@article {10.3897/zookeys.150.2193,
	title = {Scratchpads 2.0: a Virtual Research Environment supporting scholarly collaboration, communication and data publication in biodiversity science},
	journal = {ZooKeys},
	volume = {150},
	year = {2011},
	month = {28/11/2011},
	pages = {53{\textendash}70},
	publisher = {Pensoft Publishers},
	abstract = {<p> 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\&rsquo;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. </p>},
	keywords = {biodiversity, database, e-infrastructure, Taxonomy, Virtual Research Environment},
	doi = {10.3897/zookeys.150.2193},
	url = {http://dx.doi.org/10.3897/zookeys.150.2193},
	author = {Smith, Vincent and Rycroft, Simon and Brake, Irina and Scott, Ben and Baker, Ed and Livermore, Laurence and Vladimir A. Blagoderov and Roberts, David}
}
@article {44529,
	title = {Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples},
	journal = {ZooKeys},
	volume = {50},
	year = {2010},
	month = {30/06/2010},
	pages = {1-16},
	abstract = {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{\textquoteright}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.},
	keywords = {semantic enhancements, Semantic tagging, Systematics, Taxonomy},
	doi = {10.3897/zookeys.50.538},
	url = {http://pensoftonline.net/zookeys/index.php/journal/article/view/538/474},
	author = {Penev, Lyubomir and Agosti, Donat and Georgiev, Teodor and Catapano, Terrence and Miller, Jeremy and Vladimir A. Blagoderov and Roberts, David and Smith, Vincent and Brake, Irina and Rycroft, Simon and Scott, Ben and Johnson, Norman F. and Morris, Robert A. and Sautter, Guido and Chavan, Vishwas and Robertson, Tim and Remsen, David and Stoev, Pavel and Parr, Cynthia and Knapp, Sandra and Kress, W. John and Thompson, F. Christian and Erwin, Terry}
}
@article {44492,
	title = {Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys},
	journal = {ZooKeys},
	volume = {50},
	year = {2010},
	month = {30/06/2010},
	pages = {17-28},
	abstract = {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.},
	keywords = {ICBN, ICZN, Nomenclature, Online publishing, Taxonomy},
	doi = {10.3897/zookeys.50.539},
	url = {http://pensoftonline.net/zookeys/index.php/journal/article/view/539/473},
	author = {Vladimir A. Blagoderov and Brake, Irina and Georgiev, Teodor and Penev, Lyubomir and Roberts, Dave and Rycroft, Simon and Scott, Ben and Agosti, Donat and Catapano, Terrence and Smith, Vincent}
}
