Data Integration Through Protein Ontology

Data Integration Through Protein Ontology

Amandeep S. Sidhu (University of Technology Sydney, Australia), Tharam S. Dillon (University of Technology Sydney, Australia) and Elizabeth Chang (Curtin University of Technology, Perth)
DOI: 10.4018/978-1-59904-618-1.ch006
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Abstract

Traditional approaches to integrate protein data generally involved keyword searches, which immediately excludes unannotated or poorly annotated data. An alternative protein annotation approach is to rely on sequence identity, or structural similarity, or functional identification. Some proteins have high degree of sequence identity, or structural similarity, or similarity in functions that are unique to members of that family alone. Consequently, this approach can’t be generalized to integrate the protein data. Clearly, these traditional approaches have limitations in capturing and integrating data for Protein Annotation. For these reasons, we have adopted an alternative method that does not rely on keywords or similarity metrics, but instead uses ontology. In this chapter we discuss conceptual framework of Protein Ontology that has a hierarchical classification of concepts represented as classes, from general to specific; a list of attributes related to each concept, for each class; a set of relations between classes to link concepts in ontology in more complicated ways then implied by the hierarchy, to promote reuse of concepts in the ontology; and a set of algebraic operators for querying protein ontology instances.

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Table of Contents
Acknowledgment
Hector Oscar Nigro, Sandra Elizabeth Gonzalez Cisaro, Daniel Hugo Xodo
Chapter 1
Sofia Stamou, Alexandros Ntoulas, Dimitris Christodoulakis
In this paper we study how we can organize the continuously proliferating Web content into topical cate-gories, also known as Web directories. In... Sample PDF
TODE: An Ontology-Based Model for the Dynamic Population of Web Directories
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Chapter 2
Xuan Zhou, James Geller
This chapter introduces Raising as an operation which is used as a pre-processing step for Data Mining. In the Web Marketing Project, people’s... Sample PDF
Raising, to Enhance Rule Mining in Web Marketing with the Use of an Ontology
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Chapter 3
Brigitte Trousse, Marie-Aude Aufaure, Bénédicte Le Grand, Yves Lechevallier, Florent Masseglia
This chapter proposes an original approach for ontology management in the context of Web-based information systems. Our approach relies on the usage... Sample PDF
Web Usage Mining for Ontology Management
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Chapter 4
Minh Hai Pham, Delphine Bernhard, Gayo Diallo, Radja Messai, Michel Simonet
Clustering similar documents is a difficult task for text data mining. Difficulties stem especially from the way documents are translated into... Sample PDF
SOM-Based Clustering of Multilingual Documents Using an Ontology
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Chapter 5
Ana Isabel Canhoto
The use of automated systems to collect, process and analyse vast amounts of data is now integral to the operations of many corporations and... Sample PDF
Ontology-Based Interpretation and Validation of Mined Knowledge: Normative and Cognitive Factors in Data Mining
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Chapter 6
Amandeep S. Sidhu, Tharam S. Dillon, Elizabeth Chang
Traditional approaches to integrate protein data generally involved keyword searches, which immediately excludes unannotated or poorly annotated... Sample PDF
Data Integration Through Protein Ontology
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Chapter 7
Josiane Mothe, Nathalie Hernandez
This chapter introduces a method re-using a thesaurus built for a given domain, in order to create new resources of a higher semantic level in the... Sample PDF
TtoO: Mining a Thesaurus and Texts to Build and Update a Domain Ontology
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Chapter 8
Stanley Loh, Daniel Lichtnow, Thyago Borges, Gustavo Piltcher
This chapter investigates different aspects in the construction of a domain ontology to a content-based recommender system. The recommender systems... Sample PDF
Evaluating the Construction of Domain Ontologies for Recommender Systems Based on Texts
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Chapter 9
Vania Bogorny, Paulo Martins Engel, Luis Otavio Alavares
This chapter introduces the problem of mining frequent geographic patterns and spatial association rules from geographic databases. In the... Sample PDF
Enhancing the Process of Knowledge Discovery in Geographic Databases Using Geo-Ontologies
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Chapter 10
Peter Brezany, Ivan Janciak, A Min Tjoa
This chapter introduces an ontology-based framework for automated construction of complex interactive data mining workflows as a means of improving... Sample PDF
Ontology-Based Construction of Grid Data Mining Workflows
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Chapter 11
Shastri L. Nimmagadda, Heinz Dreher
Several issues of database organization of petroleum industries have been highlighted. Complex geo-spatial heterogeneous data structures complicate... Sample PDF
Ontology-Based Data Warehousing and Mining Approaches in Petroleum Industries
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Chapter 12
Evangelos Kotsifakos, Gerasimos Marketos, Yannis Theodoridis
Pattern Base Management Systems (PBMS) have been introduced as an effective way to manage the high volume of patterns available nowadays. PBMS... Sample PDF
A Framework for Integrating Ontologies and Pattern-Bases
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About the Contributors