Mining biomedical information from scientific literature

The rapid evolution and proliferation of a world-wide computerized network, the Internet, resulted in an overwhelming and constantly growing amount of publicly available data and information, a fact that was also verified in biomedicine. However, the lack of structure of textual data inhibits its direct processing by computational solutions. Information extraction is the task of text mining that intends to automatically collect information from unstructured text data sources. The goal of the work described in this thesis was to build innovative solutions for biomedical information extraction from scientific literature, through the development of simple software artifacts for developers and biocurators, delivering more accurate, usable and faster results. We started by tackling named entity recognition - a crucial initial task - with the development of Gimli, a machine-learning-based solution that follows an incremental approach to optimize extracted linguistic characteristics for each concept type. Afterwards, Totum was built to harmonize concept names provided by heterogeneous systems, delivering a robust solution with improved performance results. Such approach takes advantage of heterogenous corpora to deliver cross-corpus harmonization that is not constrained to specific characteristics. Since previous solutions do not provide links to knowledge bases, Neji was built to streamline the development of complex and custom solutions for biomedical concept name recognition and normalization. This was achieved through a modular and flexible framework focused on speed and performance, integrating a large amount of processing modules optimized for the biomedical domain. To offer on-demand heterogenous biomedical concept identification, we developed BeCAS, a web application, service and widget. We also tackled relation mining by developing TrigNER, a machine-learning-based solution for biomedical event trigger recognition, which applies an automatic algorithm to obtain the best linguistic features and model parameters for each event type. Finally, in order to assist biocurators, Egas was developed to support rapid, interactive and real-time collaborative curation of biomedical documents, through manual and automatic in-line annotation of concepts and relations. Overall, the research work presented in this thesis contributed to a more accurate update of current biomedical knowledge bases, towards improved hypothesis generation and knowledge discovery.

Traditional algarvian distillats and liqueurs historic scientific aspects

All the evidence indicates that distillation and liqueurs preparation began in Monchique mountain because this place was pointed as a possible capital of the oldest population of Algarve and an important Arabic village (Barreto, 1972: 19). It was possible to find lots of vestiges like the alembic produced by Arabic population near the X century (Telo, 1988: 77). Traditionally the Algarvian people produce the Arbutus unedo L., fig, carob, grape distillates. At the same time they produce liqueur-using maceration of parts of plants or fruits in some kinds of distillates. Most of the work about Algarvian distillates started by studying the basic compounds of Arbutus unedo spirits by gas chromatography (GC) and mass spectrometry (MS) as well as other physical-chemical properties. In a second phase aged distillates were studied by their phenolic compounds evolution using high resolution liquid chromatography (HPLC). Volatile compounds of traditional liqueurs were identified by head space micro extraction solid phase (HE-SPME) and also analysed by gas chromatography mass spectrometry (GC-MS) and when possible confirmed with standards. Total phenols were determined by Folin-Ciocalteur method. Flavenoids were studied by high performance liquid chromatography (HPLC). Sensorial analysis was also done in every drink studies. The results showed that the arbutus distillate doesn’t present a high level of methanol according to the current legislation. The excesses of acidity or ethyl acetate present normal values when the fermentation is well done (Galego, et al. 1995: 341; Galego, et al. 1995: 685). During the aging process, the colour of spirits tend to become darker, the colour changes occurred more rapidly in the arbutus spirits located in cellars with higher temperatures (Galego, et al. 2001: 432). In the sensory evaluation of samples aged during 12 months into 50 L medium toasting level oak wood barrels, panellists considered that samples of arbutus spirit had too much wood flavour and they were not able to detect the characteristic aroma of arbutus fruit (Galego, et al., 2001: 183). Differences in liqueurs were observed using HS-SPME-GC, HS-SPME-GC-MS or HPLC analysis and this observation was confirmed by a sensorial panel (Galego, et al. 2003: 60).

Automatic classification of scientific records using the German Subject Heading Authority File (SWD)

The following paper deals with an automatic text classification method which does not require training documents. For this method the German Subject Heading Authority File (SWD), provided by the linked data service of the German National Library is used. Recently the SWD was enriched with notations of the Dewey Decimal Classification (DDC). In consequence it became possible to utilize the subject headings as textual representations for the notations of the DDC. Basically, we we derive the classification of a text from the classification of the words in the text given by the thesaurus. The method was tested by classifying 3826 OAI-Records from 7 different repositories. Mean reciprocal rank and recall were chosen as evaluation measure. Direct comparison to a machine learning method has shown that this method is definitely competitive. Thus we can conclude that the enriched version of the SWD provides high quality information with a broad coverage for classification of German scientific articles.

Enabling Scientific Workflow Sharing through Coarse-Grained Interoperability

E-scientists want to run their scientific experiments on Distributed Computing Infrastructures (DCI) to be able to access large pools of resources and services. To run experiments on these infrastructures requires specific expertise that e-scientists may not have. Workflows can hide resources and services as a virtualization layer providing a user interface that e-scientists can use. There are many workflow systems used by research communities but they are not interoperable. To learn a workflow system and create workflows in this workflow system may require significant efforts from e-scientists. Considering these efforts it is not reasonable to expect that research communities will learn new workflow systems if they want to run workflows developed in other workflow systems. The solution is to create workflow interoperability solutions to allow workflow sharing. The FP7 Sharing Interoperable Workflow for Large-Scale Scientific Simulation on Available DCIs (SHIWA) project developed two interoperability solutions to support workflow sharing: Coarse-Grained Interoperability (CGI) and Fine-Grained Interoperability (FGI). The project created the SHIWA Simulation Platform (SSP) to implement the Coarse-Grained Interoperability approach as a production-level service for research communities. The paper describes the CGI approach and how it enables sharing and combining existing workflows into complex applications and run them on Distributed Computing Infrastructures. The paper also outlines the architecture, components and usage scenarios of the simulation platform.

Survival or Sustainability? Contributions of Innovatively-Managed News Ventures to the Future of Egyptian Journalism

In the repressive political climate prevailing in Egypt in 2013-15, news ventures aspiring to high standards of reporting were forced to innovate. This paper analyses three Egyptian start-ups that experimented with novel revenue streams and news services during that period, to gain insights into their approaches to managing journalism. In the process it compares different criteria for assessing sustainability and concludes that, in adverse political environments, narrow economic measures of profitability and survival may give a misleading picture as to the sustainability of the kind of journalism conducive to democratic practice. Operating collaboratively, transparently and ethically may slow productivity and profitability in the short term while laying stronger foundations for durable relations among media teams, as well as with readers and advertisers, in the long run.

From the high ground to the swamp: A model for immersive journalism research

This article examines a reflexive, praxis-based methodology for conducting journalism research from a practitioner-academic perspective. Journalism research methods that are interactive, iterative and which rest on a dynamic communicative partnership between academics and practitioners, offer the best way for understanding change in our dynamic field. This permits the researcher to coalesce and strengthen their identity as a practitioner-academic and develop research projects that are mutually beneficial for advancing scholarship and practice. Drawing on reflexive methodologies in the human sciences, such as hermeneutics, cybernetics and constructivism, this article envisions an immersive approach embracing phenomenology and Gestalt as a fully reflexive method of data collection.

New Opportunities for Development Journalism: Enlarging the Public Sphere with ICTs

The present study examines new opportunities offered by the introduction of information and communication technologies (ICTs) to enhance the development journalism practice, in order to enlarge the public sphere and empower ordinary people to participate more actively in public debate on issues affecting their development. The analysis of the achievements and challenges faced by 32 radio stations under the UNESCO project “Empowering Local Radios with ICTs” offers an overview of the introduction of ICTs in different contexts, within and among seven countries in Sub- Saharan Africa. Even though the lack of ICTs access and knowledge is still a concern in the developing world, especially in rural areas, these new tools can be adapted to each context and foster a more pluralistic and participative media in order to address people’s needs and promote social change.

Cultural journalism in a digital environment : new models, practices and possibilities

Both culture coverage and digital journalism are contemporary phenomena that have undergone several transformations within a short period of time. Whenever the media enters a period of uncertainty such as the present one, there is an attempt to innovate in order to seek sustainability, skip the crisis or find a new public. This indicates that there are new trends to be understood and explored, i.e., how are media innovating in a digital environment? Not only does the professional debate about the future of journalism justify the need to explore the issue, but so do the academic approaches to cultural journalism. However, none of the studies so far have considered innovation as a motto or driver and tried to explain how the media are covering culture, achieving sustainability and engaging with the readers in a digital environment. This research examines how European media which specialize in culture or have an important cultural section are innovating in a digital environment. Specifically, we see how these innovation strategies are being taken in relation to the approach to culture and dominant cultural areas, editorial models, the use of digital tools for telling stories, overall brand positioning and extensions, engagement with the public and business models. We conducted a mixed methods study combining case studies of four media projects, which integrates qualitative web features and content analysis, with quantitative web content analysis. Two major general-interest journalistic brands which started as physical newspapers – The Guardian (London, UK) and Público (Lisbon, Portugal) – a magazine specialized in international affairs, culture and design – Monocle (London, UK) – and a native digital media project that was launched by a cultural organization – Notodo, by La Fábrica – were the four case studies chosen. Findings suggest, on one hand, that we are witnessing a paradigm shift in culture coverage in a digital environment, challenging traditional boundaries related to cultural themes and scope, angles, genres, content format and delivery, engagement and business models. Innovation in the four case studies lies especially along the product dimensions (format and content), brand positioning and process (business model and ways to engage with users). On the other hand, there are still perennial values that are crucial to innovation and sustainability, such as commitment to journalism, consistency (to the reader, to brand extensions and to the advertiser), intelligent differentiation and the capability of knowing what innovation means and how it can be applied, since this thesis also confirms that one formula doesn´t suit all. Changing minds, exceeding cultural inertia and optimizing the memory of the websites, looking at them as living, organic bodies, which continuously interact with the readers in many different ways, and not as a closed collection of articles, are still the main challenges for some media.

Transforming scientific information with everyday thinking: A social representations perspective

Cette thèse examine la circulation et l'intégration des informations scientifiques dans la pensée quotidienne d'après la théorie des représentations sociales (TRS). En tant qu'alternative aux approches traditionnelles de la communication de la science, les transformations survenant entre le discours scientifique et le discours de sens commun sont considérées comme adaptatives. Deux études sur la circulation des informations dans les media (études 1 et 2) montrent des variations dans les thèmes de discours exposés aux profanes, et parmi les discours de ceux-ci, en fonction de différentes sources. Ensuite, le processus d'ancrage dans le positionnement préalable envers la science est étudié, pour l'explication qu'il fournit de la réception et de la transmission d'informations scientifiques dans le sens commun. Les effets d'ancrage dans les attitudes et croyances préexistants sont reportés dans différents contextes de circulation des informations scientifiques (études 3 à 7), incluant des études de type corrélationnel, experimental et de terrain. Globalement, cette thèse procure des arguments en faveur de la pertinence de la TRS pour la recherche sur la communication de la science, et suggère des développements théoriques et méthodologiques pour ces deux domaines de recherche. Drawing on the social representations theory (SRT), this thesis examines the circulation and integration of scientific information into everyday thinking. As an alternative to the traditional approaches of science communication, it considers transformations between scientific and common-sense discourses as adaptive. Two studies, focused on the spreading of information into the media (Studies 1 and 2), show variations in the themes of discourses introduced to laypersons and in the themes among laypersons' discourses, according to different sources. Anchoring in prior positioning toward science is then studied for the explanation it provides on the reception and transmission of scientific information into common sense. Anchoring effects in prior attitudes and beliefs are reported in different contexts of circulation of scientific information (Studies 3 to 7) by using results from correlational, field, and experimental studies. Overall, this thesis provides arguments for the relevance of SRT in science communication research and suggests theoretical and methodological developments for both domains of research.