Design and Development of an Information System to Manage Clinical Data about Usher Syndrome Based on Conceptual Modeling

[EN] The inefficient management of clinical data in many research environments is a problem which slows down the service provided to patients. The benefits of an Information System created following the conceptual modeling rules have been proved in multiple environments with data management difficulties. The main hurdle to overcome is the large gap between the language and concepts employed by informaticians and the ones used by biologists. The work described in this paper shows how these technologies can also be applied to the clinical domain, after a long period of mutual approaching in order to understand each other. The research clinical data of an expert research group on Usher syndrome have been studied, analyzed and redesigned using conceptual modeling, helping this group to offer a better service.It is important to highlight that this work has been done under the framework of the Cátedra Tecnologías para la Salud of the Universitat Politècnica de València financed by INDRA Systems.Burriel Coll, V.; Pastor Cubillo, MÁ.; Celma Giménez, M.; Casamayor Rodenas, JC.; Mota Herranz, L. (2013). Design and Development of an Information System to Manage Clinical Data about Usher Syndrome Based on Conceptual Modeling. IARIA XPS Press. http://hdl.handle.net/10251/75237

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.The Spanish Ministry of Science and Innovation (MICINN) [BIO2011-27069]; the Conselleria de Educacio of the Valencian Community [PROMETEO/2010/001]; National Institute of Bioinformatics (www.inab.org); CIBER de Enfermedades Raras (CIBERER), ISCIII and MICINN; Red Tematica de Investigacion Cooperativa en Cancer (RTICC) [RD06/0020/1019] ISCIII, MICINN and INNPACTO [IPT-010000-2010-43], MICINN. Funding for open access charge: MICINN [BIO2011-27069].Bleda, M.; Tarraga, J.; De María, A.; Salavert, F.; García-Alonso, L.; Celma Giménez, M.; Martín Mayordomo, A.... (2012). CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Research. 40(1):609-614. https://doi.org/10.1093/nar/gks575S609614401Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., … Lewis, S. (2007). The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. doi:10.1038/nbt1346Flicek, P., Amode, M. R., Barrell, D., Beal, K., Brent, S., Carvalho-Silva, D., … Fitzgerald, S. (2011). Ensembl 2012. Nucleic Acids Research, 40(D1), D84-D90. doi:10.1093/nar/gkr991(2011). Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Research, 40(D1), D71-D75. doi:10.1093/nar/gkr981Kozomara, A., & Griffiths-Jones, S. (2010). miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Research, 39(Database), D152-D157. doi:10.1093/nar/gkq1027Xiao, F., Zuo, Z., Cai, G., Kang, S., Gao, X., & Li, T. (2009). miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Research, 37(Database), D105-D110. doi:10.1093/nar/gkn851Hsu, S.-D., Lin, F.-M., Wu, W.-Y., Liang, C., Huang, W.-C., Chan, W.-L., … Huang, H.-D. (2010). miRTarBase: a database curates experimentally validated microRNA–target interactions. Nucleic Acids Research, 39(suppl_1), D163-D169. doi:10.1093/nar/gkq1107Friedman, R. C., Farh, K. K.-H., Burge, C. B., & Bartel, D. P. (2008). Most mammalian mRNAs are conserved targets of microRNAs. Genome Research, 19(1), 92-105. doi:10.1101/gr.082701.108Betel, D., Wilson, M., Gabow, A., Marks, D. S., & Sander, C. (2007). The microRNA.org resource: targets and expression. Nucleic Acids Research, 36(Database), D149-D153. doi:10.1093/nar/gkm995Dreszer, T. R., Karolchik, D., Zweig, A. S., Hinrichs, A. S., Raney, B. J., Kuhn, R. M., … James Kent, W. (2011). The UCSC Genome Browser database: extensions and updates 2011. Nucleic Acids Research, 40(D1), D918-D923. doi:10.1093/nar/gkr1055Hunter, S., Jones, P., Mitchell, A., Apweiler, R., Attwood, T. K., Bateman, A., … Yong, S.-Y. (2011). InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research, 40(D1), D306-D312. doi:10.1093/nar/gkr948Sherry, S. T. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Research, 29(1), 308-311. doi:10.1093/nar/29.1.308(2010). Integrating common and rare genetic variation in diverse human populations. Nature, 467(7311), 52-58. doi:10.1038/nature09298(2010). A map of human genome variation from population-scale sequencing. Nature, 467(7319), 1061-1073. doi:10.1038/nature09534Hindorff, L. A., Sethupathy, P., Junkins, H. A., Ramos, E. M., Mehta, J. P., Collins, F. S., & Manolio, T. A. (2009). Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences, 106(23), 9362-9367. doi:10.1073/pnas.0903103106Stenson, P. D., Ball, E. V., Mort, M., Phillips, A. D., Shiel, J. A., Thomas, N. S. T., … Cooper, D. N. (2003). Human Gene Mutation Database (HGMD®): 2003 update. Human Mutation, 21(6), 577-581. doi:10.1002/humu.10212Johnson, A. D., & O’Donnell, C. J. (2009). An Open Access Database of Genome-wide Association Results. BMC Medical Genetics, 10(1). doi:10.1186/1471-2350-10-6Forbes, S. A., Bindal, N., Bamford, S., Cole, C., Kok, C. Y., Beare, D., … Futreal, P. A. (2010). COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Research, 39(Database), D945-D950. doi:10.1093/nar/gkq929Kerrien, S., Aranda, B., Breuza, L., Bridge, A., Broackes-Carter, F., Chen, C., … Hermjakob, H. (2011). The IntAct molecular interaction database in 2012. Nucleic Acids Research, 40(D1), D841-D846. doi:10.1093/nar/gkr1088Croft, D., O’Kelly, G., Wu, G., Haw, R., Gillespie, M., Matthews, L., … Stein, L. (2010). Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Research, 39(Database), D691-D697. doi:10.1093/nar/gkq1018Demir, E., Cary, M. P., Paley, S., Fukuda, K., Lemer, C., Vastrik, I., … Luciano, J. (2010). The BioPAX community standard for pathway data sharing. Nature Biotechnology, 28(9), 935-942. doi:10.1038/nbt.1666Bhagat, J., Tanoh, F., Nzuobontane, E., Laurent, T., Orlowski, J., Roos, M., … Goble, C. A. (2010). BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Research, 38(Web Server), W689-W694. doi:10.1093/nar/gkq394Dowell, R. D., Jokerst, R. M., Day, A., Eddy, S. R., & Stein, L. (2001). BMC Bioinformatics, 2(1), 7. doi:10.1186/1471-2105-2-

Métodos para la comprobación de la integridad en bases de datos deductivas

La comprobación de la integridad es un problema clásico en bases de datos; los primeros métodos fueron propuestos para simplificar la comprobación de restricciones estáticas en bases de datos relacionales extendiéndose posteriormente a las bases de datos deductivas. Estos métodos se basan en la idea común de evaluar instancias de las restricciones, obtenidas a partir de actualizaciones inducidas por la transacción, y se diferencian entre sí en la estrategia seguida para la instanciación y evaluación de las restricciones. En este trabajo se presenta una clasificación de los métodos más importantes propuestos en la literatura haciendo un análisis de los mismo

Métodos para la comprobación de la integridad en base de datos deductivas

La comprobación de la integridad es un problema clásico en bases de datos; los primeros métodos fueron propuestos para simplificar la comprobación de restricciones estáticas en bases de datos relacionales extendiéndose posteriormente a las bases de datos deductivas. Estos métodos se basan en la idea común de evaluar instancias de las restricciones, obtenidas a partir de actualizaciones inducidas por la transacción, y se diferencian entre sí en la estrategia seguida para la instanciación y evaluación de las restricciones. En este trabajo se presenta una clasificación de los métodos más importantes propuestos en la literatura haciendo un análisis de los mismos

Métodos para la comprobación de la integridad en base de datos deductivas

La comprobación de la integridad es un problema clásico en bases de datos; los primeros métodos fueron propuestos para simplificar la comprobación de restricciones estáticas en bases de datos relacionales extendiéndose posteriormente a las bases de datos deductivas. Estos métodos se basan en la idea común de evaluar instancias de las restricciones, obtenidas a partir de actualizaciones inducidas por la transacción, y se diferencian entre sí en la estrategia seguida para la instanciación y evaluación de las restricciones. En este trabajo se presenta una clasificación de los métodos más importantes propuestos en la literatura haciendo un análisis de los mismos