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Molecular-biological annotation data is continuously being collected, curated and made accessible in numerous public data sources. Integration of this data is a major challenge in bioinformatics. We present the GenMapper system that physically integrates heterogeneous annotation data in a flexible way and supports large-scale analysis on the integrated data. It uses a generic data model to uniformly represent different kinds of annotations originating from different data sources. Existing associations between objects, which represent valuable biological knowledge, are explicitly utilized to drive data integration and combine annotation knowledge from different sources. To serve specific analysis needs, powerful operators are provided to derive tailored annotation views from the generic data representation. GenMapper is operational and has been successfully used for large-scale functional profiling of genes.

This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent.

This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent.

Philosophiae Doctor - PhD / This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and browsing of functional genomics data for researchers working in the field of Trypanosomiasis on the African continent. / South Africa

This paper investigates students’ attitudes towards using gestures and speech-to- text (GaST) to take notes while watching recorded lectures. A literature review regarding video based learning, an expert interview, and a background survey regarding students’ note taking habits led to the creation of the prototype AnnotEasy, a tool that allows students to use GaST to take notes. AnnotEasy was tested in three iterations against 18 students, and was updated after each iteration.  The students watched a five minute long lecture and took notes by using AnnotEasy. The participants’ perceived ease of use (PEU) and perceived usefulness (PU) was evaluated based on the TAM. Their general attitudes were evaluated in semi structured interviews.  The result showed that the students had a high PEU and PU of AnnotEasy. They were mainly positive towards taking notes by using GaST. Further, the result suggests that AnnotEasy could facilitate the process of structuring a lecture’s content. Lastly, even though students had positive attitudes towards using speech to create notes, observations showed that this was problematic when the users attempted to create longer notes. This indicates that speech could be more beneficial for taking shorter notes.

L'analyse du contenu devient une nécessité pour l'accès et l'utilisation de l'information en particulier dans le domaine de la didactique des disciplines. Nous proposons un système SRIDOP d'annotations sémantiques et d'indexation des documents pédagogiques à partir des annotations, en se basant sur la méthode d'Exploration Contextuelle qui, à un identificateur linguistique d'un concept, associe une annotation d'un segment en tenant compte d'indices contextuels gérés par des règles. SRIDOP est composé de quatre modules consécutifs : (1)Segmentation automatique des documents en paragraphes et phrases ; (2) annotation selon différents points de vue de fouille (exemple: identification de définitions, exemples, exercices, etc.) en se basant sur une ontologie linguistique de concepts associés à un point de vue de fouille (carte sémantique) et de ressources linguistiques (indicateurs de concepts, indices linguistiques et règles d'Exploration Contextuelle) ; (3) extraction d'objets pédagogiques ; (4) constitution de fiches pédagogiques exploitables par les utilisateurs. SRIDOP est évalué et comparé à d'autres systèmes. / Content analysis is a need for access and use of information especially in the field of didactics. We propose a system SRIDOP of semantic annotations and indexing of learning objects from these annotations, based on the Contextual Exploration method, that associate annotation of a segment to a linguistic identifier of a concept, taking into account contextual clues managed by rules. SRIDOP is composed of four consecutive modules: (1) Automatic segmentation of documents into paragraphs and sentences; (2) annotation from different points of view of search (eg identification of definitions, examples, exercises, etc..) based on a linguistic ontology of concepts associated with a point of view of search (semantic map) and linguistic resources (indicators of concepts, linguistic clues and contextual exploration rules); (3) extraction of learning objects, (4) establishment of learning sheets exploitable by users. SRIDOP is evaluated and compared to other systems.

隨著數位相機、智慧型手機等影像記錄產品的普及，人們可以隨時隨地按下快門，使得個人相片的數量不斷的增長。倘若照片中缺少了註釋，進行搜尋檢索大量的個人照片是困難的。雖然如此，人們卻會因為繁瑣累人的照片註釋工作而缺乏意願。 本研究藉由Kuo所發展出的PARIS (Personal Archiving and Retrieving Image System)作為來源系統架構，其系統解決了大部分個人數位影像語義標註的困難，也利用半自動註記方法減少使用者註釋負擔。但由於過去缺乏行動載具，PARIS並未開發一個現代化的行動註釋系統，來協助一般使用者進行個人影像註釋。 為了解決此問題，本研究利用使用性工程進行系統的建構，以設計及開發出一套現代化的行動影像註釋系統iPARIS (Integrated Personal Archiving and Retrieving Image System)。iPARIS擴展了PARIS設計出符合行動載具的後設資料結構與本體，包含將PARIS所定義的DDDC後設資料標準擴充為得以群眾註記之社群媒體地理標籤的iDDDC (Integrated Dozen Dimensional Digital Content)，以及在既有的STO (Spatial and Temporal Based Ontology)的空間架構中加入更具彈性的地理標籤關聯方法GRO (Geotag Related Ontology)。iPARIS並利用工作流程設計、介面線稿設計、視覺設計、系統實作、使用者參與設計等步驟來設計及開發系統，再以迭代設計方法不斷地改善系統的使用者介面及使用者體驗。iPARIS在建置完成後利用參與啟發式評估量表、手勢次數、操作時間、操作路徑、錯誤次數進行使用性測試，而其測試結果也達預期的使用性目標。更進一步，透過分析使用者操作系統的實際行為來找出系統存在的使用性問題，並提出未來系統的改進方式。 透過完整的規劃與適切的設計系統介面，讓使用者在拍照、註釋、組織及管理照片都可以在行動應用程式上完成，並使此系統能滿足具有效率、具學習性、具記憶性、低錯誤率及高滿意度等Nielsen所提出的使用性標準，以降低個人影像註釋時的負擔，並增加使用者註釋個人照片的意願，以應付日益增長地個人數位影像資料的管理需求。 / With the widespread use of photograph recording products, such as digital camera and smartphone, people take photographs easily so that the number of personal photographs increases unceasingly. If photographs are lacking of annotation, searching and retrieving the large number of personal photographs become difficult. However, people are usually reluctant to the cumbersome and exhausted annotation work. In 2004, Kuo et al. developed PARIS (Personal Archiving and Retrieving Image System) to solve these problems. Based on MPEG-7, PARIS resolved most difficulties of personal digital image semantic annotation and lightened users’ annotation burdens by semi-automatic annotation methods. However, because of the lack of mobile device at that time, PARIS did not develop a modern mobile annotation system to help ordinary people annotate personal photographs. Therefore, this thesis builds a system with usability engineering as well as designs and develops a modern mobile image annotation system iPARIS (Integrated Personal Archiving and Retrieving Image System). iPARIS expands PARIS architecture to add the support for mobile. It expands PARIS DDDC metadata standard to iDDDC (Integrated Dozen Dimensional Digital Content) which is a crowdsourcing annotation enabled by third party social networking services, and provides STO’s spatial ontology a more flexible geo-information description methodology GRO (Geotag Related Ontology). iPARIS also takes the steps of workflow design, wireframe design, visual design, system implementation, participatory design to build the system; moreover, it keeps improving the user interface and user experience by iterative design. After implementing iPARIS, we conduct usability testing including participatory heuristic evaluation, gesture times, operation time, gesture path, error times, and interview. The test results reach the expected usability goals. Furthermore, the thesis finds some usability problems by analyzing users’ behaviors when they are using the application and brings future improvement for the system. By integral planning and appropriate interface design, this system lets user take, annotate, organize, and mange personal photos in a mobile application. We hope that iPARIS can meet the usability index to lighten the burdens of personal photograph annotation, arousing users’ desire to annotate personal photographs, and meet the growing needs for the management of personal digital photograph information.

在傳統的人文研究中，人文學者大多以如古籍珍善本、歷史文獻等紙本出版形式之文本為主要研究文本型式，但是隨著資訊社會的來臨，許多研究機構陸續將這些紙本資料進行數位化並建置數位典藏資料庫，對人文研究環境與知識取得管道帶來巨大的改變，基於數位閱讀之文本研究型式也成為必然的發展趨勢。 因此，本研究發展支援數位人文研究之「文本自動標註系統」，藉由Linked Data的概念匯集來自不同資料庫的資源，並加以整合後，替文本進行自動註解，讓使用者在解讀文本時能夠即時參照其他資料庫的資源，並提供友善的具文本標註之閱讀介面，以利於人文學者透過閱讀進行資料的解讀。本研究以實驗研究法比較本研究所發展之「文本自動標註系統」與「MARKUS文本半自動標註系統」在支援人文學者進行文本資料解讀之閱讀成效與科技接受度是否具有顯著差異，並輔以半結構式深度訪談了解人文學者對於本研究發展之「文本自動標註系統」的看法及感受，也進一步分析「文本自動標註系統」閱讀成效、科技接受度及使用者行為歷程之間是否具有關聯性。 實驗結果發現，採用本研究發展之文本自動標註系統的閱讀成效高於MARKUS文本半自動標註系統，但未達顯著差異；而科技接受度分析結果則顯示文本自動標註系統之科技接受度顯著優於MARKUS文本半自動標註系統。另外，從訪談結果歸納得知，文本自動標註系統閱讀介面簡潔明瞭，比MARKUS文本半自動標註系統更適合閱讀，而閱讀介面是否易於使用與是否有用，是影響人文學者能否接受採用系統輔助數位人文研究的重要因素。此外，在兩個系統類似功能比較分析後也發現，文本自動標註系統在查詢詞彙功能、連結到來源網站功能及新增標註功能都比MARKUS文本半自動標註系統更為直覺易用。另外人文學者普遍認為斷句功能比自動斷詞功能更重要，鏈結來源資料庫則以萌典最有幫助。最後，採用文本自動標註系統之閱讀成效與使用者行為歷程之間無顯著關聯性。 / In traditional humanities research, most humanities scholars studied text-type paper-based publishing texts, such as rare ancient books and historical literature. However, many research institutes, in the information society, gradually digitalized such paper-based data and established digital archives database to result in great changes in humanities research environment and knowledge acquisition channels. The research pattern with digital reading based texts became the essential development trend. For this reason, an “automatic text annotation system” for supporting digital humanities research is developed in this study. Resources from distinct database are gathered through Linked Data and integrated for the automatic annotation of texts. It allows users immediately referring to resources from other database when interpreting texts and provides friendly reading interface with text annotation for humanities scholars interpreting data through reading. With experimental research, the “automatic text annotation system” developed in this study is compared with “MARKUS semi-automatic text annotation system” for supporting humanities scholars interpreting text data to discussed the difference in reading achievement and technology acceptance. Semi-structured in-depth interviews are also proceeded to understand humanities scholars’ opinions and perception about the “automatic text annotation system” developed in this study as well as to analyze the correlations among reading achievement, technology acceptance, and user behavior course of the “automatic text annotation system”. The experimental findings show that the reading achievement with the automatic text annotation system developed in this study is higher than that with MARKUS semi-automatic text annotation system, but not achieving the significance. The technology acceptance analysis reveals remarkably better technology acceptance of the automatic text annotation system than MARKUS semi-automatic text annotation system. According to the interviews, the reading interface of the automatic text annotation system is simple and clear that it is more suitable for reading than MARKUS semi-automatic text annotation system. The ease of use and usefulness of reading interface is a key factor in humanities scholars accepting the system for the digital humanities research. In regard to the comparison of similar functions between two systems, the functions of vocabulary enquiry, linking to source web sites, and annotation appending of the automatic text annotation system are more intuitive and easy to use than those of MARKUS semi-automatic text annotation system. What is more, humanities scholars emphasize more on the sentence segmentation function than the automatic word segmentation function, and the linked source database, Moedict, appears the best assistance. Finally, there is no significant correlation between reading achievement and user behavior course with the automatic text annotation system.

近年來隨著網路學習的發展，能夠透過網路輔以學習者進行線上合作閱讀學習的合作數位閱讀標註系統興起，並已發展出多媒體的標註模式，不但可以由學生自己針對閱讀文本進行合作閱讀標註，更可以在閱讀文本上進行標註互動討論，具有提昇閱讀理解成效的效益。而數學應用問題的閱讀理解，影響學習者對於數學應用問題的解題甚巨，但是長久以來並無好的提升數學應用問題閱讀理解策略。本研究比較採用合作數位閱讀標註系統及使用傳統同儕面對面合作學習數學應用問題的實驗組與控制組學習者，在解決數學應用問題的學習成效及學習動機上是否具有顯著差異。此外，亦探討場地獨立/場地依賴型不同認知風格及高/低不同學習能力的學習者，採用上述兩種不同學習方法進行數學應用問題學習之學習成效與學習動機是否具有顯著的差異，最後探討實驗學習者使用此合作式數位閱讀標註系統輔以數學應用問題學習之學習滿意度。 研究結果發現：（1）採用合作式數位閱讀標註系統輔以進行數學一元一次方程式應用問題學習，在學習成效與學習動機上均顯著優於傳統同儕面對面合作學習數學一元一次方程式應用問題；（2）採用合作式數位閱讀標註系統以及傳統同儕面對面合作學習輔以進行數學一元一次方程式應用問題學習的實驗組與控制組學習者，在回歸到一般學習後，實驗組在學習成效上仍顯著優於控制組學習者；（3）無論是場地獨立或場地相依認知風格學習者，採用合作式數位閱讀標註系統輔以進行數學一元一次方程式應用問題的標註學習後，在學習動機上均顯著優於採用傳統同儕面對面合作學習輔以進行數學一元一次方程式應用問題學習的控制組學習者；（4）無論是高低不同能力學習者，採用合作式數位閱讀標註系統輔以進行數學一元一次方程式應用問題的標註學習後，在學習動機上均顯著優於採用傳統同儕面對面合作學習輔以進行數學一元一次方程式應用問題學習的控制組學習者；（5）實驗組場地獨立學習者在使用合作式數位閱讀標註系統後的學習動機優於場地相依學習者；（6）實驗組高學習能力學習者在使用合作式數位閱讀標註系統後的學習動機優於低能力學習者。 綜合以上，本研究所提出採用合作數位閱讀標註系統輔以數學應用問題閱讀理解的學習模式，具有提升學習動機與閱讀理解成效的效益，可推廣至解決更複雜數學單元之閱讀理解，甚至發展為創新數學教學之翻轉教學模式。 / Along with the development of web-based learning in past years, cooperative digital reading annotation systems, which could assist learners in online cooperative reading learning through the Internet, are emerged. Besides, multimedia annotation models are also developed for students, aiming at the reading texts, proceeding cooperative reading annotation as well as annotation interactive discussion on the reading texts. It presents the benefit to enhance the reading comprehension efficiency. The reading comprehension of mathematical application problems would largely affect learners’ mathematical application problem solving. However, there has not been a good strategy to enhance the reading comprehension of mathematical application problems. In comparison with the experimental group and the control group, which respectively apply the cooperative digital reading annotation system and traditional peers’ face-to-face cooperative learning to solve mathematical application problems, the differences in the learning outcome and learning motivation are discussed in this study. Furthermore, learners with field independent/field dependent cognitive styles and high/low learning abilities are preceded above two different learning approaches for learning mathematical application problems to discuss the differences in the learning outcome and learning motivation. Finally, learners learning mathematical application problems with the cooperative digital reading annotation system in the experiment are discussed the learning satisfaction. The research findings are summarized as below. (1) Learners applying the cooperative digital reading annotation system to learn the mathematical application problems in linear equation with one unknown present better learning outcome and learning motivation than those using traditional peers’ face-to-face cooperative learning for the mathematical application problems in linear equation with one unknown. (2) The experimental group, applying the cooperative digital reading annotation system to learn mathematical application problems in linear equation with one unknown, still outperforms the experimental group, using traditional peers’ face-to-face cooperative learning, on the learning outcome after return to general learning. (3) Learners with either field independent or field dependent cognitive style present significant better learning motivation, after learning mathematical application problems in linear equation with one unknown with the cooperative digital reading annotation system, than those applying traditional peers’ face-to-face cooperative learning. (4) Learners with either high or low ability show remarkably better learning motivation, after learning mathematical application problems in linear equation with one unknown with the cooperative digital reading annotation system, than those using traditional peers’ face-to-face cooperative learning. (5) Field independent learners in the experimental group present better learning motivation than field dependent learners after using the cooperative digital reading annotation system. (6) Learners with high learning ability in the experimental group reveal better learning motivation than those with low ability after using the cooperative digital reading annotation system. In sum, the learning model for the reading comprehension of mathematical application problems with the cooperative digital reading annotation system proposed in this study could enhance the benefits of learning motivation and reading comprehension. It could be promoted to solve the reading comprehension of more complicated mathematical units and even to become the flipped teaching model for innovative mathematics teaching.