BioAssay ontology annotations facilitate cross-analysis of diverse high-throughput screening data sets

Stephan C. Schürer, Uma Vempati, Robin Smith, Mark Southern, Vance Lemmon

Research output: Contribution to journalArticlepeer-review

43 Scopus citations


High-throughput screening data repositories, such as PubChem, represent valuable resources for the development of small-molecule chemical probes and can serve as entry points for drug discovery programs. Although the loose data format offered by PubChem allows for great flexibility, important annotations, such as the assay format and technologies employed, are not explicitly indexed. The authors have previously developed a BioAssay Ontology (BAO) and curated more than 350 assays with standardized BAO terms. Here they describe the use of BAO annotations to analyze a large set of assays that employ luciferase- and ß-lactamase-based technologies. They identified promiscuous chemotypes pertaining to different subcategories of assays and specific mechanisms by which these chemotypes interfere in reporter gene assays. Results show that the data in PubChem can be used to identify promiscuous compounds that interfere nonspecifically with particular technologies. Furthermore, they show that BAO is a valuable toolset for the identification of related assays and for the systematic generation of insights that are beyond the scope of individual assays or screening campaigns. (Journal of Biomolecular Screening 2011;16:415-426)

Original languageEnglish (US)
Pages (from-to)415-426
Number of pages12
JournalJournal of Biomolecular Screening
Issue number4
StatePublished - Apr 2011


  • assay ontology
  • cheminformatics
  • compound promiscuity
  • high-throughput screening data analysis
  • reporter gene assays

ASJC Scopus subject areas

  • Analytical Chemistry
  • Drug Discovery
  • Pharmacology
  • Biochemistry
  • Molecular Medicine
  • Biotechnology


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