Adams, Nico, Hoehndorf, Robert, Gkoutos, Georgios V., Hansen, Gensine, and Hennig, Christian (2011) PIDO: the primary immunodeficiency disease ontology. Bioinformatics, 27 (22). pp. 3193-3199.

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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 toward 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 toward 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 characterizes 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

Item ID:	74838
Item Type:	Article (Research - C1)
ISSN:	1367-4811
Copyright Information:	© The Author 2011. Published by Oxford University Press. All rights reserved.
Date Deposited:	25 Jun 2024 23:52
FoR Codes:	32 BIOMEDICAL AND CLINICAL SCIENCES > 3204 Immunology > 320499 Immunology not elsewhere classified @ 20% 31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310299 Bioinformatics and computational biology not elsewhere classified @ 80%
SEO Codes:	28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280103 Expanding knowledge in the biomedical and clinical sciences @ 50% 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 50%
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