NDLI: Generating GO Slim Using Relational Database Management Systems to Support Proteomics Analysis

Content Provider	IEEE Xplore Digital Library
Author	Onsongo, G. Hongwei Xie Griffin, T.J. Carlis, J.
Copyright Year	2008
Description	Author affiliation: Dept of Comput. Sci. & Eng., Univ. of Minnesota, Minneapolis, MN (Onsongo, G.)
Abstract	The Gene Ontology Consortium built the Gene Ontology database (GO) to address the need for a common standard in naming genes and gene products. Using different names for the same concepts and different concepts with the same name makes it effectively impossible for humans and computers alike to analyze biological processes across different organisms. The consortium addresses this need by defining terms for categorizing genes and gene products. A convention in GO is that each gene or gene product is annotated to the most specific GO term in the GO database. It is, however, also useful for researchers to be able to group genesor gene products into broad biological categories that give a higher-level view of their function when analyzing results of an experiment. A GO Slim is a subset of the GO ontology that provides such a higher-level view of functions. Existing GO Slim generation tools have two important limitations: programming language dependence, and an inability to dynamically generate a GO Slim while analyzing. We have extended the relational database engine to dynamically generate a GO Slim overcoming this limitations. Using this extension, we have developed a tool (Dynamic GOSlim) that dynamically generates a GO Slim and uses the generated GO Slim to categorize genes or gene products. This tool is being used in an ongoing proteomics project aimed at identifying possible oral cancer biomarkers in saliva.
Starting Page	215
Ending Page	217
File Size	595400
Page Count	3
File Format	PDF
ISBN	9780769531656
ISSN	10637125
DOI	10.1109/CBMS.2008.77
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2008-06-17
Publisher Place	Finland
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Relational databases Proteomics Ontologies Humans Biology computing Biological processes Organisms Computer languages Engines Cancer proteomics Gene Ontology GO Slim relational databases
Content Type	Text
Resource Type	Article
Subject	Radiology, Nuclear Medicine and Imaging Computer Science Applications

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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