The Ontology of Primary Immunodeficiency Diseases (PIDs): Using PIDs to Rethink the Ontology of Phenotypes

Adams, Nico, Hennig, Christian, Hoehndorf, Robert, Oellrich, Anika, Rebholz-Schuhmann, Dietrich, and Hansen, Gesine (2010) The Ontology of Primary Immunodeficiency Diseases (PIDs): Using PIDs to Rethink the Ontology of Phenotypes. In: [Presented at the OBML 2010 Workshop]. IMISE-Report Ne 2/2010. From: OBML 2010: Ontologien in Biomedizin und Lebenswissenschaften, 9-10 September 2010, Mannheim, Germany.

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Primary immunodeficiency diseases (PIDs) are the consequence of genetic disorders and usually manifest themselves in very young patients. Because of their rarity, they are notoriously difficult to diagnose both for general practitioners and clinicians. In this paper, we present the foundations of an ontology of PIDs, which will be at the heart of an expert system designed to assist the clinician in the diagnosis of these diseases. To achieve this, the PIDOntology characterises Primary Immunodefieciencies in terms of Phenotypes. While there are a number of different ontologies already available that allow the description of phenotypes and phenotypic qualities, these have a number of associated ontological problems, which we will also address as part of this paper. We use the subtype of Hyper-IgE Syndrome caused by a STAT3 defects as an example of a primary immunodeficiency and show how the clinical phenotype of the disease can be modeled in terms of other phenotypes by introducing the notion of the “phene”. Furthermore, we develop patterns for different types of phenes and show, that these patterns can be mapped onto more traditional entity-quality statements, which are the current state of the art in phenotypic modeling.

Item ID: 74865
Item Type: Conference Item (Presentation)
Date Deposited: 18 Dec 2023 00:53
FoR Codes: 31 BIOLOGICAL SCIENCES > 3102 Bioinformatics and computational biology > 310299 Bioinformatics and computational biology not elsewhere classified @ 100%
SEO Codes: 28 EXPANDING KNOWLEDGE > 2801 Expanding knowledge > 280102 Expanding knowledge in the biological sciences @ 100%
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