《guidelines- florida state university》由会员分享，可在线阅读，更多相关《guidelines- florida state university（160页珍藏版）》请在金锄头文库上搜索。
1、THE FLORIDA STATE UNIVERSITY COLLEGE OF ARTS AND SCIENCES THE REPRESENTATION OF ASSOCIATION SEMANTICS WITH ANNOTATIONS IN A BIODIVERSITY INFORMATICS SYSTEM By DAVID A. GAITROS A Dissertation submitted to the Department of Computer Science In partial fulfillment of the Requirements for the degree of
2、Doctor of Philosophy Degree Awarded: Fall Semester, 2006 Copyright 2006 David A. Gaitros All Rights Reserved i The members of the Committee approve the Dissertation of David A. Gaitros defended on December 8th, 2006. _ Greg Riccardi Professor Directing Dissertation _ Fredrik Ronquist Outside Committ
3、ee Member _ Robert van Engelen Committee Member _ Ashok Srinivasan Committee Member Approved: _ David Whalley, Chair, Department of Computer Science _ Joseph Travis, Dean, College of Arts and Sciences The Office of Graduate Studies has verified and approved the above named committee members. ii This
4、 dissertation is dedicated to my wife Cynthia and our three children Heather, Adria, and Anthony. Without them, this work would have no meaning or purpose. iii ACKNOWLEDGEMENTS I am deeply indebted to my advisor and friend, Dr. Greg Riccardi for his guidance, support and patience all of these years.
5、 I would also like to thank Dr. Fredrik Ronquist and other members of the MorphBank research team for the opportunity to work with their research in the area of computational biology. Through the MorphBank grant we were able to accomplish something truly worthwhile. I would like to personally thank
6、the MorphBank development team of Wilfredo Blanco, Neelima Jammigumpula, Steve Winner, Karolina Maneva-Jakimoska, Debra Paul, Katja Seltmann, and Cynthia Gaitros for their hard work and dedication. There has never been a more productive team. I owe a special thanks to the late Dr. Richard W. Hamming
7、 for his encouragement to pursue this degree. Finally, I would like to thank my wife Cynthia for her love, encouragement, help, and support throughout the years. Without her, this degree would not have been possible. We always do our best work together. iv TABLE OF CONTENTS Page List of Tables vi Li
8、st of Figures vii Abstract xi 1. RESEARCH INTRODUCTION . 1 1.1 Problem Definition 3 1.2 Research Goals 5 1.3 Annotation of Metadata Relationships 7 1.4 Verification of Research Objective. 8 1.5 Research Accomplishments 8 1.6 Research Activities . 9 1.7 Research Challenges 9 1.8 Chapter Summary . 11
9、2. ANNOTATIONS IN LARGE SCIENTIFIC DATABASES. 13 2.1 Automatic Semantic Annotation. 13 2.2 Gene Sequence and DNA Annotation 15 2.3 Semantic Annotations in Image Collections. 18 2.4 Challenges of Annotations on the Web 21 2.5 Scientific Annotation Middleware (SAM) 22 2.6 Chapter Summary . 24 3. REQUI
10、REMENTS OF A WEB BASED IMAGE AND PHYLOGENETIC DATABASE SYSTEM. 25 3.1 The Motivation for MorphBank . 25 3.2 MorphBank Security Requirements . 28 3.3 Data Access Requirements 34 3.4 MorphBank Data Requirements 35 3.5 External Object Exposure 39 3.6 Rudimentary Query Requirements 42 3.7 Chapter Summar
11、y . 46 4. MORPHBANK CONCEPTUAL MODEL 48 4.1 Base Object Relationship 49 v 4.2 Image and View Relationship. 50 4.3 Specimen, Image, and Locality Relationship 51 4.4 Collection Relationships. 52 4.5 Related Objects 54 4.6 Annotation Conceptual Model . 55 4.7 Security Conceptual Model. 59 4.8 Life Scie
12、nce Identifiers. 62 4.9 Web Services 64 5. SEMANTIC ANNOTATIONS. 69 5.1 MorphBank Base Object Service 72 5.2 Biological Annotation Requirement. 73 5.3 Association Annotations. 75 5.4 Image Annotations 78 5.5 Annotation Integrity 82 5.6 Preliminary Results. 85 5.7 Conclusions. 86 6.ANNOTATION TRIALS.
13、 87 6.1 Annotation Trial Objectives 87 6.2 Trial Procedures 88 6.3 Trial Participants. 89 6.4 Initial Trial Feedback89 6.5 Image and Specimen Data Summary 90 6.6 Collection Data Summary. 92 6.7 Annotation Data Summary 93 6.8 Determination Annotation Data Summary . 97 6.9 Chapter Summary . 99 7. CONC
14、LUSION . 102 7.1 Research Results. 101 7.2 Research Objectives Achieved 102 7.3 Annotation of Metadata Relationships 102 7.4 Verification of Research. 103 7.5 Accomplishments of Research Challenges. 109 7.6 Future Work 110 vi APPENDICES 120 A MorphBank Contributors 120 BDarwin Core Standard 2.0. 122
15、 CVersion 2.5 Annotation Users Manual 128 D Example: MorphBank XML Image Annotation Schema148 BIOGRAPHICAL SKETCH 150 vii LIST OF TABLES Table 2-1: Thesaurus Reference 20 Table 3-1: Relationship Symbols. 42 Table 4-1: MorphBank Base Objects. 48 Table 4-2: Object-to-Object Relationships 55 Table 5-1:
16、 Animal Kingdom Taxonomic Rank Id. 83 Table 6-1: MorphBank Contributors . 88 viii LIST OF FIGURES Figure 1-1: Left Fore View, Female 3 Figure 2-1: Annotation of Gene Sequences 16 Figure 2-2: RDF Schema 18 Figure 2-3: “The Birthday” Painting of Chagall . 19 Figure 3-1: TreeBase Search Console . 27 Figure
