http://precedings.nature.com/tags/biodiversity%20informatics Recently posted documents tagged with 'biodiversity informatics' 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.2009.3372.1 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://precedings.nature.com/documents/3173/version/1 Although the Web has transformed science publishing, scientific papers themselves are still essentially “black boxes”, with much of their content intended for human readers only. Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical coordinates, publishers could greatly increase the scientific value of their digital content. At the same time this will provide novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic citation.As a proof of concept, my entry in the Elsevier Grand Challenge extracted extended metadata from a set of articles from the journal Molecular Phylogeny and Evolution and used it to populate a entity-attribute-value database. A simple web interface to this database enables an enhanced display of the content of an article, including a map of localities mentioned either explicitly or implicitly (through links to geotagged data), taxonomic coverage, and both data and citation links. Metadata extraction was limited to information listed in tables in the articles (such as GenBank sequences and specimen codes), the body of the article wasn’t used. This restriction was deliberate, in order to demonstrate that making extended metadata available doesn’t require a journal’s publisher to make the full-text freely available (although this is desirable for other reasons). http://precedings.nature.com/documents/3173/version/1 Fri, 24 Apr 2009 17:31:02 UTC Enhanced display of scientific articles using extended metadata hdl:10101/npre.2009.3173.1 2009-04-24 Roderic D. M. Page Nature Precedings 2009-04-24T17:31:02Z Manuscript Ecology Bioinformatics Evolutionary Biology http://creativecommons.org/licenses/by/3.0/ http://precedings.nature.com/documents/3079/version/1 Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. bioGUID is available at http://bioguid.info/. Source code is available from Google Code. http://precedings.nature.com/documents/3079/version/1 Fri, 17 Apr 2009 21:01:04 UTC bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics hdl:10101/npre.2009.3079.1 2009-04-17 Roderic Page Nature Precedings 2009-04-17T21:01:04Z Manuscript 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/