Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO)

Uma D. Vempati, Magdalena J. Przydzial, Caty Chung, Saminda Abeyruwan, Ahsan Mir, Kunie Sakurai, Ubbo E Visser, Vance Lemmon, Stephan C Schuerer

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector. The resulting experimental datasets are increasingly being disseminated via publically accessible repositories. However, existing repositories lack sufficient metadata to describe the experiments and are often difficult to navigate by non-experts. The lack of standardized descriptions and semantics of biological assays and screening results hinder targeted data retrieval, integration, aggregation, and analyses across different HTS datasets, for example to infer mechanisms of action of small molecule perturbagens. To address these limitations, we created the BioAssay Ontology (BAO). BAO has been developed with a focus on data integration and analysis enabling the classification of assays and screening results by concepts that relate to format, assay design, technology, target, and endpoint. Previously, we reported on the higher-level design of BAO and on the semantic querying capabilities offered by the ontology-indexed triple store of HTS data. Here, we report on our detailed design, annotation pipeline, substantially enlarged annotation knowledgebase, and analysis results. We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments. BAO is publically available from the NCBO BioPortal at http://bioportal.bioontology.org/ontologies/1533. BAO provides controlled terminology and uniform scope to report probe and drug discovery screening assays and results. BAO leverages description logic to formalize the domain knowledge and facilitate the semantic integration with diverse other resources. As a consequence, BAO offers the potential to infer new knowledge from a corpus of assay results, for example molecular mechanisms of action of perturbagens.

Original languageEnglish
Article numbere49198
JournalPLoS One
Volume7
Issue number11
DOIs
StatePublished - Nov 14 2012

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Preclinical Drug Evaluations
Bioassay
Biological Assay
probes (equipment)
Ontology
Assays
Screening
bioassays
screening
drugs
assays
Pharmaceutical Preparations
Throughput
Semantics
mechanism of action
Datasets
public sector
development projects
Knowledge Bases
Public Sector

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO). / Vempati, Uma D.; Przydzial, Magdalena J.; Chung, Caty; Abeyruwan, Saminda; Mir, Ahsan; Sakurai, Kunie; Visser, Ubbo E; Lemmon, Vance; Schuerer, Stephan C.

In: PLoS One, Vol. 7, No. 11, e49198, 14.11.2012.

Research output: Contribution to journalArticle

Vempati, Uma D. ; Przydzial, Magdalena J. ; Chung, Caty ; Abeyruwan, Saminda ; Mir, Ahsan ; Sakurai, Kunie ; Visser, Ubbo E ; Lemmon, Vance ; Schuerer, Stephan C. / Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO). In: PLoS One. 2012 ; Vol. 7, No. 11.
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