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Computational analysis of metabolism...

Yeh, Iwei.

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Computational analysis of metabolism for the malaria parasite.

Record Type:	Electronic resources : Monograph/item
Title/Author:	Computational analysis of metabolism for the malaria parasite./
Author:	Yeh, Iwei.
Description:	145 p.
Notes:	Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2301.
Contained By:	Dissertation Abstracts International67-05B.
Subject:	Biology, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3219417
ISBN:	9780542708596

Computational analysis of metabolism for the malaria parasite.
Yeh, Iwei.

Computational analysis of metabolism for the malaria parasite. - 145 p.

Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2301.

Thesis (Ph.D.)--Stanford University, 2006.

Biological data are accumulating rapidly with many high-throughput experiments being developed and performed. The volume and diversity of data requires computation for integration and analysis. My dissertation advances the argument that improvements in biological ontologies support the development of algorithms that execute expert-type reasoning systematically over large-scale data sets.

ISBN: 9780542708596Subjects--Topical Terms:

1018625
Biology, General.

Computational analysis of metabolism for the malaria parasite.
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100 1 $a Yeh, Iwei. $3 1917235
245 1 0 $a Computational analysis of metabolism for the malaria parasite.
300 $a 145 p.
500 $a Source: Dissertation Abstracts International, Volume: 67-05, Section: B, page: 2301.
500 $a Adviser: Russ B. Altman.
502 $a Thesis (Ph.D.)--Stanford University, 2006.
520 $a Biological data are accumulating rapidly with many high-throughput experiments being developed and performed. The volume and diversity of data requires computation for integration and analysis. My dissertation advances the argument that improvements in biological ontologies support the development of algorithms that execute expert-type reasoning systematically over large-scale data sets.
520 $a Despite the advances made in biological ontologies, there is still room for improvement. Gene Ontology is a hierarchical controlled terminology widely used to annotate genes by molecular function, biological process, and cellular component terms. I evaluate the strengths and weaknesses of Gene Ontology using a knowledge base management system, Protege. Although GO contains many concepts, its is-a and part-of hierarchies are incomplete and inconsistent. I demonstrate the usefulness of formal ontology development tools to consistency checking and logical analysis of the knowledge base. Based on this evaluation I suggest concrete improvements to GO.
520 $a The Pathway Tools ontology represents many aspects of small-molecule metabolism in a principled manner. I created PlasmoCyc, the first computational reconstruction of malaria metabolism using the Pathway Tools software. The relationships between well-organized concepts in the ontology supported the development of a novel chokepoint analysis to screen for potential drug targets. Chokepoints are greater than two-fold enriched for drug targets from the literature compared to non-chokepoints. This work demonstrates the contribution of complex ontologies analysis of large biological data sets.
520 $a Although metabolism ontologies have undergone extensive development, there are other areas of biology where ontologies could use improvement. Knowledge of cell structure informs many types of data analysis. I developed the cellular architecture ontology (CAO) which represents relationships between membranes and spaces within the cell. This ontology supports the development of rule-based analyses of protein localizations which integrate molecular functions and protein-protein interactions to refine and predict localizations. These rule-based analyses are forms of "expert-level" reasoning and the resulting refinements and predictions are validated by expert and literature review.
590 $a School code: 0212.
650 4 $a Biology, General. $3 1018625
650 4 $a Health Sciences, Pharmacology. $3 1017717
650 4 $a Health Sciences, Pathology. $3 1017854
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650 4 $a Computer Science. $3 626642
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773 0 $t Dissertation Abstracts International $g 67-05B.
790 1 0 $a Altman, Russ B., $e advisor
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791 $a Ph.D.
792 $a 2006
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3219417