Category: Uncategorized

We invite biodiversity scientists and ecologists to consider publishing in BioRisk to experience and enjoy the numerous technological innovations in publishing and dissemination of information in all branches of ecology and biodiversity science, available through the highly sophisticated, brand new journal publishing platform of Pensoft. BioRisk is extremely appropriate for publishing results of FP projects either as regular research papers or in a form of special issues, conference proceedings, thematic collections of papers, monographs, data publications and so on. All papers are open access and free to read, download, print, and distribute. There are mo restrictions in manuscript’s size neither there are restrictions or charges for publishing in color, in both the online and print versions of the journals.

You may learn a bit more on the journal’s unique features in the attached file (downloadable also at

http://87.121.150.116/triada/img/upl/file/BioRisk%20Invitation%20to%20Publish.pdf).

We welcome manuscript submissions from you and your colleagues!

 

Josef Settele (Editor in Chief) and Lyubomir Penev (Managing Editor)

www.pensoft.net/journals/biorisk | biorisk@pensoft.net

BioRisk has published an important outcome of the ALARM and CLIMIT projects, Monitoring Climatic Change With Dragonflies consisting of 15 research papers. This special issue is one more nice addition to the BioRisk collection that started with the publication of the Climatic Risk Atlas of European Butterflies (downloaded more than 30,000 times from both Pensoft’s and UFZ’s servers!) and the 1000-pages treatise Alien Terrestrial Invertebrates of Europe.

Going Fast, Linked, and Open Access!

The journals NeoBiota, Journal of Hymenoptera Research, International Journal of Myriapodology, Comparative Cytogenetics and Subterranean Biology changed their publishing model to open access and moved to the new journal publishing platform of Pensoft (www.pensoft.net/journals) in December 2010.

The journals will benefit from the accumulated technological experience of the Pensoft’s journals ZooKeys, PhytoKeys, and BioRisk. Among the most important features of the new Pensoft’s platform are:

• XML submission, editorial, publication and dissemination workflow, based on the TaxPub XML schema
• Highly automated and skilled online editorial management system, designed to serve the specific needs of publishing and dissemination of biodiversity information
• One time registration for all the platform and unified Author Guidelines
• Professional review and editorial assistance
• Quick turnaround, ranging from one to few months, from manuscript submission to publication
• No limit in manuscript length, e.g. for large revisionary works, checklists, catalogues, conference proceedings, monographs, festchrift volumes
• Professional design and layout, high quality printing and binding
• Immediate Alert Service through Email, RSS feeds and social networks to inform the society about your publication
• Immediate distribution of your publication to scientific databases, indices and search engines (Zoological Record, Web of Science, Google Scholar, CAB Abstracts, DOAJ Content and others)
• Advanced publishing technologies, possibilities for data publication and various semantic Web enhancements
• Linkage of each article and issue to several independent classification schemes, e.g., taxonomic, subject and geographical
• Possibility to customize classifications according to the specific needs of the different  journals
• No charge and restrictions for color, either in the online or printed version
• Free consultancy services and various ways to combine the new model with previous subscription and exchange programs.

More detailed information on the semantic tagging and enhnacement features offered by Pensoft can be found here. Most of them are very much relevant to biodiversity journals, namely: mandatory ZooBank or IPNI registration provided by the publisher, automated export to all new species with images to Encyclopedia of Life, indexing of new species in Wikispecies, online mapping of georeferenced localities within a paper or taxon treatments, various cross-linking mechanisms and many more.

All papers are open access and free to read, download, print, and distribute.

The journal publishing platform of Pensoft is a linked environment built upon 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 (Global Biodiversity Information Facility, Encyclopedia of Life, Biodiversity heritage Library, PubMed and PubMedCentral,  Morphbank, IPNI, Tropicos, PLANTS, ZooBank, Wikipedia, Wikispecies, etc.) through a dynamic web profile of each taxon mentioned within a paper (www.ptp.pensoft.eu).  Geo-referenced localities can be mapped within taxon treatments or for the entire paper. Each journal can be followed through its own social network profiles on Twitter, Facebook, Mendeley, as well as RSS, email newsletters and so one.

The journals will be 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; (4) XML version compatible to PubMedCentral archiving, thus providing a machine-readable copy to facilitate future data mining. Neither restriction nor charges are imposed on the use of colour illustrations.

For more details, please contact Lyubomir Penev.

 

PhytoKeys and ZooKeys created a tool to automatically export images of all new species described in both journals to EOL, in addition to text descriptions. Here is how species described in the latest issues of the journals look like on EOL:

http://www.eol.org/pages/18691590 (a new species of Solanum)
http://www.eol.org/pages/18691558 (a remarkable cave scorpion from Vietnam)

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 www.ptp.pensoft.eu. 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.

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

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

PhytoKeys builds upon the tremendous success of its sister journal ZooKeys (www.zookeys.org) 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)

On the eve of its second year’s birthday (4th of July 2008), ZooKeys published its jubilee issue No 50 (http://pensoftonline.net/zookeys/index.php/journal/issue/view/52). 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 (http://pensoftonline.net/zookeys/index.php/journal/article/view/538/469). 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 (http://sourceforge.net/projects/taxpub/) 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):  http://pmt.pensoft.eu/resources/articles/external_details.php?query=Quercus+suber, mentioned in a zoological paper (http://pensoftonline.net/zookeys/index.php/journal/article/view/504/448).  

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: http://pensoftonline.net/Parnering%20organisations-special%20issue-ZooKeys-50.pdf

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.

The open access journal BioRisk has bee approved for indexing in CABI abstracts. Titles and abstracts will be linked to the full-text articles from CABI’s database.

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 (www.plazi.org) 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!