Nanoinformatics approaches for information extraction and text mining in nanomedical research texts

La nanotecnología es un área de investigación de reciente creación que trata con la manipulación y el control de la materia con dimensiones comprendidas entre 1 y 100 nanómetros. A escala nanométrica, los materiales exhiben fenómenos físicos, químicos y biológicos singulares, muy distintos a los que manifiestan a escala convencional. En medicina, los compuestos miniaturizados a nanoescala y los materiales nanoestructurados ofrecen una mayor eficacia con respecto a las formulaciones químicas tradicionales, así como una mejora en la focalización del medicamento hacia la diana terapéutica, revelando así nuevas propiedades diagnósticas y terapéuticas. A su vez, la complejidad de la información a nivel nano es mucho mayor que en los niveles biológicos convencionales (desde el nivel de población hasta el nivel de célula) y, por tanto, cualquier flujo de trabajo en nanomedicina requiere, de forma inherente, estrategias de gestión de información avanzadas. Desafortunadamente, la informática biomédica todavía no ha proporcionado el marco de trabajo que permita lidiar con estos retos de la información a nivel nano, ni ha adaptado sus métodos y herramientas a este nuevo campo de investigación. En este contexto, la nueva área de la nanoinformática pretende detectar y establecer los vínculos existentes entre la medicina, la nanotecnología y la informática, fomentando así la aplicación de métodos computacionales para resolver las cuestiones y problemas que surgen con la información en la amplia intersección entre la biomedicina y la nanotecnología. Las observaciones expuestas previamente determinan el contexto de esta tesis doctoral, la cual se centra en analizar el dominio de la nanomedicina en profundidad, así como en el desarrollo de estrategias y herramientas para establecer correspondencias entre las distintas disciplinas, fuentes de datos, recursos computacionales y técnicas orientadas a la extracción de información y la minería de textos, con el objetivo final de hacer uso de los datos nanomédicos disponibles. El autor analiza, a través de casos reales, alguna de las tareas de investigación en nanomedicina que requieren o que pueden beneficiarse del uso de métodos y herramientas nanoinformáticas, ilustrando de esta forma los inconvenientes y limitaciones actuales de los enfoques de informática biomédica a la hora de tratar con datos pertenecientes al dominio nanomédico. Se discuten tres escenarios diferentes como ejemplos de actividades que los investigadores realizan mientras llevan a cabo su investigación, comparando los contextos biomédico y nanomédico: i) búsqueda en la Web de fuentes de datos y recursos computacionales que den soporte a su investigación; ii) búsqueda en la literatura científica de resultados experimentales y publicaciones relacionadas con su investigación; iii) búsqueda en registros de ensayos clínicos de resultados clínicos relacionados con su investigación. El desarrollo de estas actividades requiere el uso de herramientas y servicios informáticos, como exploradores Web, bases de datos de referencias bibliográficas indexando la literatura biomédica y registros online de ensayos clínicos, respectivamente. Para cada escenario, este documento proporciona un análisis detallado de los posibles obstáculos que pueden dificultar el desarrollo y el resultado de las diferentes tareas de investigación en cada uno de los dos campos citados (biomedicina y nanomedicina), poniendo especial énfasis en los retos existentes en la investigación nanomédica, campo en el que se han detectado las mayores dificultades. El autor ilustra cómo la aplicación de metodologías provenientes de la informática biomédica a estos escenarios resulta efectiva en el dominio biomédico, mientras que dichas metodologías presentan serias limitaciones cuando son aplicadas al contexto nanomédico. Para abordar dichas limitaciones, el autor propone un enfoque nanoinformático, original, diseñado específicamente para tratar con las características especiales que la información presenta a nivel nano. El enfoque consiste en un análisis en profundidad de la literatura científica y de los registros de ensayos clínicos disponibles para extraer información relevante sobre experimentos y resultados en nanomedicina —patrones textuales, vocabulario en común, descriptores de experimentos, parámetros de caracterización, etc.—, seguido del desarrollo de mecanismos para estructurar y analizar dicha información automáticamente. Este análisis concluye con la generación de un modelo de datos de referencia (gold standard) —un conjunto de datos de entrenamiento y de test anotados manualmente—, el cual ha sido aplicado a la clasificación de registros de ensayos clínicos, permitiendo distinguir automáticamente los estudios centrados en nanodrogas y nanodispositivos de aquellos enfocados a testear productos farmacéuticos tradicionales. El presente trabajo pretende proporcionar los métodos necesarios para organizar, depurar, filtrar y validar parte de los datos nanomédicos existentes en la actualidad a una escala adecuada para la toma de decisiones. Análisis similares para otras tareas de investigación en nanomedicina ayudarían a detectar qué recursos nanoinformáticos se requieren para cumplir los objetivos actuales en el área, así como a generar conjunto de datos de referencia, estructurados y densos en información, a partir de literatura y otros fuentes no estructuradas para poder aplicar nuevos algoritmos e inferir nueva información de valor para la investigación en nanomedicina. ABSTRACT Nanotechnology is a research area of recent development that deals with the manipulation and control of matter with dimensions ranging from 1 to 100 nanometers. At the nanoscale, materials exhibit singular physical, chemical and biological phenomena, very different from those manifested at the conventional scale. In medicine, nanosized compounds and nanostructured materials offer improved drug targeting and efficacy with respect to traditional formulations, and reveal novel diagnostic and therapeutic properties. Nevertheless, the complexity of information at the nano level is much higher than the complexity at the conventional biological levels (from populations to the cell). Thus, any nanomedical research workflow inherently demands advanced information management. Unfortunately, Biomedical Informatics (BMI) has not yet provided the necessary framework to deal with such information challenges, nor adapted its methods and tools to the new research field. In this context, the novel area of nanoinformatics aims to build new bridges between medicine, nanotechnology and informatics, allowing the application of computational methods to solve informational issues at the wide intersection between biomedicine and nanotechnology. The above observations determine the context of this doctoral dissertation, which is focused on analyzing the nanomedical domain in-depth, and developing nanoinformatics strategies and tools to map across disciplines, data sources, computational resources, and information extraction and text mining techniques, for leveraging available nanomedical data. The author analyzes, through real-life case studies, some research tasks in nanomedicine that would require or could benefit from the use of nanoinformatics methods and tools, illustrating present drawbacks and limitations of BMI approaches to deal with data belonging to the nanomedical domain. Three different scenarios, comparing both the biomedical and nanomedical contexts, are discussed as examples of activities that researchers would perform while conducting their research: i) searching over the Web for data sources and computational resources supporting their research; ii) searching the literature for experimental results and publications related to their research, and iii) searching clinical trial registries for clinical results related to their research. The development of these activities will depend on the use of informatics tools and services, such as web browsers, databases of citations and abstracts indexing the biomedical literature, and web-based clinical trial registries, respectively. For each scenario, this document provides a detailed analysis of the potential information barriers that could hamper the successful development of the different research tasks in both fields (biomedicine and nanomedicine), emphasizing the existing challenges for nanomedical research —where the major barriers have been found. The author illustrates how the application of BMI methodologies to these scenarios can be proven successful in the biomedical domain, whilst these methodologies present severe limitations when applied to the nanomedical context. To address such limitations, the author proposes an original nanoinformatics approach specifically designed to deal with the special characteristics of information at the nano level. This approach consists of an in-depth analysis of the scientific literature and available clinical trial registries to extract relevant information about experiments and results in nanomedicine —textual patterns, common vocabulary, experiment descriptors, characterization parameters, etc.—, followed by the development of mechanisms to automatically structure and analyze this information. This analysis resulted in the generation of a gold standard —a manually annotated training or reference set—, which was applied to the automatic classification of clinical trial summaries, distinguishing studies focused on nanodrugs and nanodevices from those aimed at testing traditional pharmaceuticals. The present work aims to provide the necessary methods for organizing, curating and validating existing nanomedical data on a scale suitable for decision-making. Similar analysis for different nanomedical research tasks would help to detect which nanoinformatics resources are required to meet current goals in the field, as well as to generate densely populated and machine-interpretable reference datasets from the literature and other unstructured sources for further testing novel algorithms and inferring new valuable information for nanomedicine.

Exploring the economic value of personal information from firms' financial statements

Currently personal data gathering in online markets is done on a far larger scale and much cheaper and faster than ever before. Within this scenario, a number of highly relevant companies for whom personal data is the key factor of production have emerged. However, up to now, the corresponding economic analysis has been restricted primarily to a qualitative perspective linked to privacy issues. Precisely, this paper seeks to shed light on the quantitative perspective, approximating the value of personal information for those companies that base their business model on this new type of asset. In the absence of any systematic research or methodology on the subject, an ad hoc procedure is developed in this paper. It starts with the examination of the accounts of a number of key players in online markets. This inspection first aims to determine whether the value of personal information databases is somehow reflected in the firms’ books, and second to define performance measures able to capture this value. After discussing the strengths and weaknesses of possible approaches, the method that performs best under several criteria (revenue per data record) is selected. From here, an estimation of the net present value of personal data is derived, as well as a slight digression into regional differences in the economic value of personal information.

Inter-organizational information systems adoption for service innovation in building sector

The building sector has experienced a significant decline in recent years in Spain and Europe as a result of the financial crisis that began in 2007. This drop accompanies a low penetration of information and communication technologies in inter-organizational oriented business processes. The market decrease is causing a slowdown in the building sector, where only flexible small and medium enterprises (SMEs) survive thanks to specialization and innovation in services, which allow them to face new market demands. Inter-organizational information systems (IOISs) support innovation in services, and are thus a strategic tool for SMEs to obtain competitive advantage. Because of the inherent complexity of IOIS adoption, this research extends Kurnia and Johnston's (2000) theoretical model of IOIS adoption with an empirical model of IOIS characterization. The resultant model identifies the factors influencing IOIS adoption in SMEs in the building sector, to promote further service innovation for competitive and collaborative advantages. An empirical longitudinal study over six consecutive years using data from Spanish SMEs in the building sector validates the model, using the partial least squares technique and analyzing temporal stability. The main findings of this research are the four ways an IOIS might contribute to service innovation in the building sector. Namely: a) improving client interfaces and the link between service providers and end users; b) defining a specific market where SMEs can develop new service concepts; c) enhancing the service delivery system in traditional customer?supplier relationships; and d) introducing information and communication technologies and tools to improve information management.

Integrated safe driving information system development: volume IV - catalog of available materials. Final report.

National Highway Traffic Safety Administration, Washington, D.C.

Acquiring highway transportation information from abroad: final report.

Federal Highway Administration, Washington, D.C.

Acquiring highway transportation information from abroad: handbook.

Federal Highway Administration, Washington, D.C.

Impact of the freedom of information and privacy acts on law enforcement agencies.

Mode of access: Internet.

Survey of specialized technical information centers. Final report.

National Highway Safety Bureau, Washington, D.C.

Proposing a systems vision of knowledge management in emergency care

This paper makes a case for taking a systems view of knowledge management within health-care provision, concentrating on the emergency care process in the UK National Health Service. It draws upon research in two casestudy organizations (a hospital and an ambulance service). The case-study organizations appear to be approaching knowledge (and information) management in a somewhat fragmented way. They are trying to think more holistically, but (perhaps) because of the ways their organizations and their work are structured, they cannot ‘see’ the whole of the care process. The paper explores the complexity of knowledge management in emergency health care and draws the distinction for knowledge management between managing local and operational knowledge, and global and clinical knowledge.

Source of legitimacy in M-government initiatives in Turkey:concerns human vs. technical resource management

Emerging markets have recently been experiencing a dramatic increased in the number of mobile phone per capita. M-government has, hence, been heralded as an opportunity to leap-frog the technology cycle and provide cheaper and more inclusive and services to all. This chapter explores, within an emerging market context, the legitimacy and resistance facing civil servants’ at the engagement stage with m-government activities and the direct implication for resource management. Thirty in depth interview, in Turkey, are drawn-upon with key ICT civil servant in local organizations. The findings show that three types of resources are perceived as central namely: (i) diffusion of information management, (ii) operating system resource management and (iii) human resource management. The main evidence suggests that legitimacy for each resource management, at local level, is an ongoing struggle where all groups deploy multiples forms of resistance. Overall, greater attention in the resource management strategy for m-government application needs to be devoted to enablers such as civil servants rather than the final consumers or citizens.

WSRF-based modeling of clinical trial information for collaborative cancer research

The CancerGrid consortium is developing open-standards cancer informatics to address the challenges posed by modern cancer clinical trials. This paper presents the service-oriented software paradigm implemented in CancerGrid to derive clinical trial information management systems for collaborative cancer research across multiple institutions. Our proposal is founded on a combination of a clinical trial (meta)model and WSRF (Web Services Resource Framework), and is currently being evaluated for use in early phase trials. Although primarily targeted at cancer research, our approach is readily applicable to other areas for which a similar information model is available.

The evolving role of information specialists:change agents in process redesign

The research investigates the past, present and potential future role of Information Specialists (ISps) in process oriented companies. It tests the proposition that ISps in companies that have undertaken formal process reengineering exercises are likely to become more proactive and more business oriented (as opposed to technically oriented) than they had previously been when their organisations were organised along traditional, functional lines. A review of existing literature in the area of Business Process Reengineering and Information Management reveals a lack of consensus amongst researchers concerning the appropriate role for ISps during and after BPR. Opinion is divided as to whether IS professionals should reactively support BPR or whether IT/IS developments should be driving these initiatives. A questionnaire based ‘Descriptive Survey’ with 60 respondents is used as a first stage of primary data gathering. This is followed by follow-up interviews with 20 of the participating organisations to gather further information on their experiences. The final stage of data collection consists of further in-depth interview with four case study companies to provide an even richer picture of their experiences. The results of the questionnaire are analysed and displayed in the form of simple means, frequencies and bar graphs. The ‘NU-DIST’ computer based discourse analysis package was tried in relation to summarising the interview findings, but this proved cumbersome and a visual collation method is preferred. Overall, the researcher contends that the supposition outlined above is proven, and she concludes the research by suggesting the implications of these findings. In particular she offers a ‘Framework for Understanding and Action’ which is deemed to be relevant to both practitioners and future researchers.

Designing a methodology for an office communication and information system:for executives in the Malaysian public sector : the Prime Minister's office

Modern managers are under tremendous pressure in attempting to fulfil a profoundly complex managerial task, that of handling information resources. Information management, an intricate process requiring a high measure of human cognition and discernment, involves matching a manager's lack of information processing capacity against his information needs, with voluminous information at his disposal. The nature of the task will undoubtedly become more complex in the case of a large organisation. Management of large-scale organisations is therefore an exceedingly challenging prospect for any manager to be faced with. A system that supports executive information needs will help reduce managerial and informational mismatches. In the context of the Malaysian public sector, the task of overall management lies with the Prime Minister and the Cabinet. The Prime Minister's Office is presently supporting the Prime Minister's information and managerial needs, although not without various shortcomings. The rigid formalised structure predominant of the Malaysian public sector, so opposed to dynamic treatment of problematic issues as faced by that sector, further escalates the managerial and organisational problem of coping with a state of complexity. The principal features of the research are twofold: the development of a methodology for diagnosing the problem organisation' and the design of an office system. The methodological development is done in the context of the Malaysian public sector, and aims at understanding the complexity of its communication and control situation. The outcome is a viable model of the public sector. `Design', on the other hand, is developing a syntax or language for office systems which provides an alternative to current views on office systems. The design is done with reference to, rather than for, the Prime Minister's Office. The desirable outcome will be an office model called Office Communication and Information System (OCIS).