ZooKeys

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Publications

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Title Author(s) Keyword(s) Language DateThis property is a special property in this wiki. Abstract R C
Creative Commons licenses and the non-commercial condition Daniel Mietchen
Robert A. Morris
Donat Agosti
Lyubomir Penev
Walter G. Berendsohn
Donald Hobern
English 28 November 2011 The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works. 0 0
A review of the millipede genus Sinocallipus Zhang, 1993 (Diplopoda, Callipodida, Sinocallipodidae), with notes on gonopods monotony vs. peripheral diversity in millipedes Pavel Stoev
Enghoff H.
Caves
Functional anatomy
Gonopod monotony
Identification key
Pensoft Wiki Convertor
Sinocallipus
Southeast Asia
Troglomorphism
English 2011 The millipede genus Sinocallipus is reviewed, with four new cave-dwelling species, S. catba, S. deharvengi, S. jaegeri and S. steineri, being described from caves in Laos and Vietnam. With the new records the number of species in the genus reaches six and the genus range is extended to Central Vietnam and North and Central Laos. Both, S. jaegeri from Khammouan Province in Laos and S. simplipodicus Zhang, 1993 from Yunnan, China, show high level of reduction of eyes, which has not been recorded in other Callipodida. Peripheral characters such as the relative lengths of antennomeres, the number of ocelli, the number of pleurotergites or even the shape of paraprocts and the coloration seem to provide more information for the distinction of the species than do the relatively uniform gonopods. The diff erences in gonopods mainly concern the shape and length of cannula, the length and shape of coxal processes g and k, and the number of the acicular projections of the femoroid. An explanation is offered for the function of the trochanteral lobe of 9 th leg-pair. It provides mechanical support for the cannula and seems to assist sperm charge and insemination during copulation. An identification key to the species in the genus is produced to accommodate the new species. The new species descriptions were automatically exported at the time of publication to a wiki (www.species-id.net) through a specially designed software tool, the Pensoft Wiki Convertor (PWC), implemented here for the first time together with a newly proposed citation mechanism for simultaneous journal/wiki publications. © P. Stoev, H. Enghoff. 0 0
A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini) Lars Hendrich
Michael Balke
Wiki
Species ID
Online species pages
Cox1
Sequence data
DNA barcoding
Molecular biodiversity assessment
English 2011 Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species' taxonomy and biology. The diving beetle Neobidessodes darwiniensis sp. n. (Coleoptera: Dytiscidae, Bidessini) is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea. 0 1
Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID Lyubomir Penev
Gregor Hagedorn
Daniel Mietchen
Teodor Georgiev
Pavel Stoev
Guido Sautter
Donat Agosti
Andreas Plank
Michael Balke
Lars Hendrich
Terry Erwin
English 2011 Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors. 9 0
Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples Lyubomir Penev
Donat Agosti
Teodor Georgiev
Terry Catapano
Jeremy Miller
Vladimir Blagoderov
David Roberts
Vincent Smith
Irina Brake
Simon Ryrcroft
Ben Scott
Norman Johnson
Robert Morris
Guido Sautter
Vishwas Chavan
Tim Robertson
David Remsen
Pavel Stoev
Cynthia Parr
Sandra Knapp
W. John Kress
Chris Thompson
Terry Erwin
Semantic tagging
Semantic enhancements
Systematics
Taxonomy
English June 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 XML-tagged 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. 0 1