PhytoKeys launched!

Fast, Linked, and Open Access – the New Plant Taxonomy Journal PhytoKeys is Launched!

We are pleased to announce launch of the journal PhytoKeys ( and publication of its inaugural issue.

PhytoKeys builds upon the tremendous success of its sister journal ZooKeys ( and offers numerous innovative ways to publish and disseminate information on the taxonomy and ecology of plants (you may see the forum paper and journal’s poster for more details). The journal will provide mandatory inclusion in the publication of IPNI records for new taxonomic names and other nomenclatural activities. All new species will be supplied to the Encyclopedia of Life (EOL) simultaneously with publication of the article. The content of the article itself will be marked-up at the level of taxonomic descriptions, taxon names, citations and references, identification keys, geo-referenced localities, and other taxon information. All papers are open access and free to read, download, print, and distribute.

PhytoKeys is more than a journal. It is a linked environment built upon its own content management software. Linking is provided at the internal level (within an article, within the journal, or within the publishing platform of Pensoft ) and to external resources (GBIF, EOL, BHL, NCBI, Morphbank, IPNI, PLANTS, Tropicos, The Gymnosperm Database, Index Herbariorum, Wikipedia, Wikispecies, etc.) through a dynamic web profile of each taxon mentioned within a paper (sample)Geo-referenced localities can be mapped within taxon treatments or for the entire paper. The journal can be followed on Twitter, Facebook, Mendeley, and several other social networks.

PhytoKeys is published in four different formats: (1) high-resolution, full-color print version (2) PDF identical to the printed version; (3) HTML to provide links to external resources and semantic enhancements to published texts for interactive reading (sample); (4) XML version compatible to PubMedCentral archiving (based on TaxPub schema), thus providing a machine-readable copy to facilitate future data mining. Neither restriction nor charges are imposed on the use of color illustrations.

PhytoKeys will cover taxonomic treatments of angiosperms, gymnosperms, monilophytes, bryophytes, and algae. Papers on fungal and lichenological studies will be welcome to be submitted to the future MycoKeys (to be launched within a few months).

PhytoKeys will be announced and presented at the forthcoming Byosystematics 2011 Congress in Berlin (21-27 February 2010) and the XVIII International Botanical Congress in Melbourne, 23-30 July 2010, as well as at several other international botanical venues. Botanists and bioinformaticians are welcome to discuss innovative publishing projects and cooperation. Candidates who may wish to serve as subject editors are welcome to contact Dr John Kress (Smithsonian), or Dr Sandra Knapp (NHM London).

The journal charges modest article processing fees, available on the website. Charges for manuscripts submitted by the end of 2010 will be waived in order to offer every botanist the chance to test the efficiency and innovative approach to publication and distribution of taxonomic information in PhytoKeys!

We welcome your manuscript submissions.

W. John Kress (Editor in Chief), Sandra Knapp (Deputy Editor), De-Zhu Li (Deputy Editor), Susanne Renner Deputy Editor), and Lyubomir Penev (Managing Editor)

Pensoft launched a new publishing platform: TRIADA

The New Publishing Platform TRIADA Launched by Pensoft

On 1 November 2010, Pensoft Publishers launched their brand new, innovative, integrated platform for publishing, disseminating and marketing of printed books, e-books and open access journals. TRIADA provides a linked environment for content, authors, reviewers, editors and customers through four independent classifications (taxonomic, subject, geographical, and geological time scale) as well through tagging and semantic mark-up. TRIADA uses a one-time registration process which allows users to submit, review or edit manuscripts, to subscribe for E-mail and RSS alerts, and to purchase Pensoft’s products.

A strong point of TRIADA is the innovative platform for open access journal publishing based on its own online editorial management system and XML-based editorial workflow. A specially designed, Pensoft Markup Tool (PMT) provides semantic mark-up of journal content and export to various formats, e.g., XML files for archiving in PubMedCentral and to facilitate future data mining, a semantically-enhanced HTML version for interactive reading, and various XML exchange formats for upload on external aggregators.

The Pensoft Taxon Profile tool creates a real-time, dynamic web page for any taxonomic name mentioned in a journal article. The tool is also open for free external use at The platform is linked to social networks, such as Facebook, Twitter, Mendeley, CiteuLike and others.

The accounts of the users of the journals ZooKeys, BioRisk and of the previous Pensoft website have been automatically transferred to the new platform. Users may use their email addresses as username and ask for a new password to enter their registration profiles.

ZooKeys publishes articles of the future

On the eve of its second year’s birthday (4th of July 2008), ZooKeys published its jubilee issue No 50 ( This special editition demonstrates how integrating the traditional part of publication with the research and dissemination processes can deliver dramatic benefits by using semantic tagging and semantic enhancements ( Several novelties are described in the two forum papers and demonstrated in four exemplar papers:

The papers are published in four different formats: (1) high-resolution, full-colour print version, to satisfy the current requirements of the ICZN, as well as the readers who prefer hardcopy, and for the purposes of paper archiving; (2) PDF to provide an electronic version identical to the printed one, to be archived in BHL and PubMedCentral; (3) HTML to provide links to external resources and semantic enhancements to published texts for interactive reading, and (4) XML version based on the TaxPub extension to the National Library of Medicine’s DTD ( to provide archiving document format for PubMedCentral and a machine-readable copy of the contents to facilitate future data mining (e.g., by EOL, GBIF, Plazi and others).

An XML-based editorial, publication and dissemination workflow was implemented, which permits acceptance of manuscripts generated either from databases (Scratchpads websites and Proctotrupoidea website) or as standard MS Word file. The XML manuscripts generated “by pushing the button” from Scratchpads are linked to the online dynamic versions of the same after publication.

A dynamic web-page for any taxonomic name mentioned in a publication is being created and explored online through the so-called Pensoft Taxon Profile tool, just by clicking on the name during the reading process.  The dynamically generated taxon profile gathers and displays information from several leading biodiversity websites, e.g., GBIF, NCBI (GenBank, PubMed and PubMedCentral), EOL, BOLD, BHL, IUCN, ZooBank, Morphbank, Wikipedia, Wikimedia and others.  An example can be a plant species, i.e., the cork oak (Quercus suber):, mentioned in a zoological paper (  

The tool offers an option to “Create your own taxon profile” for any taxonomic name of interest.

A number of additional semantic enhancements are used in the HTML versions: (i) internal cross-linking between paper sections, citations, references, tables, figures; (ii) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, citations); (iii) mapping of georeferenced localities listed in the whole paper or within separate taxon treatments; (iv) enlarging figures and visualization of literature references by pointing on citations within the text; (v) external  linking to GenBank and BOLD accession numbers, Morphbank, online maps, literature references, museum collections, and some more.
The partnering organisations are listed in:

It is anticipated that the workflow will be soon implemented also in the forthcoming PhytoKeys, a partner journal of ZooKeys.  Needless to say, the editors and authors involved in the current issue are thrilled by this development and would like to receive comments and critisim for further developing of the proposed workflow.

ZooKeys covered by PubMedCentral and Scopus

ZooKeys was recently approved for coverage in both Elsevier’s Scopus and PubMedCentral. Scopus will cover current issues as well as back list since the start of the journal in July 2008.Articles from issue 50 onwards will be archived in full-content PDF and XML formats in PubMedCentral. Bibliographic metadata and abstracts will also be indexed and available through PubMed. For XML mark up ZooKeys uses the NLM TaxPub schema, developed by the Plazi team ( to provide finer granularity mark up, for instance to delimit taxon treatments, type material, localities, etc. within a paper. This step was made possible thanks to all who supported the journal with excellent papers, reviews and editorial work. Thanks to NLM and Plazi teams for the pleasant and efficient collaboration!

ZooKeys paper on National Geographic

On 19th of November, ZooKeys has published the monograph of Paul Sereno and Hans Larsson ‘Cretaceous Crocodyliforms from the Sahara’. The study presents fascinating discoveries of a diverse fossil crocodile fauna that inhabited the present-day Sahara some 100 million years ago. Four of the five crocodile species, nicknamed as BoarCroc, RatCroc, DogCroc, DuckCroc and PancakeCroc, are new to science (three new genera) and major additions to two previously known species, Araripesuchus wegeneri and Anatosuchus minor, are published as well.

The case shows clearly the great advantage of open access publishing of scientific results. The paper was published just one hour before the start of National Geographic press-conference in Washington D.C. dedicated to this great scientific discovery and became immediately available to anyone to freely read, download and distribute. The collaboration between National Geographic and ZooKeys led to a maximum dissemination to scientists and mass public in a unprecedented manner. Shortly after publication, the new species descriptions will also be available on Encyclopedia of Life.

During the two days after publication, the paper enjoyed 11,548 visits with 1,467 and 2,153 unique visitors on Thursday and Friday, respectively!

You may learn more or have a look at these incredible creatures from the NG website or from the scientific paper itself.

The NGC documentary “When Crocs Ate Dinosaurs” was shown on Nov. 21 as part of the Channel’s second annual Expedition Week.

All five main wires — AP, Reuters, Agence France Presse, UPI and EFE — did stories, as did numerous other outlets.

Online coverage:
ABC News (Reuters)
ABC News (AP)
Chicago Tribune,0,2850583.story
Chicago Sun Times,paul-sereno-dinosaurs-111909.article
Fox News,2933,575752,00.html
US News and World Report
Seattle Times
ABC7 Chicago
Charleston Daily Mail
Science Now
Discovery News
NG News
CBC News, Canda, Spain
The Guardian, UK, UK
Daily Mail, UK
Canoe, Canada (AP)
CBCnews, Canada
Ziet News, Germany (DPA)
O Globo, Brazil
AFP, France
Le Figaro, France
Knack News, Belgium
Times of Malta, Malta
New Zealand Hearld, New Zealand
Huffington Post
Science Daily
Live Science
UTV News (Guardian)
Flesh and Stone
Idaho State Journal
Red Orbit

ZooKeys publishes interactive keys under the open access model

ZooKeys published a forum paper (doi:10.3897/zookeys.21.274) where the concepts of publication, citation and dissemination of interactive keys and other online keys under the open access model are discussed. The concept is illustrated by a sample paper by Sharkey et al. published in the same issue (doi:10.3897/zookeys.21.271) and two more papers published previously (doi:10.3897/zookeys.20.108 and doi:10.3897/zookeys.20.112).

The sample paper represents a taxonomic revision of a hymenopteran subfamily where keys to genera are published in a conventional dichotomous format and, additionally, in three different interactive formats (Intkey, Lucid and MX). The present model is based on previous experience with several existing examples of publishing online keys, however, it also suggests ways to publish, cite, preserve, disseminate and reuse the original data files under separate DOIs and metadata descriptors to the benefit of the authors, future workers, and society in general.

To be regarded as a “formal scientific publication,” an online key should satisfy the same criteria of peer review, registration, persistence, bibliographic description, etc., as conventional publications. Dynamic Web-based interactive keys meet some of these criteria (identification, citation and location), while they may lack other important features of it (persistence, archiving, indexing, science metric and citation metric services). Hence, dynamic interactive keys may benefit from publishing the first version of their underlying datasets in a form of “formal scientific publication”.

The forum paper discusses the minimum set of data files to be published for several different platforms (Intkey, Lucid2, Lucid3, MX) to ensure both (1) priority, identification, location and citation of the firstly published work and (2) future use and re-use of the keys.

GBIF and Pensoft signed a Memorandum of Cooperation


The Memorandum of Cooperation formalises the basis for the two organisations to facilitate discovery and access to ‘primary biodiversity data’ simultaneously with scholarly publication using GBIF’s infrastructure. ZooKeys calls upon its authors to submit supporting primary biodiversity data together with their manuscript, in conformance with GBIF promoted standards. ZooKeys will make the GBIF ‘Integrated Publishing Toolkit (IPT)’ available from its website. GBIF will provide ZooKeys with standards for primary biodiversity data sharing and a template, to be included in Zookeys’ ‘instructions for authors’. GBIF will also provide remote help-desk support to ZooKeys for ensuring maintenance of the IPT software.

On June 1, 2009, ZooKeys became the first open access journal in systematics to facilitate discovery and access to ‘primary biodiversity data’ simultaneously with scholarly publication using the GBIF infrastructure, when a paper by Miller, Griswold and Yin (2009) (, doi: 10.3897/zookeys.11.160, published a dataset via the GBIF data portal as part of the ZooKeys publication process, which includes the assignment of a distinct DoI for datasets, a KML file with distinct DoI, etc. (see

“Signing of MoC between ZooKeys and GBIF is a milestone step towards open access to primary biodiversity data, and an example we expect other journals will follow” says Dr. Mark Costello, President of the Society for the Management of Electronic Biodiversity Data (SMEBD). SMEBD, which recently joined GBIF as an Associate Participant, represents over 500 individual scientists who contribute to online biodiversity databases.