Bio-TDS : BioQuery Tool Discovery System

Bioinformatics and computational biology play a critical role in bioscience and biomedical research. As researchers design their experimental projects, one major challenge is to find the most relevant bioinformatics toolkits that will lead them to new knowledge discovery from their data. The Bio-TDS (BioQuery Tools Discovery Systems, http://brin.usd.edu/BioQueryTool/) has been developed to assist researchers in retrieving the most applicable computational toolkits by posing questions as free text. The Bio-TDS is a flexible, three-layer architecture retrieval system that provides users from multiple bioscience domains (e.g. genomic, proteomic, bio-imaging) the ability to query over 12,000 analytic tool descriptions integrated from well-established, community repositories. The query expressions posed by potential researchers can vary from precise questions such as “RNASeq reads mapper for mammalian” or “reads mapping”, to very domain specific free text expressions like “best tool for microbiology genome mapping using RNASeq”.One of the primary components of the Bio-TDS system is the ontology and natural language processing workflow for annotation, curation, query processing, and evaluation. The Bio-TDS’s scientific impact was evaluated using sample researcher questions retrieved from Biostars, a site focusing on biological data analysis. The Bio-TDS was compared to five similar bioscience analytic tool retrieval systems with the Bio-TDS outperforming the others in terms of relevance and completeness. The Bio-TDS provides researcher with the ability to associate their bioscience question with the most relevant computational tool-set required for the data analysis in their knowledge discovery process.