TY - JOUR T1 - No specimen left behind: industrial scale digitization of natural history collections JF - ZooKeys Y1 - 2012 DO - 10.3897/zookeys.209.3178 A1 - Vladimir A. Blagoderov A1 - Kitching, Ian A1 - Livermore, Laurence A1 - Simonsen, Thomas A1 - Smith, Vincent SP - 133–146 L2 - 50498 L3 - 51996 VL - 209 UR - http://www.pensoft.net/journals/zookeys/article/3178/abstract/no-specimen-left-behind-industrial-scale-digitization-of-natural-history-collections ER - TY - JOUR T1 - Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science JF - ZooKeys Y1 - 2011 DO - 10.3897/zookeys.150.2193 A1 - Smith, Vincent A1 - Rycroft, Simon A1 - Brake, Irina A1 - Scott, Ben A1 - Baker, Ed A1 - Livermore, Laurence A1 - Vladimir A. Blagoderov A1 - Roberts, David SP - 53–70 KW - biodiversity KW - database KW - e-infrastructure KW - Taxonomy KW - Virtual Research Environment AB -

The Scratchpad Virtual Research Environment (http://scratchpads.eu/) is a flexible system for people to create their own research networks supporting natural history science. Here we describe Version 2 of the system characterised by the move to Drupal 7 as the Scratchpad core development framework and timed to coincide with the fifth year of the project’s operation in late January 2012. The development of Scratchpad 2 reflects a combination of technical enhancements that make the project more sustainable, combined with new features intended to make the system more functional and easier to use. A roadmap outlining strategic plans for development of the Scratchpad project over the next two years concludes this article.

L2 - 48313 L3 - 49525 PB - Pensoft Publishers VL - 150 UR - http://dx.doi.org/10.3897/zookeys.150.2193 ER - TY - JOUR T1 - Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples JF - ZooKeys Y1 - 2010 DO - 10.3897/zookeys.50.538 A1 - Penev, Lyubomir A1 - Agosti, Donat A1 - Georgiev, Teodor A1 - Catapano, Terrence A1 - Miller, Jeremy A1 - Vladimir A. Blagoderov A1 - Roberts, David A1 - Smith, Vincent A1 - Brake, Irina A1 - Rycroft, Simon A1 - Scott, Ben A1 - Johnson, Norman F. A1 - Morris, Robert A. A1 - Sautter, Guido A1 - Chavan, Vishwas A1 - Robertson, Tim A1 - Remsen, David A1 - Stoev, Pavel A1 - Parr, Cynthia A1 - Knapp, Sandra A1 - Kress, W. John A1 - Thompson, F. Christian A1 - Erwin, Terry SP - 1 EP - 16 KW - semantic enhancements KW - Semantic tagging KW - Systematics KW - Taxonomy AB - Th e concept of semantic tagging and its potential for semantic enhancements to taxonomic papers is outlined and illustrated by four exemplar papers published in the present issue of ZooKeys. The four papers were created in different ways: (i) written in Microsoft Word and submitted as non-tagged manuscript (doi: 10.3897/zookeys.50.504); (ii) generated from Scratchpads and submitted as XMLtagged manuscripts (doi: 10.3897/zookeys.50.505 and doi: 10.3897/zookeys.50.506); (iii) generated from an author’s database (doi: 10.3897/zookeys.50.485) and submitted as XML-tagged manuscript. XML tagging and semantic enhancements were implemented during the editorial process of ZooKeys using the Pensoft Mark Up Tool (PMT), specially designed for this purpose. The XML schema used was TaxPub, an extension to the Document Type Definitions (DTD) of the US National Library of Medicine Journal Archiving and Interchange Tag Suite (NLM). The following innovative methods of tagging, layout, publishing and disseminating the content were tested and implemented within the ZooKeys editorial workflow: (1) highly automated, fine-grained XML tagging based on TaxPub; (2) final XML output of the paper validated against the NLM DTD for archiving in PubMedCentral; (3) bibliographic metadata embedded in the PDF through XMP (Extensible Metadata Platform); (4) PDF uploaded after publication to the Biodiversity Heritage Library (BHL); (5) taxon treatments supplied through XML to Plazi; (6) semantically enhanced HTML version of the paper encompassing numerous internal and external links and linkouts, such as: (i) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, localities, etc.); (ii) internal cross-linking between paper sections, citations, references, tables, and figures; (iii) mapping of localities listed in the whole paper or within separate taxon treatments; (v) taxon names autotagged, dynamically mapped and linked through the Pensoft Taxon Profile (PTP) to large international database services and indexers such as Global Biodiversity Information Facility (GBIF), National Center for Biotechnology Information (NCBI), Barcode of Life (BOLD), Encyclopedia of Life (EOL), ZooBank, Wikipedia, Wikispecies, Wikimedia, and others; (vi) GenBank accession numbers autotagged and linked to NCBI; (vii) external links of taxon names to references in PubMed, Google Scholar, Biodiversity Heritage Library and other sources. With the launching of the working example, ZooKeys becomes the first taxonomic journal to provide a complete XML-based editorial, publication and dissemination workfl ow implemented as a routine and cost-efficient practice. It is anticipated that XML-based workflow will also soon be implemented in botany through PhytoKeys, a forthcoming partner journal of ZooKeys. The semantic markup and enhancements are expected to greatly extend and accelerate the way taxonomic information is published, disseminated and used. L2 - 44529 L3 - 45349 VL - 50 UR - http://pensoftonline.net/zookeys/index.php/journal/article/view/538/474 ER - TY - JOUR T1 - Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys JF - ZooKeys Y1 - 2010 DO - 10.3897/zookeys.50.539 A1 - Vladimir A. Blagoderov A1 - Brake, Irina A1 - Georgiev, Teodor A1 - Penev, Lyubomir A1 - Roberts, Dave A1 - Rycroft, Simon A1 - Scott, Ben A1 - Agosti, Donat A1 - Catapano, Terrence A1 - Smith, Vincent SP - 17 EP - 28 KW - ICBN KW - ICZN KW - Nomenclature KW - Online publishing KW - Taxonomy AB - We describe a method to publish nomenclatural acts described in taxonomic websites (Scratchpads) that are formally registered through publication in a printed journal (ZooKeys). This method is fully compliant with the zoological nomenclatural code. Our approach supports manuscript creation (via a Scratchpad), electronic act registration (via ZooBank), online and print publication (in the journal ZooKeys) and simultaneous dissemination (ZooKeys and Scratchpads) for nomenclatorial acts including new species descriptions. The workflow supports the generation of manuscripts directly from a database and is illustrated by two sample papers published in the present issue. L2 - 44492 L3 - 45351 VL - 50 UR - http://pensoftonline.net/zookeys/index.php/journal/article/view/539/473 ER -