http://precedings.nature.com/tags/open%20access Recently posted documents tagged with 'open access' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3229.1 Open access in particular and changes in on-line scholarship have the potential to impact biocuration which often involves translating information currently read in papers to knowledge that is found in a variety of biological resources. The implication of these changes in scholarly communication to the biocuration process will be discussed with references to our work and that of others. http://dx.doi.org/10.1038/npre.2009.3229.1 Fri, 08 May 2009 14:21:27 UTC Changes in Scholarly Communication and the Potential Impact on Biocuration doi:10.1038/npre.2009.3229.1 2009-05-08 Nature Precedings 2009-05-08T14:21:27Z Presentation Genetics & Genomics Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3200.1 Reactome (http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2921 human proteins, 2871 reactions and 4167 literature citations. This curated dataset is integrated with a functional interaction network assembled computationally from non-curated sources of information including protein-protein interactions, gene co-expression, and gene ontology annotations, providing access. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets.Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome’s data content and software can all be freely used and redistributed under open source terms. Reactome instances are cross-referenced to corresponding ones in databases including EntrezGene, OMIM, Ensembl, UniProt, the UCSC Genome Browser, KEGG, ChEBI, and Gene Ontology. http://dx.doi.org/10.1038/npre.2009.3200.1 Sun, 03 May 2009 15:44:21 UTC Reactome – a knowledgebase of human biological pathways doi:10.1038/npre.2009.3200.1 2009-05-07 Bijay Jassal Nature Precedings 2009-05-03T15:44:21Z Poster Chemistry Genetics & Genomics Immunology Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2083.1 Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitate innovation and how this openness can be achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that prevent others from effectively reusing data. Identifying a small number of restrictions allows one to quickly appreciate which databases are open. A checklist for data openness is proposed in order to assist database curators who wish to make their data more open to make sure they do so. http://dx.doi.org/10.1038/npre.2008.2083.1 Fri, 18 Jul 2008 13:51:08 UTC Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness doi:10.1038/npre.2008.2083.1 2008-07-18 Melanie Dulong de Rosnay Nature Precedings 2008-07-18T13:51:08Z Manuscript Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1808/version/1 This article examines the relationship between Open Access to the scholarly literature and innovation. It traces the ideas of “end to end” network principles in the Internet and the World Wide Web and applies them to the scholarly biomedical literature. And the article argues for the importance of relieving not just price barriers but permission barriers. http://precedings.nature.com/documents/1808/version/1 Fri, 25 Apr 2008 16:45:07 UTC The Control Fallacy: Why OA Out-Innovates the Alternative hdl:10101/npre.2008.1808.1 2008-04-29 John Wilbanks Nature Precedings 2008-04-25T16:45:07Z Manuscript Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1655.1 We give a short introduction to open science followed by an overview of Creative Commons and open source licenses. http://dx.doi.org/10.1038/npre.2008.1655.1 Tue, 04 Mar 2008 18:07:36 UTC The What, Why and How of openness in science doi:10.1038/npre.2008.1655.1 2008-03-04 Konrad U. Foerstner Nature Precedings 2008-03-04T18:07:36Z Presentation Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1526/version/1 Open Data (OD) is an emerging term in the process of defining how scientific data may be published and re-used without price or permission barriers. Scientists generally see published data as belonging to the scientific community, but many publishers claim copyright over data and will not allow its re-use without permission. This is a major impediment to the progress of scholarship in the digital age. This article reviews the need for Open Data, shows examples of why Open Data are valuable and summarizes some early initiatives in formalizing the right of access to and re-use of scientific data. http://precedings.nature.com/documents/1526/version/1 Fri, 18 Jan 2008 19:51:35 UTC Open Data in Science hdl:10101/npre.2008.1526.1 2008-01-18 Peter Murray-Rust Nature Precedings 2008-01-18T19:51:35Z Manuscript Biotechnology Chemistry Genetics & Genomics Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1225.1 This talk aims to give scientists an introduction to the concepts of openness, freedom and transparency and their applications (not only) for science. It covers the topics of open source, open formats, Creative Commons, open access, and open science/knowledge. A video of the talk is available on the author’s website. http://dx.doi.org/10.1038/npre.2007.1225.1 Fri, 12 Oct 2007 19:01:42 UTC A quick trip through openness, freedom and transparency doi:10.1038/npre.2007.1225.1 2007-10-12 Konrad U. Foerstner Nature Precedings 2007-10-12T19:01:42Z Presentation Bioinformatics http://creativecommons.org/licenses/by/2.5/