title: PIDO: the primary immunodeficiency disease ontology.
abstract: BACKGROUND
  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.
authors.affiliation: Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. nico.adams@csiro.au
authors.forename: Nico
authors.initials: N
authors.lastname: Adams
authors.forename: Robert
authors.initials: R
authors.lastname: Hoehndorf
authors.forename: Georgios V
authors.initials: GV
authors.lastname: Gkoutos
authors.forename: Gesine
authors.initials: G
authors.lastname: Hansen
authors.forename: Christian
authors.initials: C
authors.lastname: Hennig
mesh_terms: D015415:Biomarkers / Q000032:analysis; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000175:diagnosis*; D010641:Phenotype; D012984:Software; D009626:Terminology as Topic; D014923:Wiskott-Aldrich Syndrome / Q000175:diagnosis
chemical_list: D015415:Biomarkers