The Bio-TDS (Bioscience Query Tool Discovery Systems, http://biotds.org/) has been developed to assist researchers in retrieving the most applicable analytic tools by allowing them to formulate their questions as free text. The Bio-TDS is a flexible retrieval system that affords 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. One of the primary components of the Bio-TDS is the ontology and natural language processing work-flow for annotation, curation, query processing, and evaluation. The Bio-TDS’s scientific impact was evaluated using sample questions posed by researchers 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 offers researchers the capacity to associate their bioscience questions with the most relevant computational toolsets required for the data analysis in their knowledge discovery process.