Evaluation and cross-comparison of lexical entities of biological interest (LexEBI)

MOTIVATION: Biomedical entities, their identifiers and names, are essential in the representation of biomedical facts and knowledge. In the same way, the complete set of biomedical and chemical terms, i.e. the biomedical "term space" (the "Lexeome"), forms a key resource to achieve the full integration of the scientific literature with biomedical data resources: any identified named entity can immediately be normalized to the correct database entry. This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness). RESULT: This study compiles a resource for lexical terms of biomedical interest in a standard format (called "LexEBI"), determines the overall number of terms, their reuse in different resources and the nestedness of terms. LexEBI comprises references for protein and gene entries and their term variants and chemical entities amongst other terms. In addition, disease terms have been identified from Medline and PubmedCentral and added to LexEBI. Our analysis demonstrates that the baseforms of terms from the different semantic types show only little polysemous use. Nonetheless, the term variants of protein and gene names (PGNs) frequently contain species mentions, which should have been avoided according to protein annotation guidelines. Furthermore, the protein and gene entities as well as the chemical entities, both do comprise enzymes leading to hierarchical polysemy, and a large portion of PGNs make reference to a chemical entity. Altogether, according to our analysis based on the Medline distribution, 401,869 unique PGNs in the documents contain a reference to 25,022 chemical entities, 3,125 disease terms or 1,576 species mentions. CONCLUSION: LexEBI delivers the complete biomedical and chemical Lexeome in a standardized representation (http://www.ebi.ac.uk/Rebholz-srv/LexEBI/). The resource provides the disease terms as open source content, and fully interlinks terms across resources

Organising the socio-economic relevance of university research: the case of nanomaterials research in Taiwan

This thesis is concerned with academics’ behaviour when organising research aimed at being relevant. More specifically, this study combines a sociological approach and an extensive bibliometric analysis, investigating the relationships between scientists’ perceptions of relevance, their research behaviours and their publishing activities in terms of organising nanomaterials research in Taiwan. By introducing a resource-based concept of the notion of relevance from a scientist’s perspective, it contributes to intellectual debates on changes to knowledge production and the relationship between scientific excellence and socio-economic relevance. The study finds that the ways nanomaterials scientists perceive and organise their research, specifically in terms of research orientation, industry involvement and interdisciplinary collaboration, are not entirely oriented towards socio-economic concerns. Scientists tend to adapt to the demand for relevance by demonstrating potential research applications and forming interdisciplinary collaborations. Nevertheless, they are more persistent in terms of not having industry involved in the research process. Balancing adaptation and persistence reflects scientists’ concerns with securing financial, intellectual and symbolic resources in order to establish their academic credibility. The bibliometric analysis broadly confirms the qualitative results findings, showing an increasing trend towards publishing in applied and targeted basic journals, and towards interdisciplinary collaboration. Yet, the proportion of university-industry papers has been rather stable over time. While our interviews suggest that senior scientists tend to consider interdisciplinary collaboration as a way to facilitate application, the bibliometric analysis shows that interdisciplinary co-authored papers tend to be more basic and receive more citations. The analysis also finds that junior scientists tend to feel more pressure to achieve a strong academic performance, thereby pushing them away from activities concerning achieving the envisioned socio-economic relevance of their research. Given the ambiguous notion of relevance and the inconsistency of policy practices, this thesis suggests that the real pressure is more to do with the demand for excellence than for relevance

The Value of New Scientific Communication Models for Chemistry

This paper is intended as a starting point for discussion on the possible future of scientific communication in chemistry, the value of new models of scientific communication enabled by web based technologies, and the necessary future steps to achieve the benefits of those new models. It is informed by a NSF sponsored workshop that was held on October 23-24, 2008 in Washington D.C. It provides an overview on the chemical communication system in chemistry and describes efforts to enhance scientific communication by introducing new web-based models of scientific communication. It observes that such innovations are still embryonic and have not yet found broad adoption and acceptance by the chemical community. The paper proceeds to analyze the reasons for this by identifying specific characteristics of the chemistry domain that relate to its research practices and socio-economic organization. It hypothesizes how these may influence communication practices, and produce resistance to changes of the current system similar to those that have been successfully deployed in other sciences and which have been proposed by pioneers within chemistry.National Science Foundation, Microsof

Universities' academic research and knowledge-transfer activities in a catch-up country: the case of Korea

The main research topic of this study is universities’ academic research and knowledge-transfer activities in a catch-up country, particularly the relationship between the two activities, which has been rarely examined in previous research. In order to understand this issue against existing literature, a critical review of previous studies has been attempted, considering the idiosyncratic characteristics of the Korean national innovation system. As a result, at the three analysis levels (i.e. national, organisational and individual levels), we propose three conceptual elements respectively: a tentative historical path of universities in catch-up countries; critical factors influencing knowledge transfer activities of universities in catch-up countries; and academics operating in synergy mode. Thereafter, based on the methodology integrating not only the three analysis levels but also qualitative and quantitative approaches, we analyse the data collected from the interviews with Korean academics, survey responses from Korean academics and government White Papers on the activities of Korean universities. The results show a close and positive relationship between Korean universities’ academic research and knowledge-transfer activities across the three levels. Firstly, during the last several decades, the Korean government has strongly encouraged the development of teaching, academic research and knowledge-transfer activities of Korean universities in harmony with the different developmental stages of Korean industry. This has resulted in selective patterns of the universities’ three activities (e.g. concentration of scientific activities in certain fields). Secondly, organisational factors such as scientific capacity and industry funding are important for universities’ knowledge-transfer activities in a catch-up country, which corroborates the positive relationship between the two activities. Finally, in terms of the factors influencing the synergy mode (i.e. a positive relationship between academic research and knowledge-transfer activities), academics’ career stage and disciplines are important. This is related to the rapid expansion of the Korean academic system and the selectivity found in its activities. Based on these findings, it is tempting to conclude that universities in East Asian catch-up countries have developed their own academic system different from those in developed countries, which can be characterised as having strong government control and a high level of interaction with other actors in the national innovation system. Therefore, the application of the controversy over the direct economic contribution of universities in western countries to the context of catch-up countries is quite limited

Inventor Business Card: Prof. Naila Rabbani

The launch of "Qatar University Research Magazine" marks the university's numerous achievements in the field of scientific research. It will also serve as a platform to highlight all our research related initiatives and activities carried out by the various research centers and colleges within the university

Status Report of the DPHEP Study Group: Towards a Global Effort for Sustainable Data Preservation in High Energy Physics

Data from high-energy physics (HEP) experiments are collected with significant financial and human effort and are mostly unique. An inter-experimental study group on HEP data preservation and long-term analysis was convened as a panel of the International Committee for Future Accelerators (ICFA). The group was formed by large collider-based experiments and investigated the technical and organisational aspects of HEP data preservation. An intermediate report was released in November 2009 addressing the general issues of data preservation in HEP. This paper includes and extends the intermediate report. It provides an analysis of the research case for data preservation and a detailed description of the various projects at experiment, laboratory and international levels. In addition, the paper provides a concrete proposal for an international organisation in charge of the data management and policies in high-energy physics

Serviços de integração de dados para aplicações biomédicas

Doutoramento em Informática (MAP-i)In the last decades, the field of biomedical science has fostered unprecedented scientific advances. Research is stimulated by the constant evolution of information technology, delivering novel and diverse bioinformatics tools. Nevertheless, the proliferation of new and disconnected solutions has resulted in massive amounts of resources spread over heterogeneous and distributed platforms. Distinct data types and formats are generated and stored in miscellaneous repositories posing data interoperability challenges and delays in discoveries. Data sharing and integrated access to these resources are key features for successful knowledge extraction. In this context, this thesis makes contributions towards accelerating the semantic integration, linkage and reuse of biomedical resources. The first contribution addresses the connection of distributed and heterogeneous registries. The proposed methodology creates a holistic view over the different registries, supporting semantic data representation, integrated access and querying. The second contribution addresses the integration of heterogeneous information across scientific research, aiming to enable adequate data-sharing services. The third contribution presents a modular architecture to support the extraction and integration of textual information, enabling the full exploitation of curated data. The last contribution lies in providing a platform to accelerate the deployment of enhanced semantic information systems. All the proposed solutions were deployed and validated in the scope of rare diseases.Nas últimas décadas, o campo das ciências biomédicas proporcionou grandes avanços científicos estimulados pela constante evolução das tecnologias de informação. A criação de diversas ferramentas na área da bioinformática e a falta de integração entre novas soluções resultou em enormes quantidades de dados distribuídos por diferentes plataformas. Dados de diferentes tipos e formatos são gerados e armazenados em vários repositórios, o que origina problemas de interoperabilidade e atrasa a investigação. A partilha de informação e o acesso integrado a esses recursos são características fundamentais para a extração bem sucedida do conhecimento científico. Nesta medida, esta tese fornece contribuições para acelerar a integração, ligação e reutilização semântica de dados biomédicos. A primeira contribuição aborda a interconexão de registos distribuídos e heterogéneos. A metodologia proposta cria uma visão holística sobre os diferentes registos, suportando a representação semântica de dados e o acesso integrado. A segunda contribuição aborda a integração de diversos dados para investigações científicas, com o objetivo de suportar serviços interoperáveis para a partilha de informação. O terceiro contributo apresenta uma arquitetura modular que apoia a extração e integração de informações textuais, permitindo a exploração destes dados. A última contribuição consiste numa plataforma web para acelerar a criação de sistemas de informação semânticos. Todas as soluções propostas foram validadas no âmbito das doenças raras

Lateral Strategies for Scientists and Those Who Study Them

The thesis Adapting in the Knowledge Economy investigates the strategies deployed by academic scientists when trying to adapt and maneuver within an increasingly complex mixture of scientific, industrial and governmental agendas. Chapter one “From insights to invoice” summarizes the last decade of Danish research policy as a tendency towards intensified focus on interaction between the university and “outside” actors. Looking at Danish policy documents and interview data the chapter shows how policy changes responded to an idea of “ivory tower” researchers isolating themselves in Danish universities. Furthermore, the interaction agenda was motivated by the perception that knowledge was produced but not sufficiently used. Strongly influenced by the concept of the knowledge economy and that of mode 2 knowledge production, policy changes were directed at bridging a gap between the producers and the consumers of knowledge. A series of reforms and initiatives were launched to facilitate more interaction between science and industry as well as more responsiveness towards societies’ problems on behalf of the universities. This interaction agenda was coupled with an increase in the economic investment in research and an increased focus on competition between researchers in order to ensure high quality in knowledge production...