The September 2011 issue of Thomson-Reuters Journals Citation Report announced the first impact factor of ZooKeys to be1.133.
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.
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!
On 3rd of January Lyubomir Penev visited the National Library of Medicine to discuss improvement and development of the NLM TaxPub schema for mark up and arhiving of papers in taxonomy. It was agreed our journals ZooKeys and PhytoKeys to become a pilot for testing and implementation of the improved XML marked up schema.
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!
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.
ABC News (Reuters) http://abcnews.go.com/Technology/wirestory?id=9126490&page=2
ABC News (AP) http://abcnews.go.com/Technology/wireStory?id=9126097
Chicago Tribune http://www.chicagotribune.com/news/local/chi-091119paul-sereno-dino-crocs,0,2850583.story
Chicago Sun Times http://www.suntimes.com/news/metro/1893513,paul-sereno-dinosaurs-111909.article
Fox News http://www.foxnews.com/story/0,2933,575752,00.html
US News and World Report http://www.usnews.com/science/articles/2009/11/19/new-ancient-crocodile-species-fossils-found.html?s_cid=rss:new-ancient-crocodile-species-fossils-found
Seattle Times http://seattletimes.nwsource.com/html/businesstechnology/2010307105_apusscioddcrocs.html?syndication=rss
ABC7 Chicago http://abclocal.go.com/wls/story?section=news/local&id=7128010
Charleston Daily Mail http://dailymail.com/News/NationandWorld/200911190324
Science Now http://sciencenow.sciencemag.org/cgi/content/full/2009/1119/1
Discovery News http://news.discovery.com/animals/galloping-dinosaur-eating-crocodiles-found-in-the-sahara.html
NG News http://news.nationalgeographic.com/news/2009/11/091119-dinosaurs-crocodiles-missions.html
CBC News, Canda http://www.cbc.ca/technology/story/2009/11/19/tech-fossil-crocsc.html
ABC.es, Spain http://www.abc.es/20091119/ciencia-tecnologia-paleontologia-fosiles/descubren-tres-nuevas-especies-200911191642.html
The Guardian, UK http://www.guardian.co.uk/science/2009/nov/19/galloping-dinosaur-eating-crocodiles
Telegraph.co.uk, UK http://www.telegraph.co.uk/science/science-news/6605670/BoarCroc-and-DuckCroc-among-five-ancient-species-of-crocodile-discovered.html
Daily Mail, UK http://www.mailonsunday.co.uk/sciencetech/article-1229250/Crocodiles-boar-like-teeth-pancake-flat-skulls.html
Canoe, Canada (AP) http://cnews.canoe.ca/CNEWS/Science/2009/11/19/11811911-ap.html
CBCnews, Canada http://www.cbc.ca/technology/story/2009/11/19/tech-fossil-crocsc.html
Ziet News, Germany (DPA) http://www.zeit.de/newsticker/2009/11/19/iptc-bdt-20091119-545-23047790xml
O Globo, Brazil http://oglobo.globo.com/ciencia/mat/2009/11/19/fosseis-de-crocodilos-pre-historicos-encontrados-no-saara-914834858.asp
AFP, France http://news.yahoo.com/s/afp/20091119/sc_afp/sciencepaleontologyafricaus_20091119175543
Le Figaro, France http://www.lefigaro.fr/flash-actu/2009/11/19/01011-20091119FILWWW00611-des-fossiles-d-especes-inconnues-au-sahara.php
Knack News, Belgium http://knack.rnews.be/nieuws/wetenschap/krokodillen-uit-oertijd-ontdekt/site72-section45-article42711.html
Times of Malta, Malta http://www.timesofmalta.com/articles/view/20091120/world-news/world-briefs
New Zealand Hearld, New Zealand http://www.nzherald.co.nz/world/news/article.cfm?c_id=2&objectid=10610499
Huffington Post http://www.huffingtonpost.com/huff-wires/20091119/us-sci-odd-crocs/
Science Daily http://www.sciencedaily.com/releases/2009/11/091119111327.htm
Live Science http://www.livescience.com/animals/091119-boar-duck-crocodiles.html
UTV News (Guardian) http://u.tv/News/Fossil-hunters-unearth-galloping-dinosaur-eating-crocodiles-in-Sahara/1fa80eda-6c30-42cb-ac21-76b25083db73
Flesh and Stone http://www.fleshandstone.net/healthandsciencenews/1689.html
Idaho State Journal http://www.journalnet.com/news/science/image_9f7afd87-5172-5657-880b-d6470259c97b.html
Red Orbit http://www.redorbit.com/news/science/1788844/prehistoric_supercroc_cousins_inhabit_sahara/index.html?source=r_science
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.
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) (http://www.pensoftonline.net/zookeys), 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 http://www.gbif.org/News/NEWS1243931673).
“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.
“Contributions to the systematics of North American macro-moths” (ZooKeys 9, May 2009, 134 pp.) and “Contributions …II” (ZooKeys 39, March 2010, 268 pp.) include 16 papers contributed by 22 authors on the systematics of macro-moths of North and Central America.
A revision of the noctuid genus Lasionycta (ZooKeys 30, Dec 2009, 156 pp.) included keys, descriptions, and illustrations of 43 species, 17 new.
“An annotated check list of the Lepidoptera of Alberta, Canada” (ZooKeys 38, March 2010, 549 pp.) lists 2367 species with 171 distributional or taxonomic footnotes.
“Annotated check list of the Noctuoidea of North America north of Mexico” (ZooKeys 40, March 2010, 239 pp.) lists 3693 species and includes 716 taxonomic notes and 331 literature references documenting all changes from the previous 1983 check list.