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Blagoderov V.,Natural History Museum in London | Brake I.,Natural History Museum in London | Georgiev T.,Pensoft Publishers | Penev L.,Bulgarian Academy of Science | And 6 more authors.
ZooKeys | Year: 2010

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. © Vladimir Blagoderov et al. Source


Stoev P.,National Museum of Natural History | Akkari N.,Institute Superieur Des Science Biologiques Appliquees Of Tunis | Zapparoli M.,University of Tuscia | Porco D.,University of Guelph | And 4 more authors.
ZooKeys | Year: 2010

The centipede genus Eupolybothrus Verhoeff, 1907 in North Africa is revised. A new cavernicolous species, E. kahfi Stoev & Akkari, sp. n., is described from a cave in Jebel Zaghouan, northeast Tunisia. Morphologically, it is most closely related to E. nudicornis (Gervais, 1837) from North Africa and Southwest Europe but can be readily distinguished by the long antennae and leg-pair 15, a conical dorso-median protuberance emerging from the posterior part of prefemur 15, and the shape of the male fi rst genital sternite. Molecular sequence data from the cytochrome c oxidase I gene (mtDNA-5' COI-barcoding fragment) exhibit 19.19% divergence between E. kahfi and E. nudicornis, an interspecifi c value comparable to those observed among four other species of Eupolybothrus which, combined with a low intraspecifi c divergence (0.3-1.14%), supports the morphological diagnosis of E. kahfi as a separate species. This is the fi rst troglomorphic myriapod to be found in Tunisia, and the second troglomorph lithobiomorph centipede known from North Africa. E. nudicornis is redescribed based on abundant material from Tunisia and its post-embryonic development, distribution and habitat preferences recorded. E. cloudsley-thompsoni Turk, 1955, a nominal species based on Tunisian type material, is placed in synonymy with E. nudicornis. To comply with the latest technological developments in publishing of biological information, the paper implements new approaches in cybertaxonomy, such as fi ne granularity XML tagging validated against the NLM DTD TaxPub for PubMedCentral and dissemination in XML to various aggregators (GBIF, EOL, Wikipedia), vizualisation of all taxa mentioned in the text via the dynamically created Pensoft Taxon Profi le (PTP) page, data publishing, georeferencing of all lo calities via Google Earth, and ZooBank, GenBank and MorphBank registration of datasets. An interactive key to all valid species of Eupolybothrus is made with DELTA software. © Pavel Stoev et al. Source


Arvanitidis C.,Hellenic Center for Marine Research | Faulwetter S.,Hellenic Center for Marine Research | Faulwetter S.,National and Kapodistrian University of Athens | Chatzigeorgiou G.,Hellenic Center for Marine Research | And 14 more authors.
ZooKeys | Year: 2011

This paper discusses the design and implementation of a citizen science pilot project, COMBER (Citizens' Network for the Observation of Marine Biodiv ERsity, http://www.comber.hcmr.gr, which has been initiated under the Vi BRANT EU e-infrastructure. It is designed and implemented for divers and snorkelers who are interested in participating in marine biodiversity citizen science projects. It shows the necessity of engaging the broader community in the marine biodiversity monitoring and research projects, networks and initiatives. It analyses the stakeholders, the industry and the relevant markets involved in diving activities and their potential to sustain these activities. The principles, including data policy and rewards for the participating divers through their own data, upon which this project is based are thoroughly discussed. The results of the users analysis and lessons learned so far are presented. Future plans include promotion, links with citizen science web developments, data publishing tools, and development of new scientific hypotheses to be tested by the data collected so far. Source


Penev L.,Bulgarian Academy of Science | Agosti D.,Plazi | Georgiev T.,Pensoft Publishers | Catapano T.,Plazi | And 21 more authors.
ZooKeys | Year: 2010

The 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 workflow 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. © Lyubomir Penev et al. Source


Hagedorn G.,Julius Kuhn Institute | Forstner K.U.,University of Wurzburg | Kubke M.F.,University of Auckland | Koltzenburg C.,Cellular Therapy and Transplantation | And 2 more authors.
Information Services and Use | Year: 2011

Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on Species ID - http://species-id.net; a wiki that hosts a prototype for wiki-based scholarly publishing - where it can be updated, expanded or otherwise improved. © 2011 - IOS Press and the authors. All rights reserved. Source

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