CrcTRP: a Translational Research Platform for Colorectal Cancer

Overview

Journal Comput Math Methods Med

Publisher Hindawi

Specialty Medical Informatics

Date 2013 Feb 23

PMID 23431356

Citations 3

Authors

Ning Deng

Ling Zheng

Fang Liu

Li Wang

Huilong Duan

Affiliations

Soon will be listed here.

Abstract

Colorectal cancer is a leading cause of cancer mortality in both developed and developing countries. Transforming basic research results into clinical practice is one of the key tasks of translational research, which will greatly improve the diagnosis and treatments of colorectal cancer. In this paper, a translational research platform for colorectal cancer, named crcTRP, is introduced. crcTRP serves the colorectal cancer translational research by providing various types of biomedical information related with colorectal cancer to the community. The information, including clinical data, epidemiology data, individual omics data, and public omics data, was collected through a multisource biomedical information collection solution and then integrated in a clinic-omics database, which was constructed with EAV-ER model for flexibility and efficiency. A preliminary exploration of conducting translational research on crcTRP was implemented and worked out a set of clinic-genomic relations, linking clinical data with genomic data. These relations have also been applied to crcTRP to make it more conductive for cancer translational research.

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References

Zhao P, Dai M, Chen W, Li N . Cancer trends in China. Jpn J Clin Oncol. 2010; 40(4):281-5. DOI: 10.1093/jjco/hyp187. View

Abraham S, Nobukawa B, Giardiello F, Hamilton S, Wu T . Fundic gland polyps in familial adenomatous polyposis: neoplasms with frequent somatic adenomatous polyposis coli gene alterations. Am J Pathol. 2000; 157(3):747-54. PMC: 1885693. DOI: 10.1016/S0002-9440(10)64588-9. View

Kushi L, Byers T, Doyle C, Bandera E, McCullough M, McTiernan A . American Cancer Society Guidelines on Nutrition and Physical Activity for cancer prevention: reducing the risk of cancer with healthy food choices and physical activity. CA Cancer J Clin. 2006; 56(5):254-81. DOI: 10.3322/canjclin.56.5.254. View

Siegel R, Naishadham D, Jemal A . Cancer statistics, 2012. CA Cancer J Clin. 2012; 62(1):10-29. DOI: 10.3322/caac.20138. View

Pruitt K, Tatusova T, Maglott D . NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2004; 33(Database issue):D501-4. PMC: 539979. DOI: 10.1093/nar/gki025. View

Davies H, Bignell G, Cox C, Stephens P, Edkins S, Clegg S . Mutations of the BRAF gene in human cancer. Nature. 2002; 417(6892):949-54. DOI: 10.1038/nature00766. View

Hamosh A, Scott A, Amberger J, Bocchini C, McKusick V . Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2004; 33(Database issue):D514-7. PMC: 539987. DOI: 10.1093/nar/gki033. View

Bairoch A, Apweiler R . The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 1999; 28(1):45-8. PMC: 102476. DOI: 10.1093/nar/28.1.45. View

Morikawa T, Kuchiba A, Yamauchi M, Meyerhardt J, Shima K, Nosho K . Association of CTNNB1 (beta-catenin) alterations, body mass index, and physical activity with survival in patients with colorectal cancer. JAMA. 2011; 305(16):1685-94. PMC: 3087286. DOI: 10.1001/jama.2011.513. View

10.

Shah N . Translational bioinformatics embraces big data. Yearb Med Inform. 2012; 7:130-4. PMC: 4370941. View

11.

Sarkar I . Biomedical informatics and translational medicine. J Transl Med. 2010; 8:22. PMC: 2837642. DOI: 10.1186/1479-5876-8-22. View

12.

Kakazu K, Cheung L, Lynne W . The Cancer Biomedical Informatics Grid (caBIG): pioneering an expansive network of information and tools for collaborative cancer research. Hawaii Med J. 2004; 63(9):273-5. View

13.

Butte A . Translational bioinformatics: coming of age. J Am Med Inform Assoc. 2008; 15(6):709-14. PMC: 2585538. DOI: 10.1197/jamia.M2824. View

14.

Marenco L, Nadkarni P, Skoufos E, Shepherd G, Miller P . Neuronal database integration: the Senselab EAV data model. Proc AMIA Symp. 1999; :102-6. PMC: 2232788. View

15.

Lipscomb C . Medical Subject Headings (MeSH). Bull Med Libr Assoc. 2000; 88(3):265-6. PMC: 35238. View

16.

De Silva T, Macdonald D, Paterson G, Sikdar K, Cochrane B . Systematized nomenclature of medicine clinical terms (SNOMED CT) to represent computed tomography procedures. Comput Methods Programs Biomed. 2011; 101(3):324-9. DOI: 10.1016/j.cmpb.2011.01.002. View

17.

Bodenreider O . The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2003; 32(Database issue):D267-70. PMC: 308795. DOI: 10.1093/nar/gkh061. View

18.

Maglott D, Ostell J, Pruitt K, Tatusova T . Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2010; 39(Database issue):D52-7. PMC: 3013746. DOI: 10.1093/nar/gkq1237. View

19.

Richter R, Austin T . Using MeSH (medical subject headings) to enhance PubMed search strategies for evidence-based practice in physical therapy. Phys Ther. 2011; 92(1):124-32. DOI: 10.2522/ptj.20100178. View

20.

Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C . Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29(4):365-71. DOI: 10.1038/ng1201-365. View