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
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
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 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 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 researcher
the capacity to associate their bioscience question with the most relevant computational
toolsets required for the data analysis in their knowledge discovery process.