title: ADO: a disease ontology representing the domain knowledge specific to Alzheimer's disease.
abstract: BACKGROUND
  Biomedical ontologies offer the capability to structure and represent domain-specific knowledge semantically. Disease-specific ontologies can facilitate knowledge exchange across multiple disciplines, and ontology-driven mining approaches can generate great value for modeling disease mechanisms. However, in the case of neurodegenerative diseases such as Alzheimer's disease, there is a lack of formal representation of the relevant knowledge domain.
  
  
  METHODS
  Alzheimer's disease ontology (ADO) is constructed in accordance to the ontology building life cycle. The Protégé OWL editor was used as a tool for building ADO in Ontology Web Language format.
  
  
  RESULTS
  ADO was developed with the purpose of containing information relevant to four main biological views-preclinical, clinical, etiological, and molecular/cellular mechanisms-and was enriched by adding synonyms and references. Validation of the lexicalized ontology by means of named entity recognition-based methods showed a satisfactory performance (F score = 72%). In addition to structural and functional evaluation, a clinical expert in the field performed a manual evaluation and curation of ADO. Through integration of ADO into an information retrieval environment, we show that the ontology supports semantic search in scientific text. The usefulness of ADO is authenticated by dedicated use case scenarios.
  
  
  CONCLUSIONS
  Development of ADO as an open ADO is a first attempt to organize information related to Alzheimer's disease in a formalized, structured manner. We demonstrate that ADO is able to capture both established and scattered knowledge existing in scientific text.
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany; Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Bonn, Germany.
authors.forename: Ashutosh
authors.initials: A
authors.lastname: Malhotra
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany; Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Bonn, Germany.
authors.forename: Erfan
authors.initials: E
authors.lastname: Younesi
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany.
authors.forename: Michaela
authors.initials: M
authors.lastname: Gündel
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Müller
authors.affiliation: Department of Neurology, Clinical Neurosciences Unit, University of Bonn, Bonn, Germany.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Heneka
authors.affiliation: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, Sankt Augustin, Germany; Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn-Aachen International Center for IT, Bonn, Germany. Electronic address: martin.hofmann-apitius@scai.fraunhofer.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Hofmann-Apitius
mesh_terms: D000544:Alzheimer Disease; D019295:Computational Biology; D006801:Humans; D016247:Information Storage and Retrieval; D008954:Models, Biological
keywords: Alzheimer's disease; Alzheimer's disease ontology; Neurodegeneration; Neurodegenerative diseases; Ontology; Semantic Web