http://precedings.nature.com/tags/taxonomy Recently posted documents tagged with 'taxonomy' 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.2009.3620.1 Background/Question/MethodsThe Biodiversity Heritage Library (BHL; http://www.biodiversitylibrary.org/), one of the cornerstones of the Encyclopedia of Life (eol.org), now contains nearly 13 million digitized pages of 12,000 titles comprised of 32,000 volumes of the published literature of biodiversity held in the collections of major natural history libraries. The BHL has made this literature available for open access and responsible use as a part of a global “biodiversity commons.” The BHL partnership is working with the global taxonomic community, publishers, organizations such as JSTOR and BIOONE, and the Internet Archive, to ensure that the biodiversity literature is available to all, from students to scientists with diverse interests.This poster will describe the BHL with particular focus on the taxonomic tools available and the development of international partnerships and expanded collaborations with scientists. BHL-Europe has now formed and participation by other countries and projects will augment the available literature and provide redundant repositories and mirror sites. New tools such as the PDF-generator, article repository, updated search interface and social networking tools will be reviewed. Results/ConclusionsThe BHL Portal is a transformative research environment for scientific inquiry. The tools and information in the BHL have accelerated research in life sciences. Users reach the BHL through a free, service-based portal formed by coupling existing databases with digitized, searchable images and OCR text. The array of tools for taxonomically intelligent services has expanded. These tools are designed to overcome the problem of common name versus scientific name and changes of names over time and provide easy access to the available literature on a particular organism. This scientific reference system for investigating literature offers a model that reflects, and also amplifies, scientists’ use of the natural history literature. In 2008, name finding statistics showed that 30 million name string occurrences were extracted from the BHL with 4.4 million of these being unique. Of these, 23.7 million have been verified by NameBank. Enhancement of OCR tools or manual text correction is crucial to the further development of data mining. Social networking tools may be utilized to expand OCR text correction to users and for tagging maps and illustrations. Scientists are providing bibliographies for taxonomic groups that can be incorporated into the selection process. Organizations have offered already digitized articles for deposit to the BHL. Hence, an article repository has been developed together with tools to extract pages of text, from BHL content (PDF-generator). http://dx.doi.org/10.1038/npre.2009.3620.1 Mon, 17 Aug 2009 09:21:29 UTC BHL, The Biodiversity Heritage Library: An Expanding International Collaboration doi:10.1038/npre.2009.3620.1 2009-08-18 Constance Rinaldo Nature Precedings 2009-08-17T09:21:29Z Poster Ecology Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3372.1 The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic name strings from the BHL corpus, as well as suggestions for improvement. http://dx.doi.org/10.1038/npre.2009.3372.1 Fri, 26 Jun 2009 15:25:21 UTC An evaluation of taxonomic name finding & next steps in Biodiversity Heritage Library (BHL) developments doi:10.1038/npre.2009.3372.1 2009-06-26 Chris Freeland Nature Precedings 2009-06-26T15:25:21Z Presentation Bioinformatics Earth & Environment 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://dx.doi.org/10.1038/npre.2008.1780.1 The goal of this workshop was to agree on a general strategy for developing a systematic, useful, and scientifically appropriate framework for neuroanatomical nomenclature. The workshop focused on general principles that will serve as a basis for future decisions on implementation strategies. The report discusses the problems arising from the use of different parcellation schemes and use of different terminologies and highlights the need of a universal vocabulary for describing the structural organization of the nervous system. Workshop participants encourage the creation of an International Coordinating Committee for Neuroanatomical Nomenclature and propose short- and long-term goals for such a committee. http://dx.doi.org/10.1038/npre.2008.1780.1 Tue, 08 Apr 2008 17:23:59 UTC 1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy doi:10.1038/npre.2008.1780.1 2008-04-08 Mihail Bota Nature Precedings 2008-04-08T17:23:59Z Manuscript Neuroscience Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/1760/version/1 A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers. http://precedings.nature.com/documents/1760/version/1 Thu, 03 Apr 2008 20:10:36 UTC Biodiversity informatics: the challenge of linking data and the role of shared identifiers hdl:10101/npre.2008.1760.1 2008-04-03 Roderic Page Nature Precedings 2008-04-03T20:10:36Z Manuscript Ecology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2007.1028.1 This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals. http://dx.doi.org/10.1038/npre.2007.1028.1 Tue, 18 Sep 2007 11:42:40 UTC Towards a Taxonomically Intelligent Phylogenetic Database doi:10.1038/npre.2007.1028.1 2009-03-04 Roderic Page Nature Precedings 2007-09-18T11:42:40Z Manuscript Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/2.5/