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Feltrin, Erika (2008) Contribution to OBO ontologies and application of structured vocabularies for data integration and biological reasoning. [Ph.D. thesis]

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Abstract (english)

As the amount of accessible biological data is growing exponentially, it is becoming harder and harder to extract the biological knowledge contained in thousands of databases. Biomedical scientists collect facts, often recording them in natural language, and then use their knowledge to make inferences about as yet uncharacterised observations. Therefore, to make the best use of biological databases and the knowledge they contain, different kinds of information from different sources must be integrated in ways that make sense to the scientific community. The Gene Ontology (GO) and other biomedical ontologies (OBO) are fundamental components in data integration and annotation.
This PhD project focuses on the improvement of some already existing resources, and the development of new methods that facilitate data integration and extraction, for genes, drugs and diseases, and their inter-relationships. The work consists of contributions to biological ontologies and definitions of cross-links between different semantic fields represented in several distinct databases. Significant changes in GO content and structure have been provided, resulting in the addition of hundreds of terms useful in the representation of muscle and nervous system biology. In addition, a resource has been developed to find preliminary correlations between genes, drugs and diseases. This resource integrates information from several very up-to-date sources, most of which are manually curated; and from a human disease ontology, the "Disease Ontology".
The revised ontologies will facilitate the interpretation of high-throughout experiments in the area of muscle biology and neurobiology, and more importantly, in the fields of neuromuscular and nervous system diseases. Furthermore, the developed ontology-based system will provide interoperability support for physicians and medical researchers in the interpretation of data from studies on human diseases.

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EPrint type:Ph.D. thesis
Tutor:Valle, Giorgio
Supervisor:Deegan, Jennifer
Ph.D. course:Ciclo 20 > Scuole per il 20simo ciclo > BIOCHIMICA E BIOTECNOLOGIE > BIOTECNOLOGIE
Data di deposito della tesi:24 January 2008
Anno di Pubblicazione:24 January 2008
Key Words:Gene Ontology, controlled vocabulary, ontology, functional annotation
Settori scientifico-disciplinari MIUR:Area 05 - Scienze biologiche > BIO/11 Biologia molecolare
Struttura di riferimento:Centri > Centro di ricerca Interdipartimentale Biotecnologie Innovative (CRIBI)
Codice ID:376
Depositato il:05 Nov 2008
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[1] S. Philippi and J. Kohler. Addressing the problems with life-science databases for traditional uses and systems biology. Nat Rev Genet, 7(6):482-8, 2006. Cerca con Google

[2] M. A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, S. Lewis, B. Marshall, C. Mungall, J. Richter, G. M. Rubin, J. A. Blake, C. Bult, M. Dolan, H. Drabkin, J. T. Eppig, D. P. Hill, L. Ni, M. Ringwald, R. Balakrishnan, J. M. Cherry, K. R. Christie, M. C. Costanzo, S. S. Dwight, S. Engel, D. G. Fisk, J. E. Hirschman, E. L. Hong, R. S. Nash, A. Sethuraman, C. L. Theesfeld, D. Botstein, K. Dolinski, B. Feierbach, T. Berardini, S. Mundodi, S. Y. Rhee, R. Apweiler, D. Barrell, E. Camon, E. Dimmer, V. Lee, R. Chisholm, P. Gaudet, W. Kibbe, R. Kishore, E. M. Schwarz, P. Sternberg, M. Gwinn, L. Hannick, J. Wortman, M. Berriman, V. Wood, N. de la Cruz, P. Tonellato, P. Jaiswal, T. Seigfried, and R. White. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res, 32(Database issue):D258-61, 2004. Cerca con Google

[3] T. R. Gruber. Towards principles for the design of ontologies used for knowledge sharing. In N. Guarino and R. Poli, editors, Formal Ontology in Conceptual Analysis and Knowledge Representation, Deventer, The Netherlands, 1993. Kluwer Academic Publishers. Cerca con Google

[4] P. Lambrix, M. Habbouche, and M. Perez. Evaluation of ontology development tools for bioinformatics. Bioinformatics, 19(12):1564-71, 2003. Cerca con Google

[5] R. Mack and M. Hehenberger. Text-based knowledge discovery: search and mining of life-sciences documents. Drug Discov Today, 7(11 Suppl):S89-98, 2002. Cerca con Google

[6] M. Harris and H Parkinson. Standards and Ontologies for Functional Genomics: Towards Unified Ontologies for Biology and Biomedicine. Comparative and Functional Genomics, 4(1):116-120, 2003. doi:10.1002/cfg.249. Cerca con Google

[7] M. Deng, Z. Tu, F. Sun, and T. Chen. Mapping Gene Ontology to proteins based on protein-protein interaction data. Bioinformatics, 20(6):895-902, 2004. Cerca con Google

[8] O. Bodenreider and R. Stevens. Bio-ontologies: current trends and future directions. Brief Bioinform, 7(3):256-74, 2006. Cerca con Google

[9] J. I. Clark, C. Brooksbank, and J. Lomax. It's all GO for plant scientists. Plant Physiol, 138(3):1268-79, 2005. Cerca con Google

[10] J. B. Bard and S. Y. Rhee. Ontologies in biology: design, applications and future challenges. Nat Rev Genet, 5(3):213-22, 2004. Cerca con Google

[11] T. R. Gruber. A Translation Approach to Portable Ontology Specifications. Knowledge Acquisition, 5(2):199-220, 1993. Cerca con Google

[12] B. Andersen. What is an ontology? Ontology Works (http://www.ontologyworks.com), 2001. Vai! Cerca con Google

[13] O. Bodenreider, J. A. Mitchell, and A. T. McCray. Biomedical ontologies. Pac Symp Biocomput, pages 76-8, 2005. Cerca con Google

[14] S. Schulze-Kremer. Ontologies for molecular biology and bioinformatics. In Silico Biol, 2(3):179-93, 2002. Cerca con Google

[15] J. S. Caldwell. Ontology recapitulates physiology. Chem Biol, 10(9):784-6, 2003. Cerca con Google

[16] D. Devos and A. Valencia. Intrinsic errors in genome annotation. Trends Genet, 17(8):429- 31, 2001. Cerca con Google

[17] C. Blaschke and A. Valencia. Automatic ontology construction from the literature. Genome Inform, 13:201-13, 2002. Cerca con Google

[18] B. Smith, M. Ashburner, C. Rosse, J. Bard, W. Bug, W. Ceusters, L. J. Goldberg, K. Eilbeck, A. Ireland, C. J. Mungall, N. Leontis, P. Rocca-Serra, A. Ruttenberg, S. A. Sansone, R. H. Scheuermann, N. Shah, P. L. Whetzel, and S. Lewis. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol, 25(11):1251-1255, 2007. Cerca con Google

[19] B. Smith, W. Ceusters, B. Klagges, J. Kohler, A. Kumar, J. Lomax, C. Mungall, F. Neuhaus, A. L. Rector, and C. Rosse. Relations in biomedical ontologies. Genome Biol, 6(5):R46, 2005. Cerca con Google

[20] J. A. Blake and C. J. Bult. Beyond the data deluge: data integration and bio-ontologies. J Biomed Inform, 39(3):314-20, 2006. Cerca con Google

[21] M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler, J. M. Cherry, A. P. Davis, K. Dolinski, S. S. Dwight, J. T. Eppig, M. A. Harris, D. P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. C. Matese, J. E. Richardson, M. Ringwald, G. M. Rubin, and G. Sherlock. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25(1):25-9, 2000. Cerca con Google

[22] D. M. Jones and R. C. Paton. Toward principles for the representation of hierarchical knowledge in formal ontologies. Data & Knowledge Engineering, 31(2):99-113, 1999. Cerca con Google

[23] R. Stevens, C. A. Goble, and S. Bechhofer. Ontology-based knowledge representation for bioinformatics. Brief Bioinform, 1(4):398-414, 2000. Cerca con Google

[24] J. Blake and M. Harris. The Gene Ontology Project: Structured vocabularies for molecular biology and their application to genome and expression analysis. Baxevanis, A.D. Davison, D.B. Page, R. Stormo, G. Stein, L.Current Protocols in Bioinformatics, Wiley & Sons, New York., 2003. Cerca con Google

[25] M. Harris, J. Lomax, A. Ireland, and J. I. Clark. The Gene Ontology project. John Wiley & Sons, Ltd. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. Part 4. Bioinformatics 4.7. Structuring and Integrating Data, 2005. Cerca con Google

[26] The Gene Ontology Consortium. Creating the gene ontology resource: design and implementation. Genome Res, 11(8):1425-33, 2001. Cerca con Google

[27] E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, D. Binns, N. Harte, R. Lopez, and R. Apweiler. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res, 32(Database issue):D262-6, 2004. Cerca con Google

[28] M. Bada, R. Stevens, C. Goble, Y. Gil, M. Ashburner, J.A. Blake, J.M. Cherry, M. Harris, and S. Lewis. A short study on the success of the gene ontology. Journal of Web Semantics, 1(2), 2004. Cerca con Google

[29] The Gene Ontology Consortium. The Gene Ontology project in 2008. Nucleic Acids Res, 2007. Cerca con Google

[30] A. D. Diehl, J. A. Lee, R. H. Scheuermann, and J. A. Blake. Ontology development for biological systems: immunology. Bioinformatics, 23(7):913-5, 2007. Cerca con Google

[31] J. Day-Richter, M. A. Harris, M. Haendel, and S. Lewis. OBO-Edit-an ontology editor for biologists. Bioinformatics, 23(16):2198-200, 2007. Cerca con Google

[32] E. Camon, M. Magrane, D. Barrell, D. Binns, W. Fleischmann, P. Kersey, N. Mulder, T. Oinn, J. Maslen, A. Cox, and R. Apweiler. The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro. Genome Res, 13(4):662-72, 2003. Cerca con Google

[33] E. B. Camon, D. G. Barrell, E. C. Dimmer, V. Lee, M. Magrane, J. Maslen, D. Binns, and R. Apweiler. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics, 6 Suppl 1:S17, 2005. Cerca con Google

[34] Z. Z. Hu, I. Mani, V. Hermoso, H. Liu, and C. H. Wu. iProLINK: an integrated protein resource for literature mining. Comput Biol Chem, 28(5-6):409-16, 2004. Cerca con Google

[35] S. Pyysalo, F. Ginter, T. Pahikkala, J. Boberg, J. Jarvinen, and T. Salakoski. Evaluation of two dependency parsers on biomedical corpus targeted at protein-protein interactions. Int J Med Inform, 75(6):430-42, 2006. Cerca con Google

[36] T. Z. Berardini, S. Mundodi, L. Reiser, E. Huala, M. Garcia-Hernandez, P. Zhang, L. A. Mueller, J. Yoon, A. Doyle, G. Lander, N. Moseyko, D. Yoo, I. Xu, B. Zoeckler, M. Montoya, N. Miller, D. Weems, and S. Y. Rhee. Functional annotation of the Arabidopsis genome using controlled vocabularies. Plant Physiol, 135(2):745-55, 2004. Cerca con Google

[37] F. M. Couto, M. J. Silva, V. Lee, E. Dimmer, E. Camon, R. Apweiler, H. Kirsch, and D. Rebholz-Schuhmann. GOAnnotator: linking protein GO annotations to evidence text. J Biomed Discov Collab, 1:19, 2006. Cerca con Google

[38] A. Doms and M. Schroeder. GoPubMed: exploring PubMed with the Gene Ontology. Nucleic Acids Res, 33(Web Server issue):W783-6, 2005. Cerca con Google

[39] W. A. Baumgartner, Jr, K. B. Cohen, L. M. Fox, G. Acquaah-Mensah, and L. Hunter. Manual curation is not su_cient for annotation of genomic databases. Bioinformatics, 23(13):i41-8, 2007. Cerca con Google

[40] M. R. Seringhaus and M. B. Gerstein. Publishing perishing? Towards tomorrow's information architecture. BMC Bioinformatics, 8:17, 2007. Cerca con Google

[41] S. D. Schlueter, M. D. Wilkerson, Q. Dong, and V. Brendel. xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biol, 7(11):R111, 2006. Cerca con Google

[42] M. D. Wilkerson, S. D. Schlueter, and V. Brendel. yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biol, 7(7):R58, 2006. Cerca con Google

[43] C Baral. Collaborative curation of data from bio-medical texts and abstracts and its integration. In Proceedings of the Second International Workshop on Data Integration in the Life Sciences., 2005. Cerca con Google

[44] E. J. Nestler, M. Barrot, R. J. DiLeone, A. J. Eisch, S. J. Gold, and L. M. Monteggia. Neurobiology of depression. Neuron, 34(1):13-25, 2002. Cerca con Google

[45] F. Holsboer. Stress, hypercortisolism and corticosteroid receptors in depression: implications for therapy. J A_ect Disord, 62(1-2):77-91, 2001. Cerca con Google

[46] R. M. Sapolsky. Glucocorticoids and hippocampal atrophy in neuropsychiatric disorders. Arch Gen Psychiatry, 57(10):925-35, 2000. Cerca con Google

[47] A. A. Russo-Neustadt and M. J. Chen. Brain-derived neurotrophic factor and antidepressant activity. Curr Pharm Des, 11(12):1495-510, 2005. Cerca con Google

[48] D. Nijhawan, N. Honarpour, and X. Wang. Apoptosis in neural development and disease. Annu Rev Neurosci, 23:73-87, 2000. Cerca con Google

[49] M. Hetman, K. Kanning, J. E. Cavanaugh, and Z. Xia. Neuroprotection by brain-derived neurotrophic factor is mediated by extracellular signal-regulated kinase and phosphatidylinositol 3-kinase. J Biol Chem, 274(32):22569-80, 1999. Cerca con Google

[50] P. Desjardins and S. Ledoux. The role of apoptosis in neurodegenerative diseases. Metab Brain Dis, 13(2):79-96, 1998. Cerca con Google

[51] B. S. McEwen. Stress and hippocampal plasticity. Annu Rev Neurosci, 22:105-22, 1999. Cerca con Google

[52] E. Pollanen, P. H. Ronkainen, H. Suominen, T. Takala, S. Koskinen, J. Puolakka, S. Sipila, and V. Kovanen. Muscular Transcriptome in Postmenopausal Women With or Without Hormone Replacement. Rejuvenation Res, 2007. Cerca con Google

[53] C. Bean, M. Salamon, A. Raffaello, S. Campanaro, A. Pallavicini, and G. Lanfranchi. The Ankrd2, Cdkn1c and calcyclin genes are under the control of MyoD during myogenic differentiation. J Mol Biol, 349(2):349-66, 2005. Cerca con Google

[54] T. F. Hayamizu, M. Mangan, J. P. Corradi, J. A. Kadin, and M. Ringwald. The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol, 6(3):R29, 2005. Cerca con Google

[55] J. Bard, S. Y. Rhee, and M. Ashburner. An ontology for cell types. Genome Biol, 6(2):R21, 2005. Cerca con Google

[56] D. Frank, C. Kuhn, H. A. Katus, and N. Frey. The sarcomeric Z-disc: a nodal point in signalling and disease. J Mol Med, 84(6):446-68, 2006. Cerca con Google

[57] S. Schiaffino, M. Sandri, and M. Murgia. Activity-dependent signaling pathways controlling muscle diversity and plasticity. Physiology (Bethesda), 22:269-78, 2007. Cerca con Google

[58] M. W. Berchtold, H. Brinkmeier, and M. Muntener. Calcium ion in skeletal muscle: its crucial role for muscle function, plasticity, and disease. Physiol Rev, 80(3):1215-65, 2000. Cerca con Google

[59] A. Nori, G. Valle, E. Bortoloso, F. Turcato, and P. Volpe. Calsequestrin targeting to sarcoplasmic reticulum of skeletal muscle fibers. Am J Physiol Cell Physiol, 291(2):C245- 53, 2006. Cerca con Google

[60] R. Bassel-Duby and E. N. Olson. Role of calcineurin in striated muscle: development, adaptation, and disease. Biochem Biophys Res Commun, 311(4):1133-41, 2003. Cerca con Google

[61] A. Scime and M. A. Rudnicki. Anabolic potential and regulation of the skeletal muscle satellite cell populations. Curr Opin Clin Nutr Metab Care, 9(3):214-9, 2006. Cerca con Google

[62] J. E. Anderson. The satellite cell as a companion in skeletal muscle plasticity: currency, conveyance, clue, connector and colander. J Exp Biol, 209(Pt 12):2276-92, 2006. Cerca con Google

[63] X. Shi and D. J. Garry. Muscle stem cells in development, regeneration, and disease. Genes Dev, 20(13):1692-708, 2006. Cerca con Google

[64] J. A. Timmons, O. Larsson, E. Jansson, H. Fischer, T. Gustafsson, P. L. Greenhaff, J. Ridden, J. Rachman, M. Peyrard-Janvid, C. Wahlestedt, and C. J. Sundberg. Human muscle gene expression responses to endurance training provide a novel perspective on Duchenne muscular dystrophy. FASEB J, 19(7):750-60, 2005. Cerca con Google

[65] C. A. Joslyn, S. M. Mniszewski, A. Fulmer, and G. Heaton. The gene ontology categorizer. Bioinformatics, 20 Suppl 1:i169-77, 2004. Cerca con Google

[66] A. V. Loguinov, L. M. Anderson, G. J. Crosby, and R. Y. Yukhananov. Gene expression following acute morphine administration. Physiol Genomics, 6(3):169-81, 2001. Cerca con Google

[67] M. Kanehisa, S. Goto, M. Hattori, K. F. Aoki-Kinoshita, M. Itoh, S. Kawashima, T. Katayama, M. Araki, and M. Hirakawa. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res, 34(Database issue):D354-7, 2006. Cerca con Google

[68] K. Degtyarenko, M. Ennis, and J. S. Garavelli. "Good annotation practice" for chemical data in biology. In Silico Biol, 7(2 Suppl):S45-56, 2007. Cerca con Google

[69] K. Degtyarenko, P. D. Matos, M. Ennis, J. Hastings, M. Zbinden, A. McNaught, R. Alcantara, M. Darsow, M. Guedj, and M. Ashburner. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res, 2007. Cerca con Google

[70] C. Boettcher, M. Fellermeier, C. Boettcher, B. Drager, and M. H. Zenk. How human neuroblastoma cells make morphine. Proc Natl Acad Sci U S A, 102(24):8495-500, 2005. Cerca con Google

[71] W. H. Stuart. Combination therapy for the treatment of multiple sclerosis: challenges and opportunities. Curr Med Res Opin, 2007. Cerca con Google

[72] Y. Takahashi, K. Washiyama, T. Kobayashi, and S. Hayashi. Gene expression in the brain from uoxetine-injected mouse using DNA microarray. Ann N Y Acad Sci, 1074:42-51, 2006. Cerca con Google

[73] K. Olden and S. Wilson. Environmental health and genomics: visions and implications. Nat Rev Genet, 1(2):149-53, 2000. Cerca con Google

[74] O. Bodenreider. The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res, 32(Database issue):D267-70, 2004. Cerca con Google

[75] K. G. Becker, K. C. Barnes, T. J. Bright, and S. A. Wang. The genetic association database. Nat Genet, 36(5):431-2, 2004. Cerca con Google

[76] A. Hamosh, A. F. Scott, J. S. Amberger, C. A. Bocchini, and V. A. McKusick. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res, 33(Database issue):D514-7, 2005. Cerca con Google

[77] D. S. Wishart, C. Knox, A. C. Guo, S. Shrivastava, M. Hassanali, P. Stothard, Z. Chang, and J. Woolsey. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res, 34(Database issue):D668-72, 2006. Cerca con Google

[78] M. Hewett, D. E. Oliver, D. L. Rubin, K. L. Easton, J. M. Stuart, R. B. Altman, and T. E. Klein. PharmGKB: the Pharmacogenetics Knowledge Base. Nucleic Acids Res, 30(1):163-5, 2002. Cerca con Google

[79] R. B. Altman. PharmGKB: a logical home for knowledge relating genotype to drug response phenotype. Nat Genet, 39(4):426, 2007. Cerca con Google

[80] T. Hernandez-Boussard, M. Whirl-Carrillo, J. M. Hebert, L. Gong, R. Owen, M. Gong, W. Gor, F. Liu, C. Truong, R. Whaley, M. Woon, T. Zhou, R. B. Altman, and T. E. Klein. The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Res, 2007. Cerca con Google

[81] R. G. Cote, P. Jones, R. Apweiler, and H. Hermjakob. The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries. BMC Bioinformatics, 7:97, 2006. Cerca con Google

[82] The Gene Ontology Consortium. The Gene Ontology (GO) project in 2006. Nucleic Acids Res, 34(Database issue):D322-6, 2006. Cerca con Google

[83] R. Hoffmann and A. Valencia. Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics, 21 Suppl 2:ii252-8, 2005. Cerca con Google

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