crcTRP: A Translational Research Platform for Colorectal Cancer

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.

[1]  I. Sarkar Biomedical informatics and translational medicine , 2010, Journal of Translational Medicine.

[2]  Lawrence H. Kushi,et al.  Erratum: 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 - A Cancer Journal for Clinicians (2006) 56, (254-281)) , 2007 .

[3]  Jun Nakaya The Translational Research Informatics (TRI) , 2006 .

[4]  Perry L. Miller,et al.  Neuronal database integration: the Senselab EAV data model , 1999, AMIA.

[5]  C E Lipscomb,et al.  Medical Subject Headings (MeSH). , 2000, Bulletin of the Medical Library Association.

[6]  Olivier Bodenreider,et al.  The Unified Medical Language System (UMLS): integrating biomedical terminology , 2004, Nucleic Acids Res..

[7]  F. Giardiello,et al.  Fundic gland polyps in familial adenomatous polyposis: neoplasms with frequent somatic adenomatous polyposis coli gene alterations. , 2000, The American journal of pathology.

[8]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[9]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[10]  Rolf Apweiler,et al.  The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 , 2000, Nucleic Acids Res..

[11]  Kerry K Kakazu,et al.  The Cancer Biomedical Informatics Grid (caBIG): pioneering an expansive network of information and tools for collaborative cancer research. , 2004, Hawaii medical journal.

[12]  M. Thun,et al.  American Cancer Society guidelines on nutrition and physical activity for cancer prevention , 2002, CA: a cancer journal for clinicians.

[13]  Tatiana A. Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[14]  Grace I. Paterson,et al.  Systematized nomenclature of medicine clinical terms (SNOMED CT) to represent computed tomography procedures , 2011, Comput. Methods Programs Biomed..

[15]  Min Dai,et al.  Cancer trends in China. , 2010, Japanese journal of clinical oncology.

[16]  A. Jemal,et al.  Cancer statistics, 2012 , 2012, CA: a cancer journal for clinicians.

[17]  N H Shah,et al.  Translational Bioinformatics Embraces Big Data , 2012, Yearbook of Medical Informatics.

[18]  N. Dubrawsky Cancer statistics , 1989, CA: a cancer journal for clinicians.

[19]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[20]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[21]  Tatiana Tatusova,et al.  NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..

[22]  Randy R Richter,et al.  Using MeSH (Medical Subject Headings) to Enhance PubMed Search Strategies for Evidence-Based Practice in Physical Therapy , 2011, Physical Therapy.