Interoperation of Genome Databases and Tools
Interoperation of Genome Databases and Tools
批准号:
6946756
负责人:
KEI-HOI CHEUNG
金额:
$14.62万
依托单位:
依托单位国家:
美国
项目类别:
财政年份:
2001
资助国家:
美国
项目状态:
已结题
起止时间:
2001-09-01 至 2006-08-31
关键词:
Internetcomputer data analysiscomputer program /softwarecomputer system design /evaluationdata collection methodology /evaluationdata managementgene expressiongene frequencygenomehuman population geneticsinformation retrievalmicroarray technologymolecular biology information systemparallel processing
中文摘要
说明:(由申请人提供)本申请为NIH导师
英文摘要
DESCRIPTION: (provided by applicant) This application for an NIH Mentored
Quantitative Research Career Award requests support for Dr. Kei-Hoi Cheung as
he embarks on a faculty career focused on genome-related bioinformatics. This
application presents a research career development plan in the field of
bioinformatics, bridging computer science and biology. The plan includes two
partially overlapping phases: (1) a didactic phase that emphasizes training,
including coursework and laboratory work in the area of genetics and genomics
to complement Dr. Cheung's doctoral training in Computer Science and (ii) a
development phase that focuses on intense development of the proposed research.
These two phases will be closely supervised by a steering committee of senior
scientists, who will serve as mentors or advisors, in the area of biology and
bioinformatics.
The human genome project and the rapid advance in genomic technology (e.g.,
microarrays) have produced numerous local, national, and international genome
databases, many of which are Web-accessible. To answer questions that arise in
advanced genome research projects, researchers often need to analyze a large
amount of data that are collected from multiple related databases. Therefore,
it is important to explore (1) how to integrate the databases involved in a
flexible and useful fashion and (2) how to perform large-scale data analyses as
easily and rapidly as possible. To this end, we propose two complimentary
approaches.
1. The problem of data integration or interoperation is difficult because of
the syntactic and semantic heterogeneities involved. To address this problem,
we propose a metadata-driven approach using eXtensible Markup Language (XML),
which incorporates standardized vocabulary to map heterogeneous Web-accessible
data sets into a common format that facilitates interoperability.
2. To facilitate and speed up analysis of a large quantity of data, we will
also explore a range of computational techniques including the use of
Turbogenomics, which represents collaboration with the high performance
computing group within the Yale department of Computer Science. These
techniques allow (i) integration of heterogeneous software components (analysis
tools) to be done easily and (ii) exploitation of the power of parallel
computing.
We will design, develop, test, and evaluate the approach in the context of
current database projects including: 1) TRIPLES that manages data for
large-scale yeast genome analysis (with Prof Snyder) and 2) ALFRED that stores
gene frequency data on different human populations (with Prof Kidd). We have
identified a number of related external Web-accessible databases as well as
tools that users would like to access from TRIPLES and ALFRED in an integrated
fashion. We will initially develop and apply our approach to integrate these
databases and tools. We will extend our approach to other types of genomic data
such as microarray data, which both laboratories and others will soon be
generating in large quantities.
期刊论文(4)
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DOI:
10.1107/s160053680800425x
发表时间:
2008-02-15
期刊:
Acta crystallographica. Section E, Structure reports online
影响因子:
--
作者:
[Macmillan SN, Tanski JM, Waterman R]
通讯作者:
Waterman R
DOI:
10.1186/1471-2105-5-25
发表时间:
2004-03-10
期刊:
BMC bioinformatics
影响因子:
3
作者:
[de Knikker R, Guo Y, Li JL, Kwan AK, Yip KY, Cheung DW, Cheung KH]
通讯作者:
Cheung KH
DOI:
10.1142/9789812701626_0018
发表时间:
2005-12
期刊:
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
影响因子:
--
作者:
[Kevin Y. Yip;Peishen Qi;Martin H. Schultz;D. Cheung;K. Cheung]
通讯作者:
Kevin Y. Yip;Peishen Qi;Martin H. Schultz;D. Cheung;K. Cheung
DOI:
10.1016/j.jbi.2004.05.002
发表时间:
2004
期刊:
Journal of biomedical informatics.
影响因子:
--
作者:
[Yip,KevinY, Cheung,DavidW, Ng,MichaelK, Cheung,Kei-Hoi]
通讯作者:
Cheung,Kei-Hoi
Bioinformatics and Biostatistics Core
-
批准号:8935163
-
项目类别:
-
资助金额:$34.27万
-
财政年份:2004
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Interoperation of Genome Databases and Tools
-
批准号:6367736
-
项目类别:
-
资助金额:$14.77万
-
财政年份:2001
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Interoperation of Genome Databases and Tools
-
批准号:6526869
-
项目类别:
-
资助金额:$14.3万
-
财政年份:2001
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Interoperation of Genome Databases and Tools
-
批准号:6649804
-
项目类别:
-
资助金额:$14.2万
-
财政年份:2001
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Interoperation of Genome Databases and Tools
-
批准号:6795372
-
项目类别:
-
资助金额:$14.41万
-
财政年份:2001
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Bioinformatics and Biostatistics Core
-
批准号:9282576
-
项目类别:
-
资助金额:$42.66万
-
财政年份:--
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Bioinformatics and Biostatistics Core
-
批准号:9491776
-
项目类别:
-
资助金额:$42.47万
-
财政年份:--
-
负责人:KEI-HOI CHEUNG
-
依托单位:
Bioinformatics and Biostatistics Core
-
批准号:9096100
-
项目类别:
-
资助金额:$41.97万
-
财政年份:--
-
负责人:KEI-HOI CHEUNG
-
依托单位:
海外基金