04271nas 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/538/474