BackgroundFree and open access to primary biodiversity data is essential for informed decision-making to achieve conservation of biodiversity and sustainable development. However, primary biodiversity data are neither easily accessible nor discoverable. Among several impediments, one is a lack of incentives to data publishers for publishing of their data resources. One such mechanism currently lacking is recognition through conventional scholarly publication of enriched metadata, which should ensure rapid discovery of 'fit-for-use' biodiversity data resources.DiscussionWe review the state of the art of data discovery options and the mechanisms in place for incentivizing data publishers efforts towards easy, efficient and enhanced publishing, dissemination, sharing and re-use of biodiversity data. We propose the establishment of the 'biodiversity data paper' as one possible mechanism to offer scholarly recognition for efforts and investment by data publishers in authoring rich metadata and publishing them as citable academic papers. While detailing the benefits to data publishers, we describe the objectives, work flow and outcomes of the pilot project commissioned by the Global Biodiversity Information Facility in collaboration with scholarly publishers and pioneered by Pensoft Publishers through its journals Zookeys, PhytoKeys, MycoKeys, BioRisk, NeoBiota, Nature Conservation and the forthcoming Biodiversity Data Journal. We then debate further enhancements of the data paper beyond the pilot project and attempt to forecast the future uptake of data papers as an incentivization mechanism by the stakeholder communities.ConclusionsWe believe that in addition to recognition for those involved in the data publishing enterprise, data papers will also expedite publishing of fit-for-use biodiversity data resources. However, uptake and establishment of the data paper as a potential mechanism of scholarly recognition requires a high degree of commitment and investment by the cross-sectional stakeholder communities.

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.