PIDO: The Primary Immunodeficiency Disease Ontology

Nico Adams, Robert Hoehndorf, Georgios V. Gkoutos, Gesine Hansen, Christian Hennig

Research output: Contribution to journalArticlepeer-review

5 Citations (SciVal)

Abstract

Motivation: Primary Immunodeficiency Diseases (PIDs) are Mendelian conditions of high phenotypic complexity and low incidence. They usually manifest in toddlers and infants, although they can also occur much later in life. Information about PIDs is often widely scattered throughout the clinical as well as the research literature and hard to find for both generalists as well as experienced clinicians. Semantic Web technologies coupled to clinical information systems can go some way towards addressing this problem. Ontologies are a central component of such a system, containing and centralizing knowledge about primary immunodeficiencies in both a human- and computer-comprehensible form. The development of an ontology of PIDs is therefore a central step towards developing informatics tools, which can support the clinician in the diagnosis and treatment of these diseases.

Results: We present PIDO, the Primary Immunodeficiency Disease Ontology. PIDO characterises PIDs in terms of the phenotypes commonly observed by clinicians during a diagnosis process. Phenotype terms in PIDO are formally defined using complex definitions based on qualities, functions, processes, and structures. We provide mappings to biomedical reference ontologies to ensure interoperability with ontologies in other domains. Based on PIDO, we developed the PIDFinder, an ontology-driven software prototype that can facilitate clinical decision support. PIDO connects immunological knowledge across resources within a common framework and thereby enables translational research and the development of medical applications for the domain of immunology and primary immunodeficiency diseases.

Availability: The Primary Immunodeficiency Disease Ontology is available under a Creative Commons Attribution 3.0 (CC-BY 3.0) licence at http://code.google.com/p/pido/ The most recent public release of the ontology can always be found at http://purl.org/scimantica/pido/owl/pid.owl. An instance of the PIDFinder software can be found at http://pidfinder.appspot.comContact: nico.adams@csiro.au
Original languageEnglish
Pages (from-to)3193-3199
Number of pages7
JournalBioinformatics
Volume27
Issue number22
Early online date22 Sept 2011
DOIs
Publication statusPublished - 22 Nov 2011

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