Building concordant ontologies for drug discovery

Hande Küçük-McGinty, Saurabh Mehta, Yu Lin, Nooshin Nabizadeh, Vasileios Stathias, Dusica Vidovic, Amar Koleti, Christopher Mader, Jianbin Duan, Ubbo E Visser, Stephan C Schuerer

Research output: Contribution to journalArticle

Abstract

Department of Molecular and Cellular Pharmacology, In this study we demonstrate how we interconnect three different ontologies, the BioAssay Ontology (BAO), LINCS Information FramEwork ontology (LIFEo), and the Drug Target Ontology (DTO). The three ontologies are built and maintained for three different projects: BAO for the BioAssay Ontology Project, LIFEo for the Library of Integrated Network-Based Cellular Signatures (LINCS) project, and DTO for the Illuminating the Druggable Genome (IDG) project. DTO is a new ontology that aims to formally describe drug target knowledge relevant to drug discovery. LIFEo is an application ontology to describe information in the LIFE software system. BAO is a highly accessed NCBO ontology; it has been extended formally to describe several LINCS assays. The three ontologies use the same principle architecture that allows for re-use and easy integration of ontology modules and instance data. Using the formal definitions in DTO, LIFEo, and BAO and data from various resources one can quickly identify disease-relevant and tissue-specific genes, proteins, and prospective small molecules. We show a simple use case example demonstrating knowledge-based linking of life science data with the potential to empower drug discovery.

Original languageEnglish (US)
JournalCEUR Workshop Proceedings
Volume1747
StatePublished - 2016

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Keywords

  • Bioinformatics
  • Cheminformatics
  • Drug discovery

ASJC Scopus subject areas

  • Computer Science(all)

Cite this

Küçük-McGinty, H., Mehta, S., Lin, Y., Nabizadeh, N., Stathias, V., Vidovic, D., Koleti, A., Mader, C., Duan, J., Visser, U. E., & Schuerer, S. C. (2016). Building concordant ontologies for drug discovery. CEUR Workshop Proceedings, 1747.