00679nas a2200169 4500008004100000022002500041245009000066210006900156300001400225490000800239100002900247700001800276700002400294700002100318700001900339856015100358 2012 eng d a1313-2970, 1313-298900aNo specimen left behind: industrial scale digitization of natural history collections0 aNo specimen left behind industrial scale digitization of natural a133–1460 v2091 aBlagoderov, Vladimir, A.1 aKitching, Ian1 aLivermore, Laurence1 aSimonsen, Thomas1 aSmith, Vincent uhttp://www.pensoft.net/journals/zookeys/article/3178/abstract/no-specimen-left-behind-industrial-scale-digitization-of-natural-history-collections01636nas a2200277 4500008004100000245014700041210006900188260003500257300001200292490000800304520074600312653001701058653001301075653002101088653001301109653003301122100001901155700001901174700001701193700001501210700001401225700002401239700002901263700001901292856004701311 2011 eng d00aScratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science0 aScratchpads 20 a Virtual Research Environment supporting scholar bPensoft Publishersc28/11/2011 a53–700 v1503 a
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.
10abiodiversity10adatabase10ae-infrastructure10aTaxonomy10aVirtual Research Environment1 aSmith, Vincent1 aRycroft, Simon1 aBrake, Irina1 aScott, Ben1 aBaker, Ed1 aLivermore, Laurence1 aBlagoderov, Vladimir, A.1 aRoberts, David uhttp://dx.doi.org/10.3897/zookeys.150.219301394nas a2200217 4500008004100000245013900041210006900180260001500249300001000264490000700274520069200281653001100973653001700984653001301001653001401014653001301028100002901041700001801070700001201088856007601100 2010 eng d00aParisognoriste, a new genus of Lygistorrhinidae (Diptera: Sciaroidea) from the Oise amber with redescription of Palaeognoriste Meunier0 aParisognoriste a new genus of Lygistorrhinidae Diptera Sciaroide c30/06/2010 a79-900 v503 aA new genus and a new species of Lygistorrhinidae, Parisognoriste eocenica is described from the Eocene Oise amber of the Paris Basin. Palaeognoriste sciariforme Meunier, 1904 and Palaeognoriste affine Meunier, 1912 are re-described. Lectotypes are designated for both species of Palaeognoriste. The phylogenetic positions of the new genus and Palaeognoriste Meunier are discussed. The paper is an example demonstrating a new approach in cybertaxonomy including automatic generation of manuscript within Virtual Research Environment (Scratchpads), semantic enhancements, and parallel release of the publication on paper and on-line accompanied with registration of new taxa with ZooBank.10aEocene10afossil resin10aNew taxa10aphylogeny10aTaxonomy1 aBlagoderov, Vladimir, A.1 aHippa, Heikki1 aNel, A. uhttp://pensoftonline.net/zookeys/index.php/journal/article/view/506/47204271nas a2200445 4500008004100000245009800041210006900139260001500208300000900223490000700232520298200239653002603221653002103247653001603268653001303284100002003297700001803317700002103335700002303356700001903379700002903398700001903427700001903446700001703465700001903482700001503501700002403516700002303540700001903563700002003582700001903602700001803621700001703639700001803656700001803674700001603692700002403708700001703732856007603749 2010 eng d00aSemantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples0 aSemantic tagging of and semantic enhancements to systematics pap c30/06/2010 a1-160 v503 aTh 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.10asemantic enhancements10aSemantic tagging10aSystematics10aTaxonomy1 aPenev, Lyubomir1 aAgosti, Donat1 aGeorgiev, Teodor1 aCatapano, Terrence1 aMiller, Jeremy1 aBlagoderov, Vladimir, A.1 aRoberts, David1 aSmith, Vincent1 aBrake, Irina1 aRycroft, Simon1 aScott, Ben1 aJohnson, Norman, F.1 aMorris, Robert, A.1 aSautter, Guido1 aChavan, Vishwas1 aRobertson, Tim1 aRemsen, David1 aStoev, Pavel1 aParr, Cynthia1 aKnapp, Sandra1 aKress, John1 aThompson, Christian1 aErwin, Terry uhttp://pensoftonline.net/zookeys/index.php/journal/article/view/538/47401554nas a2200301 4500008004100000245008700041210006900128260001500197300001000212490000700222520067800229653000900907653000900916653001700925653002200942653001300964100002900977700001701006700002101023700002001044700001801064700001901082700001501101700001801116700002301134700001901157856007601176 2010 eng d00aStreamlining taxonomic publication: a working example with Scratchpads and ZooKeys0 aStreamlining taxonomic publication a working example with Scratc c30/06/2010 a17-280 v503 aWe 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.10aICBN10aICZN10aNomenclature10aOnline publishing10aTaxonomy1 aBlagoderov, Vladimir, A.1 aBrake, Irina1 aGeorgiev, Teodor1 aPenev, Lyubomir1 aRoberts, Dave1 aRycroft, Simon1 aScott, Ben1 aAgosti, Donat1 aCatapano, Terrence1 aSmith, Vincent uhttp://pensoftonline.net/zookeys/index.php/journal/article/view/539/473