yOWL: An ontology-driven knowledge base for yeast biologists

Natalia Villanueva-Rosales, Michel Dumontier*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

28 Citations (Web of Science)


Knowledge management is an ongoing challenge for the biological community such that large, diverse and continuously growing information requires more sophisticated methods to store, integrate and query their knowledge. The semantic web initiative provides a new knowledge engineering framework to represent, share and discover information. In this paper, we describe our efforts towards the development of an ontology-based knowledge base, including aspects from ontology design and population using "semantic" data mashup, to automated reasoning and semantic query answering. Based on yeast data obtained from the Saccharomyces Genome Database and UniProt, we discuss the challenges encountered during the building of the knowledge base and how they were overcome.
Original languageEnglish
Pages (from-to)779-789
JournalJournal of Biomedical Informatics
Issue number5
Publication statusPublished - Oct 2008
Externally publishedYes


  • Semantic web
  • Data integration
  • Semantic query answering
  • Knowledge management
  • OWL
  • Ontology
  • Biological data
  • Yeast
  • Saccharomyces cerevisiae
  • Mashup

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