ALBERT

Description: Publishing taxonomic and systematics studies in the digital era faces major challenges and requires new approaches, many of which are currently stimulating spirited discussions amongst taxonomists and systematists. New amendments to the International Code of Zoological Nomenclature are expected to regulate electronic publishing of new taxa and create a standard form for their registration (ZooBank). Responding to a perceived need, this editorial announces establishment of ZooKeys \xc3\xa2\xc2\x80\xc2\x93 a new online and print journal in zoological taxonomy and systematics, which aims to quickly respond and adapt to the newest developments in taxonomic publishing. Open Access is accepted as mandatory for ZooKeys. The rationale for and concept of ZooKeys is discussed in detail.

Description: 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\xe2\x80\x99s 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, fi ne-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.

Description: Taxonomy is a fundamental science that provides the scaffolding for biology. But the true value of taxonomic data remains unrealized because basic biodiversity information remains fragmented and unevenly accessible. Taxonomy helps us recognize species and map their distributions by generating text descriptions, images, and records of when and where they have been observed. Current rates of species extinction, habitat loss, and climate change mean that taxonomy has never been more relevant. Biodiversity is one of the most information-rich fields of human knowledge, but advances in basic cybertaxonomic infrastructure have only recently provided the tools to organize biodiversity information in ways that respond to a wide range of user groups, including ecologists, land managers, and interested citizens, not to mention the benefits of readily accessible information to the global taxonomic community. The call to revitalize taxonomy by embracing the internet has been sounded for more than a decade. The time is ripe to significantly increase the volume of taxonomic information freely available online. But simply posting information online will not automatically reinvigorate taxonomy. There are myriad online sites dedicated to particular taxa or projects. These are useful to users interested in questions within the site\xe2\x80\x99s domains. But the greater potential lies in mechanisms for aggregating primary source data in ways that allow users to filter and recombine data easily and flexibly for whatever purposes they imagine.