Query enhancement through the practical application of ontology: the IEDB and OBI

Ontologies categorize entities, express relationships between them, and provide standardized definitions. Thus, they can be used to present and enforce the specific relationships between database components. The Immune Epitope Database (IEDB, http://www.iedb.org) utilizes the Ontology for Biomedical Investigations (OBI) and several additional ontologies to represent immune epitope mapping experiments. Here, we describe our experiences utilizing this representation in order to provide enhanced database search functionality. We applied a simple approach to incorporate the benefits of the information captured in a formal ontology directly into the user web interface, resulting in an improved user experience with minimal changes to the database itself. The integration is easy to maintain, provides standardized terms and definitions, and allows for subsumption queries. In addition to these immediate benefits, our long-term goal is to enable true semantic integration of data and knowledge in the biomedical domain. We describe our progress towards that goal and what we perceive as the main obstacles.

• Publication year

  2013

• Venue

  Journal of Biomedical Semantics

• Publication date

  2013-04-01

• Fields of study

  Medicine, Computer Science

• Identifiers
  DOI 10.1186/2041-1480-4-S1-S6PMID 23734660PMCID 3633001
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

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