NETTAB 2012 on “Integrated Bio-Search”

The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement

Development and tuning of an original search engine for patent libraries in medicinal chemistry

Background The large increase in the size of patent collections has led to the need of efficient search strategies. But the development of advanced text-mining applications dedicated to patents of the biomedical field remains rare, in particular to address the needs of the pharmaceutical & biotech industry, which intensively uses patent libraries for competitive intelligence and drug development. Methods We describe here the development of an advanced retrieval engine to search information in patent collections in the field of medicinal chemistry. We investigate and combine different strategies and evaluate their respective impact on the performance of the search engine applied to various search tasks, which covers the putatively most frequent search behaviours of intellectual property officers in medical chemistry: 1) a prior art search task; 2) a technical survey task; and 3) a variant of the technical survey task, sometimes called known-item search task, where a single patent is targeted. Results The optimal tuning of our engine resulted in a top-precision of 6.76% for the prior art search task, 23.28% for the technical survey task and 46.02% for the variant of the technical survey task. We observed that co-citation boosting was an appropriate strategy to improve prior art search tasks, while IPC classification of queries was improving retrieval effectiveness for technical survey tasks. Surprisingly, the use of the full body of the patent was always detrimental for search effectiveness. It was also observed that normalizing biomedical entities using curated dictionaries had simply no impact on the search tasks we evaluate. The search engine was finally implemented as a web-application within Novartis Pharma. The application is briefly described in the report. Conclusions We have presented the development of a search engine dedicated to patent search, based on state of the art methods applied to patent corpora. We have shown that a proper tuning of the system to adapt to the various search tasks clearly increases the effectiveness of the system. We conclude that different search tasks demand different information retrieval engines' settings in order to yield optimal end-user retrieval

NMC horizon report: 2014 library edition

The NMC Horizon Report: 2014 Library Edition, examines key trends, significant challenges, and emerging technologies for their potential impact on academic and research libraries worldwide. While there are many local factors affecting libraries, there are also issues that transcend regional boundaries and common questions; it was with these questions in mind that this report was created. The NMC Horizon Report: 2014 Library Edition was produced by the NMC in collaboration with University of Applied Sciences (HTW) Chur, Technische Informationsbibliothek (TIB) Hannover, and ETH-Bibliothek Zurich. To create the report, an international body of experts from library management, education, technology, and other fields was convened as a panel. Over the course of three months in the spring of 2014, the 2014 Horizon Project Library Expert Panel came to a consensus about the topics that would appear here in the NMC Horizon Report: 2014 Library Edition.&nbsp

Contribución de la inteligencia competitiva en el proceso de I+D+i del sector farmacéutico : el caso de España

This research focuses on the use and practice of Competitive Intelligence within the Spanich pharmaceutical sector, as a tool to be used in decision making. For that purpose, it is necessary to perform each step of the IC methdology, in order to identify strengths and weaknesses of competing firms and the own, to plan strategies for the benefit and growth of the pharmaceutical industry in Spain. This is for laboratories and companies regarless of their origin either national or foreign companies affiliated with Farmaindustria and Plan Profarma for the period 2008-2011. The research is founded on the basis of four research questions that expose the following: 1) The characteristics of Competitive intelligence and its practice within pharmaceutical companies of Spain; 2) The contribution of the CI in the process of R&D in the pharmaceutical firms; 3) Enablings and inhibiting factors of innovation, patents and CI, in Spain; and 4) The influence of CI in the chain of product development in the pharmaceutical firms in Spain. The proposal of the methodology is established by considering the aforementioned background and disciplines from which this research is based, espefically CI, R&D+i and patents. First of all, through the stages of the CI cycle, planning, evaluation of sources, information gathering, data processing, analysis (qualitative techniques) and results three work phases were established to conduct the research methodology, 1) a database of 200 pharmaceutical companies was created including fields to be filled about general data, innovation, therapies, and so on. 2) the implementation of a survey of 155 companies with open-ended questions on the themes of R&D, innovation, industrial property, CI and other questions. Finally, 3) a patents analysis though "Matheo Patent software" to identify business leaders, countries, inventors, technology, patent officess, etc. Results indicate the use of the CI in pharmaceutical firms even if the steps of the methodology are often not applied in structured form. Large enterprises give more attention to this type of activities, while SMEs lean towards other interests on the operations, on small innovations found on the way. Among the main perceived needs, it is highlighted the lack of investment in R&D, because the development of innovative new drug is long, expensive and with a rate of slow and uncertain recovery. 25% of pharmaceutical firms performing R&D, record a low rate of innovation, but the market for generic drugs and beauty products increases gradually. It was noted that a variety of information sources and tools for information on the area of interest, with the aim of providing a competitive advantage over the competition. However, there are also factors that impede the efficient and continuous development of the IC as a tool for innovation, since those are processes that must adapt to the changing political, social and cultural environmen as it is the case of research for innovative products and services that pharmaceuticl firms can provide to society. Finally and in the vace of the many possibilities the pharmaceutical industry provides, future research lines are proposed: Knowledge management (KM) to check the status of the company through the transmission of information and skills to their employees, while the external knowledge will indicate what happens in the market; patent analysis to identify whether what has been patented in the last 5-7 years, is still in the market as well as checking product whose patent is about to get due.Esta investigación se enfoca en el uso y práctica de la inteligencia competitiva dentro del sector farmacéutico español como una herramienta para ser utilizada en la toma de decisiones. Para ello, es necesario realizar cada paso de la metodología de IC, con la finalidad de identificar puntos fuertes y débiles de las empresas competidoras y las propias para planear las estrategias en beneficio y crecimiento de la industria farmacéutica en España. Esto es para: laboratorios y empresas indistintamente del origen de su procedencia, es decir, empresas nacionales y extranjeras afiliadas a Farmaindustria y al Plan Profarma en el periodo 2008-2011. La investigación se realizó a partir de cuatro preguntas de investigación que exponen lo siguiente: 1) las características de la inteligencia competitiva y sus prácticas dentro de las empresas farmacéuticas de España; 2) la contribución de la IC en el proceso de I+D en las farmacéuticas; 3) los factores facilitadores e inhibidores de innovación, de patentes y de IC en las farmacéuticas en España, así como los de la IC; y, 4) la influencia que tiene la IC en la cadena de desarrollo de productos en las firmas farmacéuticas de España. El planteamiento de la metodología se establece al considerar antecedentes expuestos y disciplinas en las que se base esta investigación, concretamente la IC, I+D+i y patentes. En primer lugar, a través de las etapas del ciclo de la IC, planeación, evaluación de fuentes, obtención de información, procesamiento de datos, análisis (técnicas cualitativas) y, resultados. Para llevar a cabo la metodología en la investigación, se establecieron tres fases de trabajo, 1) se realizó una base de datos de 200 empresas farmacéuticas que incluye campos a documentar sobre datos generales, innovación, terapias, etc. 2) aplicación de una encuesta a 155 empresas con preguntas abiertas y cerradas con temas de I+D, innovación, propiedad industrial, IC, y otros. Por último, 3) un análisis de patentes mediante en software "Matheo Patent", para identificar líderes de empresas, países, inventores, tecnologías, oficinas de patentes, etc. Los resultados indican el uso de la IC en las farmacéuticas que aunque realizan los pasos de la metodología, no suelen aplicarse en forma estructurada. Sin embargo, se distingue que las grandes empresas tienen más atención a este tipo de actividades, mientras que las pymes se inclinan hacia otros intereses de las operaciones, al igual que de las pequeñas innovaciones que van descubriendo. Entre las principales necesidades observadas, destaca la falta de inversión a la I+D, debido a que el desarrollo de nuevos fármacos innovadores son de larga duración, costosos y con una tasa de recuperación lenta e incierta. El 25% de las farmacéuticas que realizan I+D, registran un bajo índice de innovación, sin embargo el mercado para medicamentos genéricos y parafarmacia se incrementa de forma gradual. Con lo anterior se observó que existe una variedad de fuentes de información y herramientas para obtener información sobre el sector de interés, con el objetivo de proporcionar una ventaja frente la competencia. No obstante, también hay factores que impiden el desarrollo eficiente y continuo de la IC como herramienta la de Innovación, y son procesos que deben adaptarse al cambiante entorno político, social y cultural. Como es el caso de la investigación para productos y servicios innovadores que puedan ofrecer las farmacéutica a la sociedad. Para finalizar y frente a muchas posibilidades que ofrece la industria farmacéutica, se proponen futuros trabajos de investigación:la gestión del Conocimiento (GC) para conocer el status de la empresa a través de la transmisión de información y habilidades a sus empleados, mientras que el conocimiento externo indicará lo que ocurre en el mercado; el análisis de patentes para identificar si lo que se ha patentado en los últimos 5-7 años, está en el mercado al igual que los próximos productos a caducar la patent