Linking Text Mining with Ontology and Systems Biology

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Georgetown University is awarded a grant to conduct a series of BioCreative Challenge Evaluations and Biocuration Workshops to address the current barriers in using text mining tools in the biology domain. Specifically, three workshops will be organized to bring together the biological research community and developers of text mining tools for user requirement analysis, user-based evaluations and standard development for tool integration. The specific aims of the workshops are to: (i) define requirements and evaluation criteria that will maximize utilization of text mining tools by the broad biological user community; (ii) provide both system- and user-based evaluations, with metrics that measure precision and recall (system-based), as well as the effect of text mining on biocuration and knowledge discovery such as throughput and quality (user-based); and (iii) adopt, develop and recommend community standards to improve interoperability of text mining tools for data exchange and tool integration. The outcome will be to bridge the gap in linking literature to knowledge by focusing on biological use cases for database curation and knowledge discovery. The deliverables from the workshops will consist of: (i) text mining tools, including interactive and/or integrated text mining systems, that are benchmarked and evaluated by BioCreative, (ii) literature corpora used in the BioCreative evaluations, and (iii) scientific publications from these workshops in special issues of high impact journals containing results, evaluations and critical articles, including recommendations for community standards for text mining. Georgetown will collaborate with the Mitre Corporation in carrying out this workshop series.The workshops will connect the text mining and biological communities to develop common standards and user requirements, with broad impact beyond the specific text mining applications in this project. The project will provide interdisciplinary research experience for students and researchers involved in the project or participate in the workshops. The project will provide a research and educational infrastructure for broad areas of biology, allowing text mining systems to become an enabling infrastructure for biocuration and knowledge discovery. Further information on the Biocreative workshop activities may be found at http://biocreative.sourceforge.net/