title: Knowledge retrieval from PubMed abstracts and electronic medical records with the Multiple Sclerosis Ontology.
abstract: BACKGROUND
  In order to retrieve useful information from scientific literature and electronic medical records (EMR) we developed an ontology specific for Multiple Sclerosis (MS).
  
  
  METHODS
  The MS Ontology was created using scientific literature and expert review under the Protégé OWL environment. We developed a dictionary with semantic synonyms and translations to different languages for mining EMR. The MS Ontology was integrated with other ontologies and dictionaries (diseases/comorbidities, gene/protein, pathways, drug) into the text-mining tool SCAIView. We analyzed the EMRs from 624 patients with MS using the MS ontology dictionary in order to identify drug usage and comorbidities in MS. Testing competency questions and functional evaluation using F statistics further validated the usefulness of MS ontology.
  
  
  RESULTS
  Validation of the lexicalized ontology by means of named entity recognition-based methods showed an adequate performance (F score = 0.73). The MS Ontology retrieved 80% of the genes associated with MS from scientific abstracts and identified additional pathways targeted by approved disease-modifying drugs (e.g. apoptosis pathways associated with mitoxantrone, rituximab and fingolimod). The analysis of the EMR from patients with MS identified current usage of disease modifying drugs and symptomatic therapy as well as comorbidities, which are in agreement with recent reports.
  
  
  CONCLUSIONS
  The MS Ontology provides a semantic framework that is able to automatically extract information from both scientific literature and EMR from patients with MS, revealing new pathogenesis insights as well as new clinical information.
authors: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany.
authors: Ashutosh
authors: A
authors: Malhotra
authors: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany.
authors: Michaela
authors: M
authors: Gündel
authors: Merck KGaA, Darmstadt, Germany.
authors: Abdul Mateen
authors: AM
authors: Rajput
authors: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany.
authors: Heinz-Theodor
authors: HT
authors: Mevissen
authors: MS Center, Department of Neurology, Hospital Clinic of Barcelona, Barcelona, Spain; Center of Neuroimmunology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors: Albert
authors: A
authors: Saiz
authors: Department of Medical Informatics, Hospital Clinic of Barcelona-University of Barcelona, Barcelona, Spain.
authors: Xavier
authors: X
authors: Pastor
authors: Department of Medical Informatics, Hospital Clinic of Barcelona-University of Barcelona, Barcelona, Spain.
authors: Raimundo
authors: R
authors: Lozano-Rubi
authors: Elena H
authors: EH
authors: Martinez-Lapiscina
authors: Center of Neuroimmunology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors: Elena H
authors: EH
authors: Martinez-Lapsicina
authors: Center of Neuroimmunology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors: Irati
authors: I
authors: Zubizarreta
authors: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany.
authors: Bernd
authors: B
authors: Mueller
authors: Center of Neuroimmunology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors: Ekaterina
authors: E
authors: Kotelnikova
authors: Merck KGaA, Darmstadt, Germany.
authors: Luca
authors: L
authors: Toldo
authors: Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing, 53754, Sankt Augustin, Germany.
authors: Martin
authors: M
authors: Hofmann-Apitius
authors: Center of Neuroimmunology, Institut d'investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
authors: Pablo
authors: P
authors: Villoslada
mesh_terms: D000970:Antineoplastic Agents / Q000627:therapeutic use; D018501:Antirheumatic Agents / Q000627:therapeutic use; D064229:Biological Ontologies; D019295:Computational Biology / Q000379:methods; D057286:Electronic Health Records; D000068876:Fingolimod Hydrochloride / Q000627:therapeutic use; D006801:Humans; D007166:Immunosuppressive Agents / Q000627:therapeutic use; D016247:Information Storage and Retrieval; D063369:Knowledge Discovery; D008942:Mitoxantrone / Q000627:therapeutic use; D009103:Multiple Sclerosis / Q000145:classification* / Q000188:drug therapy; D039781:PubMed; D000069283:Rituximab / Q000627:therapeutic use
chemical_list: D000970:Antineoplastic Agents; D018501:Antirheumatic Agents; D007166:Immunosuppressive Agents; D000069283:Rituximab; D008942:Mitoxantrone; D000068876:Fingolimod Hydrochloride