BACKGROUND: The BioCreative challenge evaluation is a community-wide effort for 
evaluating text mining and information extraction systems applied to the 
biological domain. The biocurator community, as an active user of biomedical 
literature, provides a diverse and engaged end user group for text mining tools. 
Earlier BioCreative challenges involved many text mining teams in developing 
basic capabilities relevant to biological curation, but they did not address the 
issues of system usage, insertion into the workflow and adoption by curators. 
Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to 
address the utility and usability of text mining tools for real-life biocuration 
tasks. To support the aims of the IAT in BC-III, involvement of both developers 
and end users was solicited, and the development of a user interface to address 
the tasks interactively was requested.
RESULTS: A User Advisory Group (UAG) actively participated in the IAT design and 
assessment. The task focused on gene normalization (identifying gene mentions in 
the article and linking these genes to standard database identifiers), gene 
ranking based on the overall importance of each gene mentioned in the article, 
and gene-oriented document retrieval (identifying full text papers relevant to a 
selected gene). Six systems participated and all processed and displayed the 
same set of articles. The articles were selected based on content known to be 
problematic for curation, such as ambiguity of gene names, coverage of multiple 
genes and species, or introduction of a new gene name. Members of the UAG 
curated three articles for training and assessment purposes, and each member was 
assigned a system to review. A questionnaire related to the interface usability 
and task performance (as measured by precision and recall) was answered after 
systems were used to curate articles. Although the limited number of articles 
analyzed and users involved in the IAT experiment precluded rigorous 
quantitative analysis of the results, a qualitative analysis provided valuable 
insight into some of the problems encountered by users when using the systems. 
The overall assessment indicates that the system usability features appealed to 
most users, but the system performance was suboptimal (mainly due to low 
accuracy in gene normalization). Some of the issues included failure of species 
identification and gene name ambiguity in the gene normalization task leading to 
an extensive list of gene identifiers to review, which, in some cases, did not 
contain the relevant genes. The document retrieval suffered from the same 
shortfalls. The UAG favored achieving high performance (measured by precision 
and recall), but strongly recommended the addition of features that facilitate 
the identification of correct gene and its identifier, such as contextual 
information to assist in disambiguation.
DISCUSSION: The IAT was an informative exercise that advanced the dialog between 
curators and developers and increased the appreciation of challenges faced by 
each group. A major conclusion was that the intended users should be actively 
involved in every phase of software development, and this will be strongly 
encouraged in future tasks. The IAT Task provides the first steps toward the 
definition of metrics and functional requirements that are necessary for 
designing a formal evaluation of interactive curation systems in the BioCreative 
IV challenge.