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

Nico Adams, Christian Hennig, Robert Hoehndorf, Anika Oellrich, Dietrich Rebholz-Schuhmann, Gesine Hansen

Research output: Chapter in Book/Report/Conference proceedingConference Proceeding (Non-Journal item)


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.
Original languageEnglish
Title of host publicationProceedings of the 2nd Workshop for Ontologies in Biomedicine and Life sciences (OBML)
Publication statusPublished - 01 Sept 2010
Event3rd Workshop on Ontologies in Biomedicine and Life Sciences - Berlin, Germany
Duration: 06 Oct 201107 Oct 2011


Workshop3rd Workshop on Ontologies in Biomedicine and Life Sciences
Abbreviated titleOBML 2011
Period06 Oct 201107 Oct 2011
OtherThe series "Ontologies in Biomedicine and Life Sciences" (OBML workshop) was initiated by the workgroup for OBML of the German Society for Computer
Science in 2009. The OBML aims to bring together scientists who are working in this area to exchange ideas and discuss new results, to start collaborations and to initiate new projects. The OBML workshop is held once annually and deals with all fundamental aspects of biomedical ontologies as well as additional "hot" topics.


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