41,591 research outputs found

    Challenges of the next decade for the Asia Pacific region: 2010 International Conference in Bioinformatics (InCoB 2010)

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    The 2010 annual conference of the Asia Pacific Bioinformatics Network (APBioNet), Asia’s oldest bioinformatics organisation formed in 1998, was organized as the 9th International Conference on Bioinformatics (InCoB), Sept. 26-28, 2010 in Tokyo, Japan. Initially, APBioNet created InCoB as forum to foster bioinformatics in the Asia Pacific region. Given the growing importance of interdisciplinary research, InCoB2010 included topics targeting scientists in the fields of genomic medicine, immunology and chemoinformatics, supporting translational research. Peer-reviewed manuscripts that were accepted for publication in this supplement, represent key areas of research interests that have emerged in our region. We also highlight some of the current challenges bioinformatics is facing in the Asia Pacific region and conclude our report with the announcement of APBioNet’s 100 BioDatabases (BioDB100) initiative. BioDB100 will comply with the database criteria set out earlier in our proposal for Minimum Information about a Bioinformatics and Investigation (MIABi), setting the standards for biocuration and bioinformatics research, on which we will report at the next InCoB, Nov. 27 – Dec. 2, 2011 at Kuala Lumpur, Malaysia

    Nanoinformatics: developing new computing applications for nanomedicine

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    Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended ?nanotype? to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others

    Establishment of computational biology in Greece and Cyprus: Past, present, and future.

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    We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

    National Mesothelioma Virtual Bank: A standard based biospecimen and clinical data resource to enhance translational research

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    Background: Advances in translational research have led to the need for well characterized biospecimens for research. The National Mesothelioma Virtual Bank is an initiative which collects annotated datasets relevant to human mesothelioma to develop an enterprising biospecimen resource to fulfill researchers' need. Methods: The National Mesothelioma Virtual Bank architecture is based on three major components: (a) common data elements (based on College of American Pathologists protocol and National North American Association of Central Cancer Registries standards), (b) clinical and epidemiologic data annotation, and (c) data query tools. These tools work interoperably to standardize the entire process of annotation. The National Mesothelioma Virtual Bank tool is based upon the caTISSUE Clinical Annotation Engine, developed by the University of Pittsburgh in cooperation with the Cancer Biomedical Informatics Grid™ (caBIG™, see http://cabig.nci.nih.gov). This application provides a web-based system for annotating, importing and searching mesothelioma cases. The underlying information model is constructed utilizing Unified Modeling Language class diagrams, hierarchical relationships and Enterprise Architect software. Result: The database provides researchers real-time access to richly annotated specimens and integral information related to mesothelioma. The data disclosed is tightly regulated depending upon users' authorization and depending on the participating institute that is amenable to the local Institutional Review Board and regulation committee reviews. Conclusion: The National Mesothelioma Virtual Bank currently has over 600 annotated cases available for researchers that include paraffin embedded tissues, tissue microarrays, serum and genomic DNA. The National Mesothelioma Virtual Bank is a virtual biospecimen registry with robust translational biomedical informatics support to facilitate basic science, clinical, and translational research. Furthermore, it protects patient privacy by disclosing only de-identified datasets to assure that biospecimens can be made accessible to researchers. © 2008 Amin et al; licensee BioMed Central Ltd

    Integrating Emerging Areas of Nursing Science into PhD Programs

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    The Council for the Advancement of Nursing Science aims to “facilitate and recognize life-long nursing science career development” as an important part of its mission. In light of fast-paced advances in science and technology that are inspiring new questions and methods of investigation in the health sciences, the Council for the Advancement of Nursing Science convened the Idea Festival for Nursing Science Education and appointed the Idea Festival Advisory Committee to stimulate dialogue about linking PhD education with a renewed vision for preparation of the next generation of nursing scientists. Building on the 2010 American Association of Colleges of Nursing Position Statement “The Research-Focused Doctoral Program in Nursing: Pathways to Excellence,” Idea Festival Advisory Committee members focused on emerging areas of science and technology that impact the ability of research-focused doctoral programs to prepare graduates for competitive and sustained programs of nursing research using scientific advances in emerging areas of science and technology. The purpose of this article is to describe the educational and scientific contexts for the Idea Festival, which will serve as the foundation for recommendations for incorporating emerging areas of science and technology into research-focused doctoral programs in nursing

    Large-scale event extraction from literature with multi-level gene normalization

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    Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license
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