Development and Applications of the Bioassay Ontology (BAO) to Describe and Categorize High-Throughput Assays

Ontologies are important tools to organize information and formalize knowledge in a subject domain. In this chapter, the authors introduce Bioassay Ontology (BAO), the first ontology to describe and categorize chemical biology and drug screening assays and their results. BAO has been applied to standardize, organize and annotate assays and screening results to enable analysis and information extraction across multiple and diverse data sets, with the goal to infer new knowledge about the molecular mechanism of action of small molecules in the assay model systems. The authors provide an overview of BAO and present several applications, including the annotation of a large number of HTS assays and an assay annotation tool (BioAssayAnnotationTemplate). BAO has also been used in a software tool (BAOSearch) to enable query and exploration of assay experiments and results via a simple user interface. BAO is an evolving ontology with a growing nymber of applications and user community.