Ontology as the core discipline of biomedical informatics: Legacies of the past and recommendations for the future direction of research

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable

Machine Learning of Generic and User-Focused Summarization

A key problem in text summarization is finding a salience function which determines what information in the source should be included in the summary. This paper describes the use of machine learning on a training corpus of documents and their abstracts to discover salience functions which describe what combination of features is optimal for a given summarization task. The method addresses both "generic" and user-focused summaries.Comment: In Proceedings of the Fifteenth National Conference on AI (AAAI-98), p. 821-82

Spoken content retrieval: A survey of techniques and technologies

Speech media, that is, digital audio and video containing spoken content, has blossomed in recent years. Large collections are accruing on the Internet as well as in private and enterprise settings. This growth has motivated extensive research on techniques and technologies that facilitate reliable indexing and retrieval. Spoken content retrieval (SCR) requires the combination of audio and speech processing technologies with methods from information retrieval (IR). SCR research initially investigated planned speech structured in document-like units, but has subsequently shifted focus to more informal spoken content produced spontaneously, outside of the studio and in conversational settings. This survey provides an overview of the field of SCR encompassing component technologies, the relationship of SCR to text IR and automatic speech recognition and user interaction issues. It is aimed at researchers with backgrounds in speech technology or IR who are seeking deeper insight on how these fields are integrated to support research and development, thus addressing the core challenges of SCR

Error-Tolerant RDF Subgraph Matching for Adaptive Presentation of Linked Data on Mobile

International audienceWe present PRISSMA, a context-aware presentation layer for Linked Data. PRISSMA extends the Fresnel vocabulary with the notion of mobile context. Besides, it includes an algorithm that determines whether the sensed context is compatible with some context declarations. The algorithm finds optimal error-tolerant subgraph isomorphisms between RDF graphs using the notion of graph edit distance and is sublinear in the number of context declarations in the system

Enhancing Accessibility to Heterogeneous Sri Lankan Cultural Heritage Information across Museums through Metadata Aggregation

Thesis (Master of Science in Library and Information Studies)--University of Tsukuba, no. 36035, 2016.8.3

Concepts and Synonymy in the UMLS Metathesaurus

This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to synonymy and its relation to terms and concepts. A model theory for a segment of the Metathesaurus is then constructed, and its adequacy relative to the informal treatment is demonstrated. Finally, it is shown how this approach clarifies and addresses the puzzles educed from the informal discussion, and how the model-theoretic perspective may be employed to evaluate some fundamental criticisms of the Metathesaurus

Multi-Device Design in Contexts of Interchange and Task Migration

Com a miniaturização dos componentes digitais e o vasto desenvolvimento tecnológico dos últimos anos, a sociedade tem presenciado a redefinição dos "computadores pessoais" pelo advento dos dispositivos móveis. Além da inovação, eles introduziram o desafio do design multi-dispositivo para as aplicações desktop. Enquanto algumas abordagens criaram interfaces móveis sem aproveitar qualquer modelo, outras buscaram adaptações automáticas visando reduzir a sobrecarga de designo Em ambas, o foco do design deixou de ser o usuário, tornando as interfaces tão diferentes ao ponto de comprometerem a usabilidade na realização de uma mesma tarefa em vários dispositivos. Esta tese afirma que não existe uma abordagem de design multi-dispositivo capaz de garantir boa usabilidade em todos os contextos porque o usuário pode escolher apenas uma forma de acesso à aplicação ou alternar seu uso por meio de vários dispositivos. No primeiro caso, o usuário aprende a usar a interface para realizar suas tarefas, sendo relevante uma abordagem que aproveite os recursos do dispositivo e trate suas limitações. No segundo, o usuário já conhece uma das interfaces, o que gera uma expectativa no uso das demais. Logo, é necessário combinar abordagens com objetivos diferentes para atender ao usuário de acordo com o seu contexto de uso. Neste sentido, propõe-se o design multi-dispositivo por meio da preservação de uma hierarquia de prioridades de consistência definida em três níveis. Enquanto os dois primeiros dão suporte à expectativa do usuário em contextos de uso alternado (propensos à execução de tarefas em dispositivos diferentes) e migração de tarefas (iniciando tarefas com um dispositivo e concluindo com outro), o terceiro nível garante a personalização das tarefas de maior interesse visando eficiência e satisfação de uso em um dispositivo específico. A avaliação desta metodologia foi feita por meio de um experimento com três interfaces de pocket PC construídas a partir de uma aplicação desktop do domínio de Educação a Distância: a primeira delas era uma réplica da original (Migração Direta), a segunda não mantinha consistência de layout e era baseada em um processo de design personalizado adequado ao dispositivo (Linear) e a terceira aplicava apenas os dois primeiros níveis da hierarquia de prioridades (Overview). Os resultados da avaliação subjetiva mostraram que a abordagem Overview foi capaz de manter o modelo mental do usuário com maior precisão por preservar os atributos de facilidade, eficiência e segurança de uso na interação inter-dispositivo. Além disso, os resultados medidos para a eficácia (exatidão das respostas) e eficiênciá (tempo médio de execução das tarefas) foram iguais ou melhores com essa abordagem. Por outro lado, os usuários revelaram uma preferência pela personalização de tarefas presente na abordagem Linear. Este resultado dá suporte à proposta desta tese, mostrando que a eficácia gerada pelos dois primeiros níveis da hierarquia de prioridades (percepção e execução das tarefas) deve ser combinada com o terceiro nível de personalização. Para isso, sugere-se a disponibilização de padrões de interface criados pelo designer para escolha do usuário durante a interação. Essa combinação deve garantir usabilidade no acesso a uma aplicação feito sempre por um mesmo dispositivo ou em contextos de uso alternado e migração de tarefasWith the miniaturization of digital components and the vast technological development of the past years, society has remarked the redefinition of "personal computers" by the advent of modern mobile devices. Besides the innovation, these handhelds also introduced the challenge to develop multi-device interfaces for today's desktop applications. While some created mobile interfaces from scratch to get the best from the devices, others looked for automatic adaptations to reduce the load imposed to the designeI. In both cases, the user wasn't the focus anymore, which resulted interfaces so different from each other to the point of compromising usability when peHorming one task on many devices. This thesis claims that there is no multi-device approach capable to provi de full usability in every context because the user may choose only one interface to access the application or interchange its use via many devices. In the first case, the user learns to perform tasks with the given device, which makes relevant an approach that takes advantage of its resources and solves its limitations. In the second, the user already knows one of the available interfaces, which generates an expectation for the others. Therefore, it is necessary to combine approaches with different goals and suit the user according to the appropriate context. In this sense, we propose multi-device design via maintenance of a consistency priorities hierarchy defined in three levels. The first two levels give support to the user's expectation in contexts of interchange (prone to task execution with different devices) and task migration (starting tasks with one device and finishing with other). On the other side, the third level provides task personalization according to the user's interest towards higher efficiency and satisfaction of use with a specific device. The evaluation of this methodology was conducted by an experiment with three pocket PC interfaces designed from an e-learning desktop application: the first interface was an exact replica of the original desktop version (Direct Migration), the second didn't maintain layout consistency and was based in a personalized design process adequate to the device (Linear) while the third applied only the first two levels of the consistency priorities hierarchy (Overview). The subjective evaluation results pointed the Overview approach as the best to maintain the user's mental model by preserving easiness, efficiency and safety of use on inter-device interaction. Additionally, both measured efficacy (task result accuracy) and efficiency (task execution mean time) were the same or even better with this approach. On the other hand, users revealed their preference for the task personalization present in the Linear approach. This result gives support to our proposal, corroborating that the efficacy generated by the first two levels of the consistency priorities hierarchy (task perception and execution) should be combined with the third level of personalization. This could be done by letting designers create interface patterns and make them available to users during interaction. Such combination should guarantee usability while constantly accessing one application through the same device or in contexts of alternated use and task migratio