An object-oriented framework to organize genomic data

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dc.contributor.advisor Adelson , David en_US
dc.contributor.committeeMember Elsik , Christine en_US
dc.creator Wei , Ning en_US 2010 -01 -15T00 :12 :39Z 2014 -02 -19T19 :32 :19Z 2010 -01 -15T00 :12 :39Z 2014 -02 -19T19 :32 :19Z 2008 -05 en_US 2009 -05 -15 en_US
dc.identifier.uri http : / /hdl .handle .net /1969 .1 /ETD -TAMU -2690
dc.description.abstract Bioinformatics resources should provide simple and flexible support for genomics research . A huge amount of gene mapping data , micro -array expression data , expressed sequence tags (EST ) , BAC sequence data and genome sequence data are already , or will soon be available for a number of livestock species . These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data . In term of exploring complex -intertwined genomic data , the way to organize them will be addressed in this study . Therefore , we investigated two issues in this study : one is an independent informatics framework including both back end and front end ; another is how an informatics framework simplifies the user interface to explore data . We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data , and allow for query results to be presented via a user friendly web interface . A genome object -oriented framework (GOOF ) was proposed with object -oriented Java technology and is independent of any database system . This framework seamlessly links the database system and web presentation components . The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data , meaning that users avoid constructing queries within the interface layer . Moreover , the module -based interface provided by GOOF could allow different users to access data in different interfaces and ways . In another words , GOOF not only gives a whole solution to informatics infrastructure , but also simplifies the organization of data modeling and presentation . In order to be a fast development solution , GOOF provides an automatic code engine by using meta -programming facilities in Java , which could allow users to generate a large amount of routine program codes . Moreover , the pre -built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema . In summary , we studied the way to model genomic data into an informatics framework , a one -stop approach , to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data . en_US
dc.format.medium electronic en_US
dc.format.mimetype application /pdf en_US
dc.language.iso en _US en_US
dc.subject Bioinformatics en_US
dc.title An object -oriented framework to organize genomic data en_US
dc.type Book en
dc.type.genre Electronic Dissertation en_US
dc.type.material text en_US
dc.format.digitalOrigin born digital en_US


An object-oriented framework to organize genomic data. Available electronically from http : / /hdl .handle .net /1969 .1 /ETD -TAMU -2690 .

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