Epilepsy and seizure ontology: towards an epilepsy informatics infrastructure for clinical research and patient care

OBJECTIVE Epilepsy encompasses an extensive array of clinical and research subdomains, many of which emphasize multi-modal physiological measurements such as electroencephalography and neuroimaging. The integration of structured, unstructured, and signal data into a coherent structure for patient care as well as clinical research requires an effective informatics infrastructure that is underpinned by a formal domain ontology. METHODS We have developed an epilepsy and seizure ontology (EpSO) using a four-dimensional epilepsy classification system that integrates the latest International League Against Epilepsy terminology recommendations and National Institute of Neurological Disorders and Stroke (NINDS) common data elements. It imports concepts from existing ontologies, including the Neural ElectroMagnetic Ontologies, and uses formal concept analysis to create a taxonomy of epilepsy syndromes based on their seizure semiology and anatomical location. RESULTS EpSO is used in a suite of informatics tools for (a) patient data entry, (b) epilepsy focused clinical free text processing, and (c) patient cohort identification as part of the multi-center NINDS-funded study on sudden unexpected death in epilepsy. EpSO is available for download at http://prism.case.edu/prism/index.php/EpilepsyOntology. DISCUSSION An epilepsy ontology consortium is being created for community-driven extension, review, and adoption of EpSO. We are in the process of submitting EpSO to the BioPortal repository. CONCLUSIONS EpSO plays a critical role in informatics tools for epilepsy patient care and multi-center clinical research.

[1]  T. Kurashige,et al.  Proposal for Revised Classification of Epilepsies and Epileptic Syndromes , 1989, No to hattatsu = Brain and development.

[2]  Philippe Balbiani,et al.  Formal Concept Analysis, Foundations and Applications , 2005 .

[3]  H. Lüders,et al.  Presurgical evaluation of epilepsy. , 2001, Brain : a journal of neurology.

[4]  Chien-Hung Chen,et al.  Electrophysiological Signal Analysis and Visualization using Cloudwave for Epilepsy Clinical Research , 2013, MedInfo.

[5]  H. Lüders,et al.  Modern technology calls for a modern approach to classification of epileptic seizures and the epilepsies , 2012, Epilepsia.

[6]  H. Lüders,et al.  Semiological Seizure Classification * , 1998, Epilepsia.

[7]  M. T. Medina,et al.  Mutations in EFHC1 cause juvenile myoclonic epilepsy , 2004, Nature Genetics.

[8]  Michael Wong.  Epilepsy is both a symptom and a disease: A proposal for a two‐tiered classification system , 2011, Epilepsia.

[9]  Guo-Qiang Zhang,et al.  VISAGE: A Query Interface for Clinical Research , 2010, Summit on translational bioinformatics.

[10]  Sean Bechhofer,et al.  The OWL API: A Java API for OWL ontologies , 2011, Semantic Web.

[11]  C. Kellinghaus,et al.  Vorschlag für eine neue patientenorientierte Epilepsieklassifikation , 2006, Der Nervenarzt.

[12]  Olivier Bodenreider,et al.  Bio-ontologies: current trends and future directions , 2006, Briefings Bioinform..

[13]  Meng Zhao,et al.  OPIC: Ontology-driven Patient Information Capturing System for Epilepsy , 2012, AMIA.

[14]  Linda L Kloss.  AHIMA Letter to the Secretary of HHS on Funding the Office of the National Coordinator for Health Information Technology (ONCHIT) , 2004 .

[15]  J. H. Cross,et al.  Revised terminology and concepts for organization of seizures and epilepsies: Report of the ILAE Commission on Classification and Terminology, 2005–2009 , 2010, Epilepsia.

[16]  Nicola Guarino,et al.  Sweetening Ontologies with DOLCE , 2002, EKAW.

[17]  James Cheney,et al.  PROV-O: The PROV ontology:W3C recommendation 30 April 2013 , 2013 .

[18]  Munir Pirmohamed,et al.  Exploring the genomic basis of pharmacoresistance in epilepsy: an integrative analysis of large-scale gene expression profiling studies on brain tissue from epilepsy surgery. , 2011, Human molecular genetics.

[19]  C. Elger,et al.  Epileptic Seizures and Epilepsy: Definitions Proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE) , 2005, Epilepsia.

[20]  F. Mostashari.  Office of the National Coordinator for Health Information Technology Attention: Governance RFI , 2005 .

[21]  Michael F. Goodchild,et al.  Interoperating Geographic Information Systems , 2012 .

[22]  Peter F. Patel-Schneider,et al.  OWL 2 Web Ontology Language Primer (Second Edition) , 2012 .

[23]  Rudolf Wille,et al.  Restructuring Lattice Theory: An Approach Based on Hierarchies of Concepts , 2009, ICFCA.

[24]  Amit P. Sheth,et al.  Changing Focus on Interoperability in Information Systems:From System, Syntax, Structure to Semantics , 1999 .

[25]  E. So.  What is known about the mechanisms underlying SUDEP? , 2008, Epilepsia.

[26]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[27]  Amit P. Sheth,et al.  An ontology-driven semantic mashup of gene and biological pathway information: Application to the domain of nicotine dependence , 2008, J. Biomed. Informatics.

[28]  Andrew D. Spear.  Ontology for the Twenty First Century: An Introduction with Recommendations , 2006 .

[29]  Deborah L. McGuinness,et al.  PROV-O: The PROV Ontology , 2013 .

[30]  Francisco Sales,et al.  Ontology and Knowledge Management System on Epilepsy and Epileptic Seizures , 2010, SWAT4LS.

[31]  Tobias Loddenkemper,et al.  A proposal for a five-dimensional patient-oriented epilepsy classification. , 2005, Epileptic disorders : international epilepsy journal with videotape.

[32]  Guo-Qiang Zhang.  Large-Scale, Exhaustive Lattice-Based Structural Auditing of SNOMED CT , 2010, KSEM.

[33]  Stuart J. Nelson,et al.  Normalized names for clinical drugs: RxNorm at 6 years , 2011, J. Am. Medical Informatics Assoc..

[34]  W. Hauser,et al.  Comment on Epileptic Seizures and Epilepsy: Definitions Proposed by the International League Against Epilepsy (ILAE) and the International Bureau for Epilepsy (IBE) , 2005, Epilepsia.

[35]  C. Panayiotopoulos,et al.  The new ILAE report on terminology and concepts for organization of epileptic seizures: A clinician’s critical view and contribution , 2011, Epilepsia.

[36]  Iftikhar U. Sikder,et al.  Modeling a Classification Scheme of Epileptic Seizures Using Ontology Web Language , 2010, Int. J. Comput. Model. Algorithms Medicine.

[37]  Jerome Engel,et al.  The etiologic classification of epilepsy , 2011, Epilepsia.

[38]  Christopher G. Chute,et al.  The National Center for Biomedical Ontology , 2012, J. Am. Medical Informatics Assoc..

[39]  L. Nashef,et al.  Risk Factors in Sudden Death in Epilepsy (SUDEP): The Quest for Mechanisms , 2007, Epilepsia.

[40]  N. Barbaro,et al.  Common data elements in epilepsy research: Development and implementation of the NINDS epilepsy CDE project , 2011, Epilepsia.

[41]  Jung-Hsien Chiang,et al.  MeKE: Discovering the Functions of Gene Products from Biomedical Literature Via Sentence Alignment , 2003, Bioinform..

[42]  Sunghwan Sohn,et al.  Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications , 2010, J. Am. Medical Informatics Assoc..

[43]  Hans-Jörg Schek,et al.  Interoperating Geographic Information Systems , 1999, Lecture Notes in Computer Science.

[44]  A. Rector.  Thesauri and Formal Classifications: Terminologies for People and Machines , 1998, Methods of Information in Medicine.

[45]  Allen D. Malony,et al.  Development of NeuroElectroMagnetic ontologies(NEMO): a framework for mining brainwave ontologies , 2007, KDD '07.

[46]  Yi Liu,et al.  Using ontology-based annotation to profile disease research , 2012, J. Am. Medical Informatics Assoc..

[47]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[48]  Jan Komorowski,et al.  Learning Rule-based Models of Biological Process from Gene Expression Time Profiles Using Gene Ontology , 2003, Bioinform..

[49]  José L. V. Mejino,et al.  A reference ontology for biomedical informatics: the Foundational Model of Anatomy , 2003, J. Biomed. Informatics.

[50]  Jérôme Euzenat,et al.  A Survey of Schema-Based Matching Approaches , 2005, J. Data Semant..

[51]  B Diehl,et al.  [Suggestion for a new, patient-oriented epilepsy classification]. , 2006, Der Nervenarzt.

[52]  Guo-Qiang Zhang,et al.  EpiDEA: Extracting Structured Epilepsy and Seizure Information from Patient Discharge Summaries for Cohort Identification , 2012, AMIA.