Media channels play an important role in the flow, construction, and curation of knowledge in software development. Understanding how developers use media channels is key to improving developer practices and supporting channel evolution. In this thesis, I investigate the way developers use media channels to curate knowledge within the R software development community. By applying a case study methodology consisting of mining archival data and survey methods, I investigate the R community on Stack Overflow and the R-help mailing list, using a qualitative approach. The findings reveal that Stack Overflow and mailing lists foster knowledge co-construction differently---crowd-sourced and participatory respectively. Furthermore, developers use actively both channels to optimize knowledge exchange and curation. My thesis contributes to the understanding of knowledge curation by developer communities, and describes a model for a systematic comparison of two or more media channels, within a community of practice. This model allows knowledge categorization and can be used in future studies to explore knowledge flow within multiple media channels. Moreover, based on my observations in conjunction with the survey data analysis, I extracted a set of recommendations to assist practitioners in the use of multiple Question and Answer (Q&A) channels. / Graduate

This thesis is an archaeological and ethnographic exploration of historic military sites associated with the Cold War. It takes a multi-sited approach to former radar installations in the UK and examines the range of meanings and values that surround them, as well as their mediation, management and curation in the contemporary landscape. This thesis provides a detailed study of a range of related (although not necessarily overlapping) practices, which have accumulated around these places since the 1990s. Much has been written about the ruined-aesthetic of abandoned military sites. Moreover, conservation professionals have undertaken extensive research and granted heritage status to a number of key sites. However, little academic research has been carried out concerning the contemporary social life of former military installations. Furthermore, despite valuable archaeological research concerning the character and form of Cold War historic sites, little attention has been given to the ways in which they are involved in the production of ideas surrounding the Cold War and Cold War heritage in the present; this thesis aims to cover both of these issues. Each of the main chapters in this thesis focuses on a particular set of practices or relationships surrounding historic radar sites, which have been treated in a relatively sporadic and uneven fashion – some have been demolished, others left in ruination and limbo, whereas as a few have been designated as nationally important heritage sites. Therefore, a number of heritage and memory practices are covered, including conservation management, militarisation and nostalgia, as well as the museumification of Cold War sites and objects and the (often) disparate memory practices of former radar veterans. Principally, the analysis in this thesis focuses on extensive ethnographic research undertaken by the author at a number of sites in the UK. This includes semi-structured interviews, participant observation and archival research undertaken in England and Scotland. The key case-studies are the listed and scheduled monuments at RAF Neatishead in Norfolk; the Air Defence Radar Museum, which is located on the same site; and a former early warning site at Saxa Vord in Unst, Shetland. Research conducted at a number of other Cold War sites and museums is also discussed. The principal aim of this thesis is to contribute a set of nuanced and detailed accounts surrounding the archaeology and heritage of the recent past. The Cold War was a varied and complex phenomenon – one which is much debated. Manifold legacies of the Cold War also continue to shape and influence the contemporary world. In a similar manner, concepts and practices surrounding heritage and memory are widely studied, but remain slippery and resist straightforward interpretation. Therefore, the complexities surrounding these phenomena are magnified when they are combined in the present through the notion of Cold War heritage. In order to add some specificity to these related issues, this thesis focuses on two main questions (which are really two-sides of the same coin): what kind of heritage emerges in relation to historic Cold War radar sites? And, what kind of Cold War is produced in the context of heritage and memory practices? Throughout the thesis, it is argued that the Cold War is an uneven, complex and occasionally difficult heritage to deal with in the UK. Mostly, this relates to practical problems such as the complexities surrounding the ownership of former military sites, as well as a number of other conceptual and philosophical issues. For example, in the context of designation and management, this emerges as a tension between the idea of the Cold War as avant-garde heritage and modern conservation principles that underpin contemporary heritage management practices. Furthermore, the emphasis placed on materiality, place and continuity in heritage and memory practices are also brought into relief. At times, these are shown to be complicated by the (at times) elusive, unpredictable and uncertain character of the Cold War in the present. Using radar sites as a microcosm, it is argued that former Cold War sites are seldom the product of coherent or unified approaches to heritage and memory. Instead, they are often at the centre of a variety of converging, conflicting and confounding agendas. Practices surrounding radar sites also present a number of ethical and political challenges. Moreover, it is also argued that radar sites, despite their billing as Cold War heritage, cannot simply be reduced or collapsed into the concept of the Cold War. Nonetheless, the author argues that this kind of fragmentation and complexity might form the basis of a more comprehensive approach to the Cold War and the recent past in the present. Therefore, in the conclusions to this thesis, the author presents a number of avenues for future research and examines the implications of his findings.

This thesis is the written result of a practice-based PhD. The thesis presents a 'located' model of curatorial practice that aims to actively benefit the cultural landscape of host regions. It challenges existing definitions of 'the curatorial', taking a multidisciplinary understanding of curatorial practice and evaluating curatorial methods in light of recent geo-political developments. Concerned with the effects of changes in European cultural policy, and the geopolitical position of the Mediterranean basin, this thesis evaluates contemporary curatorial practices in the Euro-Mediterranean Partnership context and, through practice-based interventions, suggests ways to develop situated curatorial processes, appropriate to their geographical context. Specifically, I argue that the temporary, large-scale exhibition formats financially supported by EU policies, such as the European Regional Development Fund, are not necessarily the most appropriate or beneficial to the cultural development of their host regions. I therefore propose an alternative set of methods, tools and considerations for a self-reflexive model of curatorial practice. This proposal takes the form of a curatorial initiative 'Vessel'; a long-term practice-based research project that seeks models of practice that effectively enable local engagement in cultural production, allowing culture to flourish independently of larger hegemonies. Several of Vessel's experimental initiatives are presented here, and appraised in order to build a theoretical understanding of 'located' curatorial practices that can inform alternative approaches. This research is developed through case studies of Manifesta, Liminal Spaces, Matadero and Intermediae; all of them testing grounds for 'Vessel', a curatorial initiative based in Puglia, Italy. Puglia has been chosen as a site for this research because of its central role in the current Mediterranean situation. This thesis illustrates the theoretical, geographical and historical context of this investigative project, and documents the evolution and outcomes of the curatorial initiative attempted. This thesis represents the first practice-based study of contemporary curatorial practices in the Euro-Mediterranean Partnership (EUROMED) context, which seeks primarily to develop situated curatorial processes appropriate to their geographical context. The thesis discusses aspects of human geography, cultural studies, social science and European studies, all filtered through practical implementation and reflective examination of the main discipline of interest: curatorial studies. This research acknowledges the role of the curator as a mediator between cultural producers and the political and bureaucratic conditions for cultural production. This role offers the opportunity to develop an awareness of the potential influence of those conditions on the artists, their work and their audiences. In other words, the curator is in a unique position to have an overview of the practices, interests and concerns of cultural producers, as well as those of policy makers and administrative bodies, and any potential conflicts of interest that may arise. Thus, curators are in a privileged position to operate as proactive agents, particularly when they observe that cultural policies are not achieving the aim of fostering cultural development. This thesis, therefore, invites curators to consider their responsibility to critically assess the long-term effects of their practice on cultural and epistemological development in Europe. The thesis is divided into four chapters. Chapter 1 presents the research questions, clarifying their terminology and broadly discussing their rationale, context and theoretical focus. The chapter questions current EU cultural and economic strategies and suggests that they may be misguided. In Chapter 2, the level of analysis shifts from the geo-political context to a more specific situation: the position of art practitioners involved in the above situation, and the outcomes produced. Since the exhibition format is popular and has been envisioned by the EU cultural agenda as one of the most effective instruments for creating a dialogue between different geographical areas, Chapter 2 challenges this understanding of the format and the ways of production embedded in it. Chapter 3 presents a series of alternative curatorial approaches coming from the South and related to the four theoretical pillars of the self-reflexive approach: geography, time, process and epistemology. Starting with the methods used to investigate the case studies, the chapter traces connections between theory and practice. The chapter moves through close readings of the alternative case studies and comparative analysis, to the use of self- reflexive practice. Chapter 4 is at the heart of the thesis: it presents the methodologies underpinning both the approach to case study analysis and the practical research. This involves the curatorial proposal put forward and practised through Vessel. Vessel is therefore presented, in Chapter 4, as a self-reflexive model of located curatorial practice that is appropriate for located curatorial engagement. The conclusion addresses the capacity of curatorial practices to cultivate local epistemologies. I propose the outcome of the Vessel research project, and associated case studies as a set of curatorial methods and considerations for a 'located' model of curatorial practice.

Doctor of Philosophy / Genetics Interdepartmental Program / Jesse A. Poland / Wheat is perhaps the most important component in human diet introduced since the conception of modern agriculture, which provides about 20% of the daily protein and calorie intake to billions of people. Adaptable to wide range of climates, wheat is grown worldwide, lending it the potential to mitigate the imminent risk of food security for future population of 9.5 billion people. For developing improved crop varieties in the future, genetic diversity is a key factor in plant breeding. Constraints in wheat evolution and artificial selection practices have resulted in erosion of this ingredient in elite germplasm. However, wheat wild relatives, such as Ae. tauschii, D-genome donor of wheat, are a storehouse for unexploited genetic diversity that can be used for improving wheat for disease and insect resistance, yield, quality, and tolerance to abiotic stresses. More than 1700 genebanks around the world hold over 7 million accessions of these wild relatives. These genebanks are expensive to maintain, therefore, efficient curation is necessary. We developed and implemented a protocol to identify duplicate accessions using genomic tools. Implementing this approach with three genebanks, we identified over 50% duplicated accessions across genebanks. There are over a million Triticeae accessions held collectively, and it is likely as more number of genebanks are tested, there will be decreasing number of unique accessions. Selecting and utilizing the wild genetic diversity is no easy task. Historically, breeders and geneticists have chosen the accessions primarily based on associated phenotypic data. Unless focusing on a targeted trait, this practice is imperfect in capturing the genetic diversity with some other limitations, such as confounding phenotypic data with the testing environment. Utilizing next-generation sequencing methods, we selected a MiniCore consisting of only 40 accessions out of 574 capturing more than 95% of the allelic diversity. This MiniCore will facilitate the use of genetic diversity present in Ae. tauschii for wheat improvement including resistance to leaf rust, stem rust, Hessian fly, and tolerance to abiotic stresses. Hessian fly is an important insect pest of wheat worldwide. Out of 34 known resistance genes, only six have been mapped on the D sub-genome. With swift HF evolution, we need to rapidly map and deploy the resistance genes. Some of the undefeated HF resistance genes, such as H26 and H32, were introgressed from Ae. tauschii. In this study, we mapped three previously known genes, and a new gene from Ae. tauschii accession KU2147. Genes were mapped on chromosomes 6B, 3D, and 6D. Further, identification and cloning of resistance genes will enhance our understanding about its function and mode of action. In conclusion, wild wheat relatives are genetically diverse species, and utilizing the novel genetic diversity in Ae. tauschii will be fruitful for wheat improvement in the wake of climate change to ensure future food security to expected 2 billion newcomers by 2050.

Submitted by KAREN KAHN (karenkipnis@yahoo.com.br) on 2018-05-16T23:19:26Z No. of bitstreams: 1 Dissertação_Mestrado_Karen_Kahn_maio_pdf.pdf: 4705611 bytes, checksum: 869c1cc805d03b2a42e697ef57340c5c (MD5) / Approved for entry into archive by Telma Jaqueline Dias Silveira null (telmasbl@marilia.unesp.br) on 2018-05-17T14:34:20Z (GMT) No. of bitstreams: 1 kahn_k_me_mar.pdf: 4705611 bytes, checksum: 869c1cc805d03b2a42e697ef57340c5c (MD5) / Made available in DSpace on 2018-05-17T14:34:20Z (GMT). No. of bitstreams: 1 kahn_k_me_mar.pdf: 4705611 bytes, checksum: 869c1cc805d03b2a42e697ef57340c5c (MD5) Previous issue date: 2018-04-24 / Não recebi financiamento / Fazeres pós-custodiais em ambiência digital de tradicionais Instituições da Informação, como arquivos, bibliotecas e museus, exigem novos saberes e novas representações padronizadas de dados. Tais dados devem convergir com linguagens computacionais que os traduzam para efetivas interoperabilidades entre sistemas para o armazenamento, a preservação, o acesso e compartilhamento da informação em processo de Curadoria Digital. No Museu da Pessoa, observa-se a convergência do Design da Informação (DI) com demais sistemas complexos, como a Curadoria Digital e a Ciência da Informação, para a construção intencional de memórias de pessoas ou comunidades na Web 2. 0. Atores informacionais que interagem nas interfaces das ambiências digitais destas instituições atuam como designers da informação. Os agentes institucionais devem capacitar-se para ações que justapõem disciplinas a fim de minimizar o risco de obsolescência digital e valorização das informações, idealmente armazenadas em repositórios digitais confiáveis para seu aceso e preservação a longo prazo. O estudo observa o papel do DI no processo de Curadoria Digital do Museu da Pessoa. O objetivo geral da pesquisa é descrever como o DI, definido em e para sua Curadoria Digital, estrutura e organiza as interfaces Homepage e Conte sua História (CSH) do portal do Museu e das páginas Principal e Nova História da base de dados. Ao objetivo geral da pesquisa, somam-se os objetivos específicos: levantar as transformações tecnológicas do Museu desde sua origem (1991); conhecer como se desenham e se apresentam os conteúdos informacionais em interfaces do seu ambiente digital a partir de suas Homepage (back-end e front-end); identificar convergências de linguagens e interoperabilidades entre o subsistema e sistemas digitais, recursos de DI previstos em Curadoria Digital; verificar as implicações do DI nas interações entre sujeitos e o ambiente digital do Museu e reconhecer o papel do DI nos processos contínuos e interativos do ciclo de vida da Curadoria Digital do Museu. A pesquisa descritiva parte de exploração por observação participativa indireta em livros, dissertações, artigos acadêmicos e sites; e observação participativa direta ou etnografia virtual para imersão e verificação do princípio de mutualidade sujeitoambiente. Justifica-se por contribuir para o entendimento epistemológico, acadêmico e transdisciplinar do Museu e por dar um passo necessário em direção à compreensão técnico-científica sobre como o DI prevê convergências de linguagens, codificações multimodais e interoperabilidades entre sistemas. Do ponto de vista político-social, a descrição do processo de Curadoria Digital do Museu da Pessoa poderá servir de modelo a sistemas memoriais que objetivem a socialização da informação mediada por Tecnologias de Informação e Comunicação (TIC). Destaca que no acervo do Museu, resultante de emergências bottom-up facilitadas por simulacro top-down (DI), o fato museal, memórias intangíveis, representam-se por metadados (DI). Descreve o papel estruturante do DI em camadas visíveis e invisíveis do sistema digital; bem como organizador da apresentação e representação de informações previstas em e para a Curadoria Digital. Observa possíveis atualizações na Curadoria Digital do Museu para que o acesso e compartilhamento da informação possa ser garantia de sua preservação a futuras gerações. / Post-custodial practices on digital environments of traditional information institutions such as archives, libraries and museums demand new knowledge and new standardized representation of data. Such data should converge with computational languages that translate them into effective interoperability across systems for the storage, preservation, access and sharing of information in the process of Digital Curation. In Museu da Pessoa, the convergence of Information Design (ID) with other complex systems, such as Digital Curation and Information Science is observed, for the intentional construction of memories of people or communities on the Web 2.0. Informational actors interacting at the interfaces of the digital environments of these institutions act as information designers. Institutional agents should be empowered to take actions that juxtapose disciplines in order to minimize the risk of digital obsolescence and information valorization, ideally stored in reliable digital repositories for their access and long-term preservation. The study discusses the role of ID in the process of Digital Curation of Museu da Pessoa. The general objective of the research is to describe how Information Design resources, defined in and for its Digital Curation, structure the interfaces of Homepage and Conte sua História (CSH) of the museum's digital ambience, and Principal and Nova História from the database. To the general objective of the research, the specific objectives are added: to raise the technological transformations of the museum from its origin (1991); to know how the information contents are designed and presented on the interfaces of their digital environment from Homepage (back-end and front-end); to identify language convergences and interoperability across the subsystem and digital systems, ID resources planned in the Digital Curation; to verify the implications of ID in the interactions between subjects and the digital environment of the museum and to recognize the role of ID in the Digital Curation of Museu da Pessoa. The descriptive research is based on bibliographical and documentary review, historical study and indirect participation in planned observation in sites, dissertations, theses, scientific articles and academic journals, documents and books; and direct participatory observation or virtual ethnography for immersion and verification of the principle of subject-environment mutuality. It is justified because it seeks to contribute to the epistemological, academic and transdisciplinary understanding of the museum and to take a step towards the technical-scientific understanding about how ID plans language convergences, multimodal coding and interoperability across systems. From the political-social point of view, to describe the Digital Curation process of Museu da Pessoa may serve as a model for memory systems aimed at socializing information mediated by Information and Communication Technologies (ICT). We highlight that in the Museum's collection, resulting from bottom-up emergencies facilitated by top-down simulations (ID), the museum fact, intangible memories, are represented by metadata (ID). We describe the structuring role of ID in visible and invisible layers of the digital system; as well as organizer of the presentation and representation of information provided in and for Digital Curation. We observe possible updates in the Digital Curation of the Museum so that the information access and sharing can be guarantee of its preservation to future generations.

Thesis submitted in fulfilment of the requirements for the degree Master of Technology: Information Technology In the Faculty of Informatics and Design at the Cape Peninsula University of Technology / Data sources often emerge with the potential to transform, drive and allow deriving never-envisaged business value. These data sources change the way business enacts and models value generation. As a result, sellers are compelled to capture value by collecting data about business elements that drive change. Some of these elements, such as the customer and products, generate data as part of transactions which necessitates placement of the business element at the centre of the organisation’s data curation journey. This is in order to reveal changes and how these elements affect the business model. Data in business represents information translated into a format convenient for transfer. Data holds the relevant markers needed to measure business elements and provide the relevant metrics to monitor, steer and forecast business to attain enterprise goals. Data forms the building blocks of information within an organisation, allowing for knowledge and facts to be obtained. At its lowest level of abstraction, it provides a platform from which insights and knowledge can be derived as a direct extract for business decision-making as these decisions steer business into profitable situations. Because of this, organisations have had to adapt or change their business models to derive business value for sustainability, profitability and transformation. An organisation’s business model reflects a conceptual representation on how the organisation obtains and delivers value to prospective customers (the service beneficiary). In the process of delivering value to the service beneficiaries, data is generated. Generated data leads to business knowledge which can be leveraged to re-engineer the business model. The business model dictates which information and technology assets are needed for a balanced, profitable and optimised operation. The information assets represent value holding documented facts. Information assets go hand in hand with technology assets. The technology assets within an organisation are the technologies (computers, communications and databases) that support the automation of well-defined tasks as the organisation seeks to remain relevant to its clientele. What has become apparent is the fact that companies find it difficult to leverage the opportunities that data, and for that matter Big Data (BD), offers them. A data curation journey enables a seller to strategise and collect insightful data to influence how business may be conducted in a sustainable and profitable way while positioning the curating firm in a state of ‘information advantage’. While much of the discussion surrounding the concept of BD has focused on programming models (such as Hadoop) and technology innovations usually referred to as disruptive technologies (such as The Internet of Things and Automation of Knowledge Work), the real driver of technology and business is BD economics, which is the combination of open source data management and advanced analytics software coupled with commodity-based, scale-out architectures which are comparatively cheaper than prevalent sustainable technologies known to industry. Hadoop, though hugely misconstrued, is not an integration platform; it is a model the helps determine data value while it brings on-board an optimised way of curating data cheaply as part of the integration architecture. The objectives of the study were to explore how BD can be used to utilise the opportunities it offers the organisation, such as leveraging insights to enable business for transformation. This is accomplished by assessing the level of BD integration with the business model using the BD Business Model Maturation Index. Guidelines with subsequent recommendations are proposed for curation procedures aimed at improving the curation process. A qualitative research methodology was adopted. The research design outlines the research as a single case study; it outlines the philosophy as interpretivist, the approach as data collection through interviews, and the strategy as a review of the method of analysis deployed in the study. Themes that emerged from categorised data indicate the diverging of business elements into primary business elements and secondary supporting business elements. Furthermore, results show that data curation still hinges firmly on traditional data curation processes which diminish the benefits associated with BD curation. Results suggest a guided data curation process optimised by persistence hybridisation as an enabler to gain information advantage. The research also evaluated the level of integration of BD into the case business model to extrapolate results leading to guidelines and recommendations for BD curation.

Orientador: Marcelo El Khouri Buzato / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Estudos da Linguagem / Made available in DSpace on 2018-08-24T15:08:24Z (GMT). No. of bitstreams: 1 Barros_NayaraNataliade_M.pdf: 4553829 bytes, checksum: 2db82890158abe5e58189a69db1cda28 (MD5) Previous issue date: 2014 / Resumo: Esta dissertação tem por objetivo caracterizar a curadoria digital como um novo letramento que aponta para a hibridização empírica entre narrativa e banco de dados na cultura digital, como previsto por Lev Manovich no início dos anos 2000. A base teórica incorpora os conceitos de cultura digital, apropriação tecnológica, hibridismo digital, hipermodalidade, novos letramentos/letramentos digitais, curadoria, gatekeeping/ gatewatching, produsagem e remix. Toma-se como contexto a plataforma de curadoria Storify, serviço que permite que os curadores selecionem e combinem itens de mídia a partir de diferentes mídias sociais. As stories de O Estado de S. Paulo são tomadas como objeto de análise, uma vez que era do interesse do estudo retratar como as práticas de um produtor de conteúdo estabelecido e aquelas de usuários comuns de mídias sociais influenciam o processo de convergência. Um corpus de dez histórias hipermodais do usuário OESP foi elaborado através de um processo de seleção com base em taxas de visualização. As stories foram analisadas em associação com o conteúdo discursivo de uma entrevista semi-estruturada com um dos jornalistas responsáveis por esses textos, à luz de um conjunto de dados secundários (uma revisão da história do jornal Estadão. A análise foi pautada em duas questões de pesquisa: (1) Até que ponto as teorias sobre textos digitais disponíveis na literatura dão conta de descrever o objeto, e que facetas do objeto escampam a cada uma dessas teorias? (2) Dada essa mesma complexidade e a multiplicação de possibilidades práticas, discursivas e semióticas oferecidas pelo objeto, de que maneira o usuário OESP se apropriou do serviço para elaborar suas stories? As ferramentas analíticas empregadas foram tomadas da teoria da Análise do Discurso Mediado por Computador. Os resultados sugerem que as stories constituem um exemplo empírico de hibridismo entre a narrativa como forma cultural dominante da cultura impressa e o banco de dados como uma forma cultural típica da cultura digital, semelhante a mashups agregativos e/ ou remixes regenerativos encontrados em outros contextos de compartilhamento de mídia na internet. O produtor de mídia tradicional se apropriou do Storify por meio de uma prática de curadoria no meio termo entre gatekeeping e gatewatching, que oferece aos usuários de mídias sociais "oportunidades de participar" em "retratos da realidade", reforçando a bem estabelecida relação fornecedor ¿ cliente, entre o jornal e o leitor / Abstract: This dissertation aims to characterize digital curation as a new literacy that points out to the empirical hybridization between narrative and database in digital culture as foreshadowed by Lev Manovich in the early 2000s. The theoretical basis embodies the concepts of digital culture, technological appropriation, digital hybridism, hypermodality, new literacies/ digital literacies, curation, gatekeeping/gatewatching, produsage and remix. The curation platform Storify is taken as a context. It is a service that allows curators to select and combine media items from different social media. O Estado de S. Paulo's stories are taken as the object of analysis since it was in the interest of the study to portray how the practices of an established content producer and those of ordinary social media users would influence the process of convergence. A corpus of ten hypermodal OESP stories was put together through a selection process based on viewing rates. The stories were analysed in association with the discusrsive content of a semi-structured interview with one of the journalists responsible for those texts, in the light of a secondary data (a review of the history of the Estadão journal). The analysis was focused on two research questions: (1) To what extent do the theories on digital text available in the literature can account to describe the object and what aspects of the object are not contemplated by each of those theories? (2) Given such complexity and the multiple practical, discursive and semiotic possibilities offered by the object, in which ways has the user O Estado de S. Paulo appropriated the service to elaborate their stories? The analytical tools employed were taken from Computer Mediated Discourse Analysis theory. The findings suggest that the stories constitute an empirical instance of hybridization between the narrative as dominant cultural form of print culture and the database as a typical cultural form of digital culture akin to aggregative mashups and/or regenerative remixes found in other internet media sharing contexts. The traditional media producer has appropriated Storify by the means of a curator practice in the middle ground between gatekeeping and gatewatching, which offers social media users "opportunities to participate" in "portraits of reality" while reinforcing the well established provider-client relationship between the newspaper and the reader / Mestrado / Linguagem e Sociedade / Mestra em Linguística Aplicada

Molecular interactions enable us to understand the complexity of the human living system and how it can be exploited or malfunction to cause disease. The biomedical literature presents detailed knowledge of molecular functions and therefore represents a valuable reservoir of data for studying disease. However, extracting this data efficiently is difficult as it is spread over millions of publications in text that is not machine-readable. In this thesis we investigate how text mining can be used to automatically extract data for molecular interactions and their context relevant to disease. We focus on two globally relevant classes of diseases of which manifest from contrasting mechanisms: pain-related diseases and diseases caused by pathogenic organisms. Using HIV-1 as a case study, we first show that text mining can be used to partially recreate a large, manually curated database of HIV-1-human molecular interactions derived from the literature. We highlight both weaknesses in the quality of the data produced by the text-mining approach and strengths in it being able to extract this data rapidly, identifying instances missed in the manual curation and its potential as a support tool. We then expand on this approach by showing how an entirely new database of protein interactions relevant to pain can be created efficiently and accurately using text mining to generate the data and manual curation to validate the data quality. The following chapter then presents an analysis of 1,002 unique pain-related protein-protein interactions derived from this database, showing that it is of greater relevance to pain research than databases of pain interactions created from other common starting points. We highlight its value by, for example, identifying new drug repurposing opportunities and exploring differences in specific pain diseases using the contextual detail afforded by the text mining. Finally, we expand further on our approach to extracting molecular interactions from the literature, by showing how interactions between human proteins and pathogens can be curated across pathogenic organisms. We demonstrate how these techniques can be used to expand our knowledge of human pathogen related interaction data already stored in public databases, by identifying 42 new HIV-1-human molecular interactions, 108 new interactions between pathogen species and human proteins and 33 new human proteins that were found to interact with pathogens. Together, the results show that contexualised text mining, when supported by manual curation, can be used to extract molecular interactions for contrasting disease types in an efficient and accurate manner.

D. Litt. et Phil. / The use of data in science has evolved to a new level in e-science. Collaboration in e- science is important as scientists, engineers and technologists work together to solve scientific problems, through the collection and analysis of large data sets. These experiments can generate enormous amounts of data, creating a need for more efficient storage, management and processing of data. Data needs to be managed effectively to ensure possible future use for secondary analysis and further experimentation. The practice of data curation deals with the management of data, with the objective of sustaining data as a resource for future use. A number of frameworks and models have been developed to address the curation of data, but only the Open Archival Information System (OAIS) has been accepted internationally. The World Data Centre (WDC) is an organisation that was established to ensure access to scientific data for a number of different scientific disciplines. This organisation consists of 52 individual data centres (iWDCs) that are members of the WDC, and are responsible for the curation of scientific data. Because the data curation practices and needs of each iWDC differ, the purpose of this study is to determine to what extent it is possible to develop a framework for the curation of data in the WDC. This study used a mixed method research design through the collection of data from an online survey (quantitative data) and a multiple-case case study (qualitative data). All the iWDCs were invited to participate in the online survey, which was created to quantify OAIS functional model compatibility, sampling for the case study was conducted based on the OAIS functional model compatibility scores. v Based on the findings from this study, suggestions towards a suitable framework for the curation of data in the WDC are made. The key outcomes from this research included a quantitative OAIS functional model compatibility test and suggestions towards a suitable framework for the curation of data. The suggestions towards a suitable framework for the curation of data in the WDC should in future be tested in the newly formed World Data System (WDS) and adjustments made to create a viable framework for curating data in the WDS.

Cieľom tejto práce je vytvorenie novej databázy dát pre proteínovú stabilitu, ktorá bude udržiavať a poskytovať experimentálne dáta. Výsledkom práce je databáza FireProtDB, ktorá poskytuje manuálne overené experimentálne dáta z dostupných zdrojov a implementuje grafické užívateľské rozhranie, ktoré poskytuje dôležité informácie o dátach spoločne s možnosťou vyhľadávania umožňujúcim vytvárať dotazy na mieru a cieliacim na užívateľov, ktorí hľadajú dáta pre vytváranie dátových sád pre nástroje využívajúce strojové učenie.