. To address the barriers in using TM in biocuration, BioCreative has been conducting user requirements analysis and user-based evaluations, and fostering standards development for TM tool re-use and integration. IV included a panel session, sponsored by the Department of Energy (DOE), on the TM needs of the metagenomics community which studies the genetic material recovered directly from environmental samples The discussions from this session inspired the participation of a team in the IAT task to address the extraction of environmental and species metadata from free text. In parallel to IAT track, BioCreative V has introduced the Collaborative Biocurator Assistant Task (BioC) [11], which explores the integration of the BioC format [12] output from different TM modules to provide a system for literature curation of protein–protein interactions tailored for the BioGrid Database [13]. The current article describes the IAT task, the workflow of the IAT activities, the participating TM systems and the results from the user evaluation
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