TY - JOUR
T1 - ICOD
T2 - An integrated clinical omics database based on the systems-pathology view of disease
AU - Shimokawa, Kazuro
AU - Mogushi, Kaoru
AU - Shoji, Satoshi
AU - Hiraishi, Atsuko
AU - Ido, Keisuke
AU - Mizushima, Hiroshi
AU - Tanaka, Hiroshi
N1 - Funding Information:
Development of iCOD has been conducted as a government-commissioned national project, under the direction of Information Center for Medical Sciences at Tokyo Medical and Dental University, in collaboration with National Cancer Center for providing additional cases, former RIKEN Genome Science Center, and Advanced Industrial Science and Technology for collaborating with the development of multi-hierarchical omics database scheme and sharing each other database (12). Our iCOD, which integrates omics information and other comprehensive clinico-pathological information, is also one of the subprojects of the “Integrated Database Project” funded by MEXT(the Ministry of Education, Culture, Sports, Science and Technology of Japan) with the purpose to integrate the databases in Japan in the field of life science directed by DBCLS (Database Center for Life Science). We thank the Hitachi Software company for supporting to develop this database, Tokyo Medical and Dental University Hospital for clinical collaboration. We thank Dr. Dana Ichinotsubo for checking this manuscript. This work was sponsored by MEXT, under the direction of Information Center for Medical Sciences at Tokyo Medical and Dental University. This article has been published as part of BMC Genomics Volume 11 Supplement 4, 2010: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S4.
PY - 2010/12/2
Y1 - 2010/12/2
N2 - Background: Variety of information relating between genome and the pathological findings in disease will yield a wealth of clues to discover new function, the role of genes and pathways, and future medicine. In addition to molecular information such as gene expression and genome copy number, detailed clinical information is essential for such systematic omics analysis.Results: In order to provide a basic platform to realize a future medicine based on the integration of molecular and clinico-pathological information of disease, we have developed an integrated clinical omics database (iCOD) in which comprehensive disease information of the patients is collected, including not only molecular omics data such as CGH (Comparative Genomic Hybridization) and gene expression profiles but also comprehensive clinical information such as clinical manifestations, medical images (CT, X-ray, ultrasounds, etc), laboratory tests, drug histories, pathological findings and even life-style/environmental information. The iCOD is developed to combine the molecular and clinico-pathological information of the patients to provide the holistic understanding of the disease. Furthermore, we developed several kinds of integrated view maps of disease in the iCOD, which summarize the comprehensive patient data to provide the information for the interrelation between the molecular omics data and clinico-pathological findings as well as estimation for the disease pathways, such as three layer-linked disease map, disease pathway map, and pathome-genome map.Conclusions: With these utilities, our iCOD aims to contribute to provide the omics basis of the disease as well as to promote the pathway-directed disease view. The iCOD database is available online, containing 140 patient cases of hepatocellular carcinoma, with raw data of each case as supplemental data set to download. The iCOD and supplemental data can be accessed at. http://omics.tmd.ac.jp/icod_pub_eng.
AB - Background: Variety of information relating between genome and the pathological findings in disease will yield a wealth of clues to discover new function, the role of genes and pathways, and future medicine. In addition to molecular information such as gene expression and genome copy number, detailed clinical information is essential for such systematic omics analysis.Results: In order to provide a basic platform to realize a future medicine based on the integration of molecular and clinico-pathological information of disease, we have developed an integrated clinical omics database (iCOD) in which comprehensive disease information of the patients is collected, including not only molecular omics data such as CGH (Comparative Genomic Hybridization) and gene expression profiles but also comprehensive clinical information such as clinical manifestations, medical images (CT, X-ray, ultrasounds, etc), laboratory tests, drug histories, pathological findings and even life-style/environmental information. The iCOD is developed to combine the molecular and clinico-pathological information of the patients to provide the holistic understanding of the disease. Furthermore, we developed several kinds of integrated view maps of disease in the iCOD, which summarize the comprehensive patient data to provide the information for the interrelation between the molecular omics data and clinico-pathological findings as well as estimation for the disease pathways, such as three layer-linked disease map, disease pathway map, and pathome-genome map.Conclusions: With these utilities, our iCOD aims to contribute to provide the omics basis of the disease as well as to promote the pathway-directed disease view. The iCOD database is available online, containing 140 patient cases of hepatocellular carcinoma, with raw data of each case as supplemental data set to download. The iCOD and supplemental data can be accessed at. http://omics.tmd.ac.jp/icod_pub_eng.
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U2 - 10.1186/1471-2164-11-S4-S19
DO - 10.1186/1471-2164-11-S4-S19
M3 - Article
C2 - 21143802
AN - SCOPUS:78649801861
SN - 1471-2164
VL - 11
JO - BMC Genomics
JF - BMC Genomics
IS - SUPPL. 4
M1 - S19
ER -