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ZooKeys published a large taxonomic revision (Talamas et al. 2011) where all occurrence data and the taxon checklist have been published both in text and also as supplementary files in Darwin Core Archive format. Such an approach permits occurrence data to be downloaded, indexed, published through the GBIF data portal and others, used and re-used. The present monograph may serve as a sample to follow. It also may help in fostering the links between the data creators and scholarly publishers.

Darwin Core Archive (DwC-A) is an international biodiversity informatics data standard and the preferred format for publishing data through the Global Biodiversity Information Facility (GBIF) network. Each Darwin Core Archive consists of at least three files: (1) one or more data files keeping all records of the particular dataset in a tabular format such as a comma-separated or tab-separated list; (2) the archive descriptor (meta.xml) file describing the individual data file columns used and mapping them to DwC terms; and (3) a metadata file describing the entire dataset which GBIF recommends to be EML (Ecological Metadata Language) 2.1.1 based. The format is defined in the Darwin Core text guidelines. Darwin Core is no longer strictly bound to occurrence data, and together with Dublin Core (on which its ideas are based), it is used by GBIF and others to encode data about organism names, taxonomies and species information.

The Darwin Core Archive dataset of the present paper was simultaneously published in and is also available through the GBIF’s  Integrated Publishing Toolkit (IPT) –
http://gbrds.gbif.org/browse/agent?uuid=12a6bf1f-f66e-408c-8c6c-771af210e6a8 .

ZooKeys and PhytoKeys would like to encourage taxonomists to review this revision and consider publishing your own data in conjunction with your manuscript.  The journals provide a ready-made solution for supporting this.

On February 8th,  Pensoft published the first gold Open Access and NLM Taxpub-based issue of the Journal of Hymenoptera Research. It is one of the first journals that Pensoft publishes for a scientific society  – The International Society of Hymenopterists – besides its own in-house journals (www.pensoft.net/journals), such as Zookeys. The implications are going beyond changing from a traditional pdf to a semantically enhanced version allowing immediate distribution of its content to a set of external aggregators such as Encylopedia of Life,  Plazi, Wikispecies or the Global Biodiversity Information Facility (GBIF), and so on.

The Journal of Hymenoptera Research will be published in four different formats: (a) Print format, (b) PDF format, identical to the print version, (c) Semantically enhanced HTML to provide interactive readings and links to external resources, and (d) XML version to be archived in PubMedCentral and other archives, to facilitate future use and reuse of the content. One may learn more on the advanced technologies of publication and dissemination from the journal’s Press Release. 

The Journal of Hymenoptera Research created its own Twitter, Facebook , and Mendeley  profiles in addition to the RSS and email alerts. Despite the contradicting opinions on the role of social networks, all these profiles greatly help to keep you informed on all published papers and news coming from the journal’s website.

If you are or intend to become a member of any of these social networks, it would be really helpful if you suggest the journal to be followed by your friends and colleagues, to increase the range of users unforeseen before, just by few clicks! This could happen by clicking the button "Follow" in Twitter. In Facebook, you could share the journal’s page with friends through the "Share" link at bottom left side of the page. You can then choose to share it via a post on their profiles, which may appear in their friends’ News Feeds, or with specific friends via a message. In the academic network Mendeley , there is a "Share this group" box at bottom right side of the journal’s page.

ZooKeys published a paper (Hendrich L, Balke M (2011) A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini). ZooKeys 79: 11–20. doi: 10.3897/zookeys.79.803) showing simultaneous description of a new species and creation of a wiki page for the taxon on www.species-id.net. The link to the wiki page (www.species-id.net/wiki/Neobidessodes_darwiniensis) is published in the original description under the ZooBank’s LSID, so that readers may always link to the wiki page to see if there is a new information on the taxon there. Vice versa, readers of the wiki page will have always the possibility to link to the original journal description that will stay unchanged as in any other conventional journal article.

While the original authors should always be credited through citing the journal article, further contributors to the wiki page (either the authors themselves or other interested students of that taxon) may edit/add content and be credited consequently as well. Conseguent changes could be tracked by using the wiki "page history" option.

We consider that such an approach could help in resolving the lively discussed contradiction between the "fixed" character of conventional academic publications and the dynamic nature of scientific research and of Internet as media.

Species-id.net is a wiki-based environment that aims at creating species pages (descriptions, data on ecology, biology, distribution, keys, etc.) in addition to Wikispecies (catalogue) and Wikimedia Commons (image repository), as well as to any other biodiversity platform  that may wish to link to it. Species-id is expected to be used/edited mostly by biologists with professional interests in a particular taxon.

The fourth issue of BioRisk, Alien Terrestrial Invertebrates in Europe,  has been positively reviewed by Entomologische Berichten! You can read the review here.

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.

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

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)

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)