'Data Management and Curation' Breakout session from the Living the Future 8 Conference, April 23-24, 2012, University of Arizona Libraries, Tucson, AZ.

Experimentally determining the biological function of a protein is a process known as protein characterization. Establishing the role a specific protein plays is a vital step toward fully understanding the biochemical processes that drive life in all its forms. In order for researchers to efficiently locate and benefit from the results of protein characterization experiments, the relevant information is compiled into public databases. To populate such databases, curators, who are experts in the biomedical domain, must search the literature to obtain the relevant information, as the experiment results are typically published in scientific journals. The database curators identify relevant journal articles, read them, and then extract the required information into the database. In recent years the rate of biomedical research has greatly increased, and database curators are unable to keep pace with the number of articles being published. Consequently, maintaining an up-to-date database of characterized proteins, let alone populating a new database, has become a daunting task. In this thesis, we report our work to reduce the effort required from database curators in order to create and maintain a database of characterized proteins. We describe a system we have designed for automatically identifying relevant articles that discuss the results of protein characterization experiments. Classifiers are trained and tested using a large dataset of abstracts, which we collected from articles referenced in public databases, as well as small datasets of manually labeled abstracts. We evaluate both a standard and a modified naïve Bayes classifier and examine several different feature sets for representing articles. Our findings indicate that the resulting classifier performs well enough to be considered useful by the curators of a characterized protein database. / Thesis (Master, Computing) -- Queen's University, 2010-01-28 18:45:17.249

This paper examines the feasibility of establishing reliable repositories intended for the use of the average individual for the preservation of personal digital objects. Observers of technological change warn of the coming of a "digital dark age." Rather than being systematic, the attempts of the average individual to preserve his or her personal digital objects - photos, documents, music - are ad hoc, at best. Digital archiving involves challenges both in terms of hardware reliability and software obsolescence, and requires a blend of technology platforms, legal and public policies, and organizational structure. These three areas must be combined in a cohesive manner in order to facilitate the preservation of personal digital objects for periods of decades or even centuries. Regarding the issue of technological feasibility, I present an examination of work that has already been performed in the field of digital preservation, including an assessment ofDSpace, an open source platform used in institutional repositories to encapsulate data for long term archival. I then introduce my development of Alexandria@CyberStreet.com as an exploration of how a DSpace installation may be modified to suit the needs of personal archiving. Next, I present an examination of the legal and public policy issues concerning such a repository. Finally, I examine organizations that are devoted to the oversight of long-term endeavors and draw conclusions as to an appropriate administrative structure. I conclude that there are sufficient technological tools, public policies and organizational models in place to enable establishment of reliable, long term repositories for personal digital objects.

As computer users increasingly rely on digital tools for daily tasks, the complexity of their working environments continues to grow. Modern knowledge workers must navigate a diverse array of digital resources, including documents, websites, applications, and other information. This complexity presents challenges in managing multiple activities to maintain productivity, such as handling interruptions, resuming tasks, curating resources, recalling context, retrieving previously closed digital resources, and fostering self-reflection. Despite these challenges, there has been limited research on leveraging visual cues to help users reconstruct their previous mental contexts, retrieve digital resources, and enhance self-reflection for behavioral change. Therefore, this Ph.D. dissertation addresses these gaps by focusing on: (1) investigating the existing challenges users face in curating digital resources, (2) designing and implementing supportive applications for task resumption, (3) developing methods that utilize screenshots and metadata for reconstructing mental context and retrieving resources, and (4) enhancing the processes of self-reflection and behavioral change to improve overall productivity. / Doctor of Philosophy / In our increasingly digital world, people are spending more time on computers to complete their daily tasks. However, as there are increasing resources and information involved, managing tasks has become more complex because individuals need to juggle various digital tools at the same time, like documents, websites, and applications. This can lead to difficulties such as dealing with interruptions, picking up where they left off, organizing information, remembering what they were working on, and reflecting on their habits to make positive changes. Surprisingly, there has been little research on how common-seen visual tools, like screenshots, can help people better handle these challenges. Screenshots can serve as visual reminders, helping users remember what they were doing and easily find the resources they need. Hence, this Ph.D. dissertation explores these issues by: (1) examining the problems people face when organizing digital resources, (2) creating tools to help users quickly resume their tasks, (3) using screenshots and additional information to help users remember their previous work, and (4) improving the way people reflect on their behavior to encourage positive changes.

Yes / Radiography has frequently been used during palaeopathological research, and plays an important role in the differential diagnosis of many diseases, including Paget¿s disease and carcinomas. Traditionally, radiographs were taken in hospitals with clinical equipment. However industrial radiography techniques have gradually become more commonly used, as their superior image quality and improved potential for diagnoses become recognised. The introduction of radiographic scanners has facilitated the digitisation of these images for dissemination and publication. However this is not all that radiographic digitisation can offer the researcher. Digital image processing (DIP) allows the researcher to focus on an area of interest and to adjust the brightness and contrast of the captured image. This allows the investigation of areas of high radio-opacity and radio-lucency, providing detailed images of the internal structures of bone and pathological lesions undetectable by the naked eye. In addition 3D effects, edge enhancement and sharpening algorithms, available through commonly used image processing software, can be very effective in enhancing the visibility of specific features. This paper will reveal how radiographic digitisation and manipulation can enhance radiographic images of palaeopathological lesions and potentially further our understanding of the bony manifestations of disease.

No / This volume grew out of an interdisciplinary discussion held in the context of the Leverhulme-funded project 'Changing Beliefs in the Human Body', through which the image of the body in pieces soon emerged as a potent site of attitudes about the body and associated practices in many periods. Archaeologists routinely encounter parts of human and animal bodies in their excavations. Such fragmentary evidence has often been created through accidental damage and the passage of time - nevertheless, it can also signify a deliberate and meaningful act of fragmentation. As a fragment, a part may acquire a distinct meaning through its enchained relationship to the whole or alternatively it may be used in a more straightforward manner to represent the whole or even act as stand-in for other variables. This collection of papers puts bodily fragmentation into a long-term historical perspective. The temporal spread of the papers collected here indicates both the consistent importance and the varied perception of body parts in the archaeological record of Europe and the Near East. By bringing case studies together from a range of locations and time periods, each chapter brings a different insight to the role of body parts and body wholes and explores the status of the body in different cultural contexts. Many of the papers deal directly with the physical remains of the dead body, but the range of practices and representations covered in this volume confirm the sheer variability of treatments of the body throughout human history. Every one of the contributions shows how looking at how the human body is divided into pieces or parts can give us deeper insights into the beliefs of the particular society which produced these practices and representations.

La quantité d'informations sur Internet aujourd'hui accable la plupart des utilisateurs. La découverte d'informations pertinentes (p. Ex. Des nouvelles à lire ou des vidéos à regarder) prend du temps et est fastidieuse; pourtant, elle fait partie du travail quotidien d'au moins 80% des employés en Amérique du Nord. Plusieurs systèmes de filtrage d'informations pour le Web peuvent faciliter cette tâche pour les utilisateurs. Les exemples se retrouvent dans des familles telles que les réseaux sociaux, les systèmes de notation sociale et les systèmes de bookmarking social. Tous ces systèmes exigent que l'engagement de l'utilisateur fonctionne (par exemple, la soumission ou l'évaluation du contenu). Ils fonctionnent bien dans une communauté Internet, mais souffrent dans le cas des petites communautés. En effet, dans les petites communautés, l'apport des utilisateurs est plus rare. Nous nous concentrons sur les communautés d'un endroit qui sont des communautés qui regroupent les gens qui vivent, travaillent ou étudient dans la même région. Exemples de communautés d'un lieu: (i) les étudiants d'un campus, (ii) les personnes vivant dans un quartier ou (iii) les chercheurs travaillant sur le même site. Anecdote nous savons que seulement 0,3% des travailleurs contribuent quotidiennement à leur réseau social d'entreprise. Cette information montre qu'il ya un manque d'engagement des utilisateurs dans les communautés d'un endroit.Dans cette thèse, nous tirons parti de l'observation passive des communautés d'un endroit pour réduire les frais généraux pour les utilisateurs de participer à des systèmes de filtrage de l'information. Nous obtenons une nouvelle source riche d'informations que nous utilisons pour (i) concevoir WeBrowse, un outil de restauration de contenu pour les communautésLa quantité d'informations sur Internet aujourd'hui accable la plupart des utilisateurs. La découverte d'informations pertinentes (p. Ex. Des nouvelles à lire ou des vidéos à regarder) prend du temps et est fastidieuse; pourtant, elle fait partie du travail quotidien d'au moins 80% des employés en Amérique du Nord. Plusieurs systèmes de filtrage d'informations pour le Web peuvent faciliter cette tâche pour les utilisateurs. Les exemples se retrouvent dans des familles telles que les réseaux sociaux, les systèmes de notation sociale et les systèmes de bookmarking social. Tous ces systèmes exigent que l'engagement de l'utilisateur fonctionne (par exemple, la soumission ou l'évaluation du contenu). Ils fonctionnent bien dans une communauté Internet, mais souffrent dans le cas des petites communautés. En effet, dans les petites communautés, l'apport des utilisateurs est plus rare. Nous nous concentrons sur les communautés d'un endroit qui sont des communautés qui regroupent les gens qui vivent, travaillent ou étudient dans la même région. Exemples de communautés d'un lieu: (i) les étudiants d'un campus, (ii) les personnes vivant dans un quartier ou (iii) les chercheurs travaillant sur le même site. Anecdote nous savons que seulement 0,3% des travailleurs contribuent quotidiennement à leur réseau social d'entreprise. Cette information montre qu'il ya un manque d'engagement des utilisateurs dans les communautés d'un endroit. / The amount of information on the Internet today overwhelms most users. Discovering relevant information (e.g. news to read or videos to watch) is time-consuming and tedious and yet it is part of the daily job of at least 80% of the employees in North America. Several information filtering systems for the web can ease this task for users. Examples fall into families such as Social Networks, Social Rating Systems and Social Bookmarking Systems. All these systems require user engagement to work (e.g. submission or rating of content). They work well in an Internet-wide community but suffer in the case smaller communities. Indeed, in smaller communities, the users' input is more scarce. We focus on communities of a place that are communities that group people who live, work or study in the same area. Examples of communities of a place are: (i) the students of a campus, (ii) the people living in a neighborhood or (iii) researchers working in the same site. Anecdotally we know that only 0.3% of workers contribute daily to their corporate social network. This information shows that there is a lack of user engagement in communities of a place.

No description available.

Rural place is often overlooked in interaction design research. This thesis is centered around an analog interaction between humans and a 35 ton stone in a danish forest, on the rural island of Bornholm. With a methodological approach influenced by Donna Haraway's essay 'Situated Knowledges' the author approaches her site-specific topic both as a local, a tourist and a researcher. The thesis offers a close study of the interaction with the stone, and explains how this natural occurring interaction, has physically shaped the landscape around it, but also reveals the curation imposed upon rural place and and how this curation affects our sense of place. The researcher suggests that counter-curations can be used as a method for site-specific interaction designers, and exemplifies this by curating a natural site as well as a rural village site. The stone in the forest opens up for a project about the multiple identities of rural place and how theses are shaped in deep intertwining and tension between the past and present, human and nature.

L'émergence de nouvelles plateformes décentralisées pour la création de données, tel que les plateformes mobiles, les capteurs et l'augmentation de la disponibilité d'open data sur le Web, s'ajoute à l'augmentation du nombre de sources de données disponibles et apporte des données massives sans précédent à être explorées. La notion de curation de données qui a émergé se réfère à la maintenance des collections de données, à la préparation et à l'intégration d'ensembles de données (data set), les combinant avec une plateforme analytique. La tâche de curation inclut l'extraction de métadonnées implicites et explicites ; faire la correspondance et l'enrichissement des métadonnées sémantiques afin d'améliorer la qualité des données. La prochaine génération de moteurs de gestion de données devrait promouvoir des techniques avec une nouvelle philosophie pour faire face au déluge des données. Ils devraient aider les utilisateurs à comprendre le contenue des collections de données et à apporter une direction pour explorer les données. Un scientifique peut explorer les collections de données pas à pas, puis s'arrêter quand le contenu et la qualité atteignent des niveaux satisfaisants. Notre travail adopte cette philosophie et la principale contribution est une approche de curation des données et un environnement d'exploration que nous avons appelé CURARE. CURARE est un système à base de services pour curer et explorer des données volumineuses sur les aspects variété et variabilité. CURARE implémente un modèle de collection de données, que nous proposons, visant représenter le contenu structurel des collections des données et les métadonnées statistiques. Le modèle de collection de données est organisé sous le concept de vue et celle-ci est une structure de données qui pourvoit une perspective agrégée du contenu des collections des données et de ses parutions (releases) associées. CURARE pourvoit des outils pour explorer (interroger) des métadonnées et pour extraire des vues en utilisant des méthodes analytiques. Exploiter les données massives requière un nombre considérable de décisions de la part de l'analyste des données pour trouver quelle est la meilleure façon pour stocker, partager et traiter les collections de données afin d'en obtenir le maximum de bénéfice et de connaissances à partir de ces données. Au lieu d'explorer manuellement les collections des données, CURARE fournit de outils intégrés à un environnement pour assister les analystes des données à trouver quelle est la meilleure collection qui peut être utilisée pour accomplir un objectif analytique donné. Nous avons implémenté CURARE et expliqué comment le déployer selon un modèle d'informatique dans les nuages (cloud computing) utilisant des services de science des donnés sur lesquels les services CURARE sont branchés. Nous avons conçu des expériences pour mesurer les coûts de la construction des vues à partir des ensembles des données du Grand Lyon et de Twitter, afin de pourvoir un aperçu de l'intérêt de notre approche et notre environnement de curation de données / The emergence of new platforms for decentralized data creation, such as sensor and mobile platforms and the increasing availability of open data on the Web, is adding to the increase in the number of data sources inside organizations and brings an unprecedented Big Data to be explored. The notion of data curation has emerged to refer to the maintenance of data collections and the preparation and integration of datasets, combining them to perform analytics. Curation tasks include extracting explicit and implicit meta-data; semantic metadata matching and enrichment to add quality to the data. Next generation data management engines should promote techniques with a new philosophy to cope with the deluge of data. They should aid the user in understanding the data collections’ content and provide guidance to explore data. A scientist can stepwise explore into data collections and stop when the content and quality reach a satisfaction point. Our work adopts this philosophy and the main contribution is a data collections’ curation approach and exploration environment named CURARE. CURARE is a service-based system for curating and exploring Big Data. CURARE implements a data collection model that we propose, used for representing their content in terms of structural and statistical meta-data organised under the concept of view. A view is a data structure that provides an aggregated perspective of the content of a data collection and its several associated releases. CURARE provides tools focused on computing and extracting views using data analytics methods and also functions for exploring (querying) meta-data. Exploiting Big Data requires a substantial number of decisions to be performed by data analysts to determine which is the best way to store, share and process data collections to get the maximum benefit and knowledge from them. Instead of manually exploring data collections, CURARE provides tools integrated in an environment for assisting data analysts determining which are the best collections that can be used for achieving an analytics objective. We implemented CURARE and explained how to deploy it on the cloud using data science services on top of which CURARE services are plugged. We have conducted experiments to measure the cost of computing views based on datasets of Grand Lyon and Twitter to provide insight about the interest of our data curation approach and environment