Abstract
Hypertrophic cardiomyopathy (HCM) is a complex genetic disease characterized by a variable clinical presentation and onset, as well as a high number of associated mutations.
Therefore, this disease is a good candidate for a translational medicine approach to assist in its prognosis. For this purpose, we propose a framework containing two components: one for data integration, and another for data analysis based on clinical-genetic associations obtained with data mining techniques.
In this article we present the implementation of the first component. At its basis is a semantic data model developed in OWL representing the clinical and genetic data necessary for the characterization of HCM patients. This model follows a modular approach and includes mappings to controlled vocabularies such as the NCI Thesaurus and SNOMED-Clinical Terms.
The development of the model has been done in collaboration with biomedical experts, who are also the providers of the data to populate it.
Keywords
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References
Maron, B.J., Maron, M.S., Wigle, E.D., Braunwald, E.: The 50-Year History, Controversy, and Clinical Implications of Left Ventricular Outflow Tract Obstruction in Hypertrophic Cardiomyopathy: from Idiopathic Hypertrophic Subaortic Stenosis to Hypertrophic Cardiomyopathy. J. Am. Coll. Cardiol. 54, 191–200 (2009)
Alcalai, R., Seidman, J.G., Seidman, C.E.: Genetic Basis of Hypertrophic Cardiomyopathy: from Bench to the Clinics. J. Cardiovasc. Electrophysiol. 19, 104–110 (2008)
Harvard Sarcomere Mutation Database, http://genepath.med.harvard.edu/~seidman/cg3/
Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene Ontology: Tool for the Unification of Biology. Nat. Genet. 25, 25–29 (2000)
Systematized Nomenclature of Medicine-Clinical Terms (SNOMED), http://www.ihtsdo.org/snomed-ct/
Berners-Lee, T., Hendler, J., Lassila, O.: The Semantic Web. Sci. Am., 29–37 (2001)
World Wide Web Consortium, http://www.w3.org/
RDF Primer, http://www.w3.org/TR/2004/REC-rdf-primer-20040210/
OWL Web Ontology Language Current Status, http://www.w3.org/standards/techs/owl#w3call
Gudivada, R.C., Qu, X.A., Chen, J., Jegga, A.G., Neumann, E.K., Aronow, B.J.: Identifying Disease-Causal Genes Using Semantic Web-based Representation of Integrated Genomic and Phenomic Knowledge. J. Biomed. Inform. 41, 717–729 (2008)
Agorastos, T., Koutkias, V., Falelakis, M., Lekka, I., Mikos, T., Delopoulos, A., Mitkas, P.A., Tantsis, A., Weyers, S., Coorevits, P., Kaufmann, A.M., Kurzeja, R., Maglaveras, N.: Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: the ASSIST Approach. Cancer Inform. 8, 31–44 (2009)
Colombo, G., Merico, D., Boncoraglio, G., Paoli, F.D., Ellul, J., Frisoni, G., Nagy, Z., van der Lugt, A., Vassányi, I., Antoniotti, M.: An Ontological Modeling Approach to Cerebrovascular Disease Studies: the NEUROWEB Case. J. Biomed. Inform. 43, 469–484 (2010)
Noy, N.F., McGuinness, D.L.: Ontology Development 101: A Guide to Creating Your First Ontology. Technical report number KSL-01-05, Knowledge Systems, AI Laboratory, Stanford University (2001)
Protégé Ontology Editor, http://protege.stanford.edu
Hermit OWL Reasoner, http://hermit-reasoner.com/
Noy, N.F., Shah, N.H., Whetzel, P.L., Dai, B., Dorf, M., Griffith, N., Jonquet, C., Rubin, D.L., Storey, M.-A., Chute, C.G., Musen, M.A.: BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse. Nucleic Acids Res. 37, W170–W173 (2009)
Machado, C.M., Couto, F., Fernandes, A.R., Santos, S., Cardim, N., Freitas, A.T.: Semantic Characterization of Hypertrophic Cardiomyopathy Diseases. In: First Workshop on Knowledge Engineering, Discovery and Dissemination in Health, KEDDH 2010 (2010)
Sioutos, N., Coronado, S., Haber, M.W., Hartel, F.W., Shaiu, W.L., Wright, L.W.: NCI Thesaurus: a Semantic Model Integrating Cancer-Related Clinical and Molecular Information. J. Biomed. Inform. 40, 30–43 (2007)
The Ontology of Clinical Research (OCRe), http://rctbank.ucsf.edu/home/ocre.html
Beisswanger, E., Lee, V., Kim, J., Rebholz-Schuhmann, D., Splendiani, A., Dameron, O., Schulz, S., Hahn, U.: Gene Regulation Ontology (GRO): Design Principles and Use Cases. St. Heal. T. 136, 9–14 (2008)
Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R., Ashburner, M.: The Sequence Ontology: a Tool for the Unification of Genome Annotations. Genome Biol. 6, R44 (2005)
Jonquet, C., Musen, M.A., Shah, N.H.: Building a Biomedical Ontology Recommender Web Service. J. Biomed. Semantics 1(suppl. 1), S1 (2010)
Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L.J., Eilbeck, K., Ireland, A., Mungall, C.J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Scheuermann, R.H., Shah, N., Whetzel, P.L., Lewis, S.: The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration. Nat. Biotech. 25, 1251–1255 (2007)
Gersh, B.J., Maron, B.J., Bonow, R.O., Dearani, J.A., Fifer, M.A., Link, M.S., Naidu, S.S., Nishimura, R.A., Ommen, S.R., Rakowski, H., Seidman, C.E., Towbin, J.A., Udelson, J.E., Yancy, C.W.: ACCF/AHA Guideline for the Diagnosis and Treatment of Hypertrophic Cardiomyopathy: A Report of the American College of Cardiology Foundation/American Heart Association Task Force on Practice Guidelines. Circulation 124, e783–e831 (2011)
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Machado, C.M., Couto, F.M., Fernandes, A.R., Santos, S., Freitas, A.T. (2012). Toward a Translational Medicine Approach for Hypertrophic Cardiomyopathy. In: Böhm, C., Khuri, S., Lhotská, L., Renda, M.E. (eds) Information Technology in Bio- and Medical Informatics. ITBAM 2012. Lecture Notes in Computer Science, vol 7451. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32395-9_12
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DOI: https://doi.org/10.1007/978-3-642-32395-9_12
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