Overview of the interactive task in BioCreative V

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

The BioGRID interaction database: 2017 update

“…The BioGRID team has strongly supported the biomedical text-mining community through the BioCreative initiative (52) by providing curation expertise and manually annotated gold standard reference datasets (53,54). For example, in the most recent BioCreative competition in 2015 one particular task focused on the development of a curation interface designed specifically for BioGRID curators (55), based on the BioC standard, an extensible mark-up language created to allow interoperability between biomedical text processing systems (56).…”

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

“…The BioCreative V Workshop was held in September 2015 and consisted of five tasks: the Collaborative Biocurator Assistant Task (BioC task) (5), the CHEMDNER-patents task (6), the CDR task (7), the BEL task (8, 9) and the User Interactive Task (10). Our focus is the BioC task.…”

On expert curation and sustainability: UniProtKB/Swiss-Prot as a case study

“…Many of the tools are developed as part of a research proposal and/or for proof of concept, in isolation from their potential users and not with the end goal of adoption. There is an ongoing effort in BioCreative to promote interaction between the biocuration and text-mining communities to lower these barriers (Wang, S, et al, 2016). In fact, Pubtator is a product of the BioCreative 2012 challenge (Arighi, Carterette, et al, 2013).…”