THESIS ONTOLOGY DEVELOPMENT FOR AGRICULTURAL RESEARCH KNOWLEDGE MANAGEMENT: A CASE STUDY FOR THAI RICE AREE THUNKIJJANUKIJ A Thesis Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy (Tropical Agriculture) Graduate School, Kasetsart University 2009 This work is licensed under a Creative Commons Attribution- Noncommercial-No Derivative Works 3.0 Unported License http://creativecommons.org/licenses/by-nc-nd/3.0/" ACKNOWLEDGEMENTS When I first started on this thesis I anticipated only the benefits of the results: the Rice Production Ontology may help to manage agricultural research knowledge in Thailand, and hopefully it will be a prototype for other ontology development in the future. At the beginning, I did not know how difficult it was, as this is a pioneer work in plant production domain, to conceptualize the research framework and to synthesize the lessons learned. Therefore, it is very obvious that this study would have never been completed without support and encouragement from the people involved. First, I would like to thank Johannes Keizer, Information Systems Officer at the United Nations Food and Agriculture Organization (FAO), who helped me conceive the idea for this study since the 1st Agricultural Ontology Service Workshop (AOS Workshop) in Rome from the year 2000 and facilitated all necessary support during my research process. Thank Dr. Dargobert Soergel from College of Information Studies, Maryland University who advised and gave me idea for conceptualizing the ontology. I am very grateful to all of my three advisors, Professor Dr. Supamard Panichsakpatana, Associate Professor Dr. Asanee Kawtrakul and Associate Professor Uamporn Veesommai. In addition to valuable advices about my research, they also provided encouragement and supports when I needed. The technical part and data conversion of this research were formidable. So, I am exceptionally thankful to those who gave me supports, namely Thiranan Damrongson, Dussadee Thamvijit, and Daoyos Noikongka. My special thanks also go to the experts from Faculty of Agriculture, Kasetsart University and researchers in Rice Department, Ministry of Agriculture and Cooperatives for their information provision. I am thankful to Director of Kasetsart University Research and Development Institute, Professor Dr. Rangsit Suwanmonkha and Dr. Apichart Pongsrihadulchai, the former Director General of Rice Department for allowing the valuable interview. I would like to thank Sudjai Lochaloen, Ratchanee Pattaravayo, Thararat Maneenuam, Suraporn Khongphon, and Chanjira Ayawong for their support in data collection. My special thanks go to Chanattika Khamdee for her exceptional performance as my coordinating assistant. Other form of support was to make my thesis readable. Margherita Sini, Michael Victor, and Suriyon Thunkijjanukij played a crucial part in this area. I thank all of them from my heart. I would like to express gratitude also to those experts who had to answer my questionnaires twice. I only hoped that my questionnaires did not make them too stressful. A number of my colleagues and friends also provided me unforgettable support and encouragement during my rough time. They are Phanpaporn Wittayadecha, Napalai Thongpun, Napa Chiewchuwong, Areerat Thongbai and all of the Thai AGRIS staff. In addition, I would like to express my special gratitude to the person who has been my admirable technical supporter and advisor, Ms. Margherita Sini. She is an Information Management Specialist at FAO. Her invaluable supports came in many forms and her willingness to help was beyond the call of duty. I do deeply appreciate that. Last but not least are my husband and my kids. I love them for their support, encouragement and tolerance for my lack of participation in family matter during the chaotic period associated to this work. They regard my success as their success, and we are happy to see that we completed this valuable study together. Finally, I would like to say that although many people have contributed significantly to this research, any deficiency or inappropriateness of this thesis is exclusively due to the author, and I will be appreciate those who provide constructive feedback. Aree Thunkijjanukij February 2009 I authorized FAO to store, diseminate and preserve my thesis from the FAO Document Repository i TABLE OF CONTENTS Page TABLE OF CONTENTS i LIST OF TABLES ii LIST OF FIGURES v INTRODUCTION 1 OBJECTIVES 3 LITERATURE REVIEW 4 MATERIALS AND METHODS 67 Materials 68 Methods 70 RESULTS AND DISCUSSION 101 Results 101 Discussion 188 CONCLUSION AND RECOMMENDATION 199 LITERATURE CITED 201 APPENDICES 208 Appendix A Delphi participant list 209 Appendix B Questionnaire 211 Appendix C CS WB User Manual 224 Appendix D Guidelines for plant production ontology construction 232 Appendix E Rice production and agricultural knowledge resources 242 CIRRICULUM VITAE 249 ii LIST OF TABLES Table Page 1 Environmental and biological factors affecting crop production management on a field scale 34 2 AGRIS/CARIS Subject Categorization Scheme related with plant production 38 3 Term level relationship 46 4 Concept level relationship 48 5 Rice production related factors 75 6 Rice taxonomy summary 76 7 Rice cultivar summary defined by composition, cultivation ecology and photoperiod sensitivity 76 8 Rice cultivar summary defined by diseases resistant, disease susceptible, pest resistant and pest susceptible properties 77 9 Weed taxonomy summary 78 10 Weed characteristic properties summary 79 11 Weed control method and chemical control substance summary 79 12 Pathogen taxonomy summary 80 13 Diseases name and pathogen name summary 80 14 Diseases control, epidemiology and ecological factor defined by disease name summary 81 15 Agricultural substance type defined by type of pesticide, fertilizer and plant growth substance summary 82 16 Datasheet for formalizing concept lexicalization 89 17 Datasheet for formalizing concept and hierarchical relationship 90 18 Datasheet for formalizing concept and associative relationship 90 19 Query of the competency questions define by query approach 94 20 Class concept of rice production ontology 102 21 Number of rice production ontology relationships 103 22 Number of rice production ontology concepts and terms 104 iii LIST OF TABLES (Continued) Table Page 23 Description of rice production ontology relationships 105 24 Jasmine rice terms and synonym 116 25 Plant production subject categories 117 26 Example of concept and relation “hasBiologicalControlAgent” 119 27 Example of biological control agent terms and synonyms 119 28 Example of concepts of relation “hasDisease” 122 29 Example of disease terms and synonyms 122 30 Example of pathogen terms and synonyms 122 31 Chemical fertilizers concept and subclass concepts 124 32 Chemical fertilizers terms and synonyms 125 33 Organic fertilizers concept and child concepts 126 34 Organic fertilizers terms and synonym 126 35 Example of concept and relation “hasPest” 132 36 Example of pest concept with type “field pest” 132 37 Example of field pest terms and synonym 132 38 Example of pest concept with type “stored product pest” 133 39 Example of stored product pest terms and synonym 133 40 Example of pest control concept and child concept 134 41 Example of pest control terms and synonym 134 42 Example of control method concept and subclass concept 135 43 Example of control method terms and synonym 135 44 Example of pesticide concepts and subclasses 136 45 Example of pesticide terms and synonym 136 46 Query result from the conventional search 137 47 Query result search by using ontology 139 48 Query results compared between conventional search approach and ontology-based search approach 141 49 Comparison of results in the first round and second round questionnaire 144 iv LIST OF TABLES (Continued) Table Page 50 Degree of agreement on each criteria defined by number of experts 154 51 Rice production ontology concept categories 162 52 Relations and inverse relations of the equivalence relationships 170 53 Pattern and example of equivalence relationships 171 54 Relation and inverse relation of hierarchical relationships 172 55 Pattern and example of hierarchical relationships 172 56 Relation and inverse relation of associative relationships 173 57 Pattern and example of associative relationship 175 v LIST OF FIGURES Figure Page 1 Whole plant model and flow of energy, water and nutrient 31 2 Meaning Triangle of Communication 39 3 Human and Machine Communication 40 4 Pilot ontology of semantic relationships based on the UMLS Semantic Network 53 5 Conceptual Framework of Rice Production Ontology Development 68 6 Ontology structure model 83 7 Identify concept by top-down and bottom-up approach 85 8 Concept and relationship of rice and pest insect 86 9 Conceptual model of rice production ontology 102 10 Thai Rice Production Ontology in the full view display 108 11 Thai Rice Production Ontology concept hierarchy displayed with the Thai Agricultural Ontology Visualization Tool in CS WB 109 12 Section of the Thai Rice Production Ontology related to concept[rice] 110 13 Description table of term relationships for the selected concept in the Thai Rice Production Ontology 111 14 Thai Rice Production Ontology concept with associative relationships 113 15 Thai Rice Production Ontology Visualization with search function and search results 112 16 Conventional search mechanism 113 17 Ontology search mechanism 114 18 Conventional search result as a simple list 114 19 Ontology search result defined by disease