Pensoft Publishers

Sofia, Bulgaria

Pensoft Publishers

Sofia, Bulgaria
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Miller J.A.,Naturalis Biodiversity Center | Agosti D.,Www.Plazi.org | Penev L.,Pensoft | Sautter G.,Karlsruhe Institute of Technology | And 7 more authors.
Biodiversity Data Journal | Year: 2015

Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Corecompatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions. © Miller J et al.


Deltshev C.,Bulgarian Academy of Science | Komnenov M.,Macedonian Museum of Natural History | Blagoev G.,University of Guelph | Georgiev T.,Pensoft Publishers | And 3 more authors.
Biodiversity Data Journal | Year: 2013

A total of 294 species from 31 families have been found in Galichitsa Mt. Of them, 85 species are new to the mountain, while 20 are also new to the fauna of FYR of Macedonia. According to their current distribution the established species can be assigned to 17 zoogeographical categories, grouped into 5 complexes (Cosmopolitan, Holarctic, European, Mediterranean, Endemics of Balkans). Dominant are Holarctic species (66.0%) followed by European (16.5%) and Mediterranean (9.3%). The endemics (6.2%) and Southeast European species (1.7%) emphasize the local character of this fauna, but its low percentage suggests an important process of colonization. © Deltshev C et al.


Penev L.,Bulgarian Academy of Science | Lyal C.H.C.,Natural History Museum in London | Weitzman A.,Smithsonian Institution | Morse D.R.,Open University Milton Keynes | And 6 more authors.
ZooKeys | Year: 2011

We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of "taxon treatment" from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes.


PubMed | Karlsruhe Institute of Technology, Naturalis Biodiversity Center, Pensoft, Open University Milton Keynes and 3 more.
Type: | Journal: Biodiversity data journal | Year: 2015

Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions.


Arriaga-Varela E.,Charles University | Seidel M.,Charles University | Deler-Hernandez A.,Charles University | Senderov V.,Pensoft Publishers | And 2 more authors.
ZooKeys | Year: 2017

The representatives of the genus Cercyon Leach occurring in the Greater Antilles are reviewed. Ten species are recorded, of which five are described here as new: C. gimmeli sp. n. (Dominican Republic), C. armatipenis sp. n. (Dominican Republic), C. taino sp. n. (Dominican Republic), C. sklodowskae sp. n. (Jamaica) and C. spiniventris sp. n. (Dominican Republic). Diagnoses and detailed distributional data are also provided for C. floridanus Horn, 1890 (distributed in southeastern United States of America and Cayman Islands), C. insularis Chevrolat, 1863 (endemic to the Antilles), C. praetextatus (Say, 1825) (widely distributed in the New World incl. Greater Antilles), C. quisquilius (Linnaeus, 1761) (an adventive species of Paleartic origin) and C. nigriceps (Marshall, 1802) (an adventive species probably of Oriental origin). Cercyon armatipenis, C. gimmeli, C. taino form a group of closely related species only distinguishable by male genitalia and DNA sequences. A key to the Great Antillean Cercyon is provided and important diagnostic characters are illustrated. The larvae of C. insularis and C. taino were associated with adults using COI barcode sequences, illustrated and diagnosed. Full occurrence data, additional images and COI barcode sequences were submitted to open access on-line depositories in an effort to provide access to complete data. © Emmanuel Arriaga-Varela et al.


Stoev P.,National Museum of Natural History | Akkari N.,Institute Superieur Des Science Biologiques Appliquees Of Tunis | Zapparoli M.,University of Tuscia | Porco D.,University of Guelph | And 4 more authors.
ZooKeys | Year: 2010

The centipede genus Eupolybothrus Verhoeff, 1907 in North Africa is revised. A new cavernicolous species, E. kahfi Stoev & Akkari, sp. n., is described from a cave in Jebel Zaghouan, northeast Tunisia. Morphologically, it is most closely related to E. nudicornis (Gervais, 1837) from North Africa and Southwest Europe but can be readily distinguished by the long antennae and leg-pair 15, a conical dorso-median protuberance emerging from the posterior part of prefemur 15, and the shape of the male fi rst genital sternite. Molecular sequence data from the cytochrome c oxidase I gene (mtDNA-5' COI-barcoding fragment) exhibit 19.19% divergence between E. kahfi and E. nudicornis, an interspecifi c value comparable to those observed among four other species of Eupolybothrus which, combined with a low intraspecifi c divergence (0.3-1.14%), supports the morphological diagnosis of E. kahfi as a separate species. This is the fi rst troglomorphic myriapod to be found in Tunisia, and the second troglomorph lithobiomorph centipede known from North Africa. E. nudicornis is redescribed based on abundant material from Tunisia and its post-embryonic development, distribution and habitat preferences recorded. E. cloudsley-thompsoni Turk, 1955, a nominal species based on Tunisian type material, is placed in synonymy with E. nudicornis. To comply with the latest technological developments in publishing of biological information, the paper implements new approaches in cybertaxonomy, such as fi ne granularity XML tagging validated against the NLM DTD TaxPub for PubMedCentral and dissemination in XML to various aggregators (GBIF, EOL, Wikipedia), vizualisation of all taxa mentioned in the text via the dynamically created Pensoft Taxon Profi le (PTP) page, data publishing, georeferencing of all lo calities via Google Earth, and ZooBank, GenBank and MorphBank registration of datasets. An interactive key to all valid species of Eupolybothrus is made with DELTA software. © Pavel Stoev et al.


News Article | December 18, 2015
Site: www.nanotech-now.com

Abstract: Controlled manipulation of matter on the scale of atoms is the topic of a new cutting edge Austrian Science Fund (FWF) project "Heteroatom quantum corrals and nanoplasmonics in graphene" (HeQuCoG), led by Finnish-born physicist Toma Susi. The project is the first to openly publish its proposal via the innovative platform of the Research Ideas & Outcomes (RIO) Journal, designed to uncover the entire research cycle. The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. The journal harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research outputs than those traditionally made public. RIO offers one of the most transparent, open and public peer-review processes, including pre-submission and post-publication peer-review options. The journal is designed to encourage collaboration between scientists within and across disciplines by making the entire research cycle open, and by mapping the social impact for its publications. Dr. Susi, based at the University of Vienna in Austria, shares why he chose to make his research accessible to peers and the wider public from the proposal stage. "I must be honest: it was an instinctively scary prospect to publish a grant proposal, even a funded one. However, once I carefully weighed the potential pros and cons and discussed the idea with my close peers, I concluded that those fears most likely were unfounded. Moreover, there really can be no doubt that science as a whole would benefit if this became common practice." The aim of the HeQuCoG project is to create atomically precise structures consisting of silicon and phosphorus atoms embedded in the lattice of graphene using a combination of ion implantation, first principles modeling and electron microscopy. The expected outcome is a systematic demonstration of atomic-level material design and the creation of freestanding "quantum corral" structures for the first time. "We are happy to have such an exciting and ambitious project as one of the first to publish its proposal in RIO. This goes to show that the platform is an ideal hub for forward-thinking young researchers wishing to take science to a new level of collaboration and real-world impact" comments Prof. Lyubomir Penev, co-founder of RIO. ### Additional information: The Austrian Science Fund FWF is devoted to the support of the ongoing development of Austrian science and basic research at a high international level. In this way, the FWF makes a significant contribution to cultural development, to the advancement of a knowledge-based society, and to the creation of value and wealth in Austria and abroad. About Pensoft Publishers The Research Ideas and Outcomes (RIO) Journal publishes all outputs of the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform offering one of the most transparent, open and public peer-review processes. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.


Penev L.,Bulgarian Academy of Science | Paton A.,International Plant Name Index IPNI and Index Fungorum IF | Nicolson N.,International Plant Name Index IPNI and Index Fungorum IF | Kirk P.,International Plant Name Index IPNI and Index Fungorum IF | And 8 more authors.
ZooKeys | Year: 2016

Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper. © Lyubomir Penev et al.


Blagoderov V.,Natural History Museum in London | Brake I.,Natural History Museum in London | Georgiev T.,Pensoft Publishers | Penev L.,Bulgarian Academy of Science | And 6 more authors.
ZooKeys | Year: 2010

We describe a method to publish nomenclatural acts described in taxonomic websites (Scratchpads) that are formally registered through publication in a printed journal (ZooKeys). This method is fully compliant with the zoological nomenclatural code. Our approach supports manuscript creation (via a Scratchpad), electronic act registration (via ZooBank), online and print publication (in the journal ZooKeys) and simultaneous dissemination (ZooKeys and Scratchpads) for nomenclatorial acts including new species descriptions. The workflow supports the generation of manuscripts directly from a database and is illustrated by two sample papers published in the present issue. © Vladimir Blagoderov et al.


PubMed | ZooBank, International Plant Name Index IPNI and Index Fungorum IF, Pensoft Publishers, Bulgarian Academy of Science and Fungal Biodiversity Center
Type: | Journal: ZooKeys | Year: 2016

Collaborative effort among four lead indexes of taxon names and nomenclatural acts (International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.

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