Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Editorial
. 2013 Apr 15;4 Suppl 1(Suppl 1):S6.
doi: 10.1186/2041-1480-4-S1-S6. Epub 2013 Apr 15.

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

Randi Vita  1 , James A Overton, Jason A Greenbaum, Alessandro Sette; OBI consortium; Bjoern Peters
Affiliations
Editorial

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

Randi Vita et al. J Biomed Semantics. .

Abstract

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Conversion of IEDB assay types from a static list to terms in OBI used to generate new search interface utilizing a hierarchical tree.
Figure 2
Figure 2
Export of IEDB data into RDF format makes SPARQL queries possible. This example demonstrates the ability to utilize the role branch of the ChEBI ontology to determine ‘pharmaceuticals’ with T cell responses in the IEDB. See http://ontology.iedb.org.
See this image and copyright information in PMC

References

    1. Vita R, Peters B, Sette A. The curation guidelines of the immune epitope database and analysis resource. Cytometry A. 2008;73(11):1066–70. - PMC - PubMed
    1. The Open Biological and Biomedical Ontologies. http://obofoundry.org
    1. The OBI Consortium. http://purl.obolibrary.org/obo/obi
    1. Greenbaum JA, Vita R, Zarebski L, Emami H, Sette A, Ruttenberg A, Peters B. ONTology of Immune Epitopes (ONTIE) Representing the Immune Epitope Database in OWL. The 12th Annual Bio-Ontologies Meeting, ISMB. 2009. pp. 45–48.
    1. Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B. The immune epitope database 2.0. Nucleic Acids Res. 2010;38(Database issue):D854–62. - PMC - PubMed

Publication types

LinkOut - more resources