Pensoft and ARPHA welcome three biodiversity-themed journals in their portfolio

The scholarly publisher and technology provider Pensoft and its self-developed publishing platform ARPHA welcome three journals to their distinguished and growing portfolio of biodiversity-themed journals. The international, peer-reviewed and open-access journals Acta Ichthyologica et PiscatoriaCaucasiana and Zitteliana are now fully operable and open for submissions through their new websites and technologically advanced user interfaces.

By moving to ARPHA, the three scholarly outlets will not only revamp their websites and technological backbone, but will also take advantage from ARPHA’s signature fast-track, end-to-end publishing system, which is to benefit all journal users: authors, reviewers and editors alike. In addition, the journals will use all unique services offered by ARPHA, such as data publishing, linked data tables, semantic markup and enhancements, automated export of sub-article elements and data to aggregators, web-service integrations with over 40 world-class indexing and archiving databases, sub-article-level usage metrics, and more. Published articles are to be available in PDF, machine-readable JATS XML formats and semantically enriched HTML, so that they guarantee better reader experience to ensure they are easy to discover, access, cite and reuse.

Acta Ichthyologica et Piscatoria

Launched in 1970, Acta Ichthyologica et Piscatoria (AIeP) publishes research about all aspects of ichthyology and fisheries, concerning true fishes (fin-fishes), including taxonomy, biology, morphology, anatomy, physiology, pathology, parasitology, reproduction and zoogeography. To be accepted, manuscripts need to be based on original experimental data or experimental methods, or new analyses of already existing data. The journal stands against the publication of “isolated” research, linked neither to the “past” nor the “future” of science. Likewise, “salami science” is also discouraged. AIeP is indexed by all major indexers, including Web of Science and Scopus. The journal’s first Impact Factor was released in 2010, and currently stands at 0.629 (2019).

Caucasiana

As a successor of the Proceedings of the Institute of Zoology of the Georgian Academy of Science, the Caucasiana is to give new life to the historical, print-only zoological by becoming a full-fledged, exclusively digital scholarly journal, focused on the still poorly known biodiversity in the Caucasus region and its adjacent areas. Caucasiana‘s aim is to accumulate primary biodiversity data urgently needed to understand the big picture of the biodiversity in the area: from individuals to ecosystems. To support the mission of uncovering the secrets of the Caucasus, the journal operates a no-APCs policy.

While the journal will be considering all biodiversity-related studies, based on their merits and quality of research, Caucasiana places special attention to taxonomic inventories and systematics. Thereby, in addition to traditional research outputs, the journal also publishes data papers, annotated checklists, monographs and conference proceedings, making use of the suite of biodiversity data publishing innovations, tools and know-how available from Pensoft.

Zitelliana

In 2021, Zitelliana is celebrating its 50th anniversary in a brand new gear in an excellent example of tradition working perfectly together with innovation and modernity. Since its launch in 1961, Zitelliana, a scholarly journal devoted to all fields of paleontology and geobiology, and owned by the Bavarian State Collection of Palaeontology and Geology (SNSB), has changed several names (i.e. Mitteilungen der Bayerischen Staatssammlung für Paläontologie und historische Geologie, Zitteliana A (Abhandlungen) and Zitteliana B (Mitteilungen)) and has extended its scope to cover research from outside Bavaria and adjacent regions or materials deposited in the SNSB’s collections.

Today, Zitteliana welcomes both modern and traditional research outputs, including palaeobiology, geobiology, palaeogenomics, biodiversity, stratigraphy, sedimentology, regional geology, systematics, phylogeny, and cross-disciplinary studies. Thanks to the support of the SNSB, authors in Zitteliana publish free of charge.

“At Pensoft, we take pride in our experience and achievements in the field of biodiversity research publishing and dissemination, so we’re particularly pleased to welcome these three wonderful journals and share our know-how with them at all levels: readership, editorship, publication and dissemination,” comments Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

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Upcoming Special Issue of Biodiversity Data Journal to feature data papers on European Russia

Partners GBIF, FinBIF and Pensoft to support publication of data papers that describe datasets from Russia west of the Ural Mountains

Original post via GBIF

GBIF—the Global Biodiversity Information Facility—in collaboration with the Finnish Biodiversity Information Facility (FinBIF) and Pensoft Publishers, are happy to issue a call for authors to submit and publish data papers on European Russia (west of the Urals) in an upcoming special issue of Biodiversity Data Journal (BDJ).

Between now and 31 August 2020, the article processing fee (normally €450) will be waived for the first 20 papers, provided that the publications are accepted and meet the following criteria that the data paper describes a dataset:

The manuscript must be prepared in English and is submitted in accordance with BDJ’s instructions to authors by 31 August 2020. Late submissions will not be eligible for APC waivers.

Sponsorship is limited to the first 20 accepted submissions meeting these criteria on a first-come, first-served basis. The call for submissions can therefore close prior to the stated deadline of 31 August. Authors may contribute to more than one manuscript, but artificial division of the logically uniform data and data stories, or “salami publishing”, is not allowed.

BDJ will publish a special issue including the selected papers by the end of 2020. The journal is indexed by Web of Science (Impact Factor 1.029), Scopus (CiteScore: 1.24) and listed in РИНЦ / eLibrary.ru

For non-native speakers, please ensure that your English is checked either by native speakers or by professional English-language editors prior to submission. You may credit these individuals as a “Contributor” through the AWT interface. Contributors are not listed as co-authors but can help you improve your manuscripts.

In addition to the BDJ instruction to authors, it is required that datasets referenced from the data paper a) cite the dataset’s DOI and b) appear in the paper’s list of references.

Authors should explore the GBIF.org section on data papers and Strategies and guidelines for scholarly publishing of biodiversity data. Manuscripts and datasets will go through a standard peer-review process.

To see an example, view this dataset on GBIF.org and the corresponding data paper published by BDJ.

Questions may be directed either to Dmitry Schigel, GBIF scientific officer, or Yasen Mutafchiev, managing editor of Biodiversity Data Journal.

Definition of terms

Datasets with more than 5,000 records that are new to GBIF.org

Datasets should contain at a minimum 5,000 new records that are new to GBIF.org. While the focus is on additional records for the region, records already published in GBIF may meet the criteria of ‘new’ if they are substantially improved, particularly through the addition of georeferenced locations.

Justification for publishing datasets with fewer records (e.g. sampling-event datasets, sequence-based data, checklists with endemics etc.) will be considered on a case-by-case basis.

Datasets with high-quality data and metadata

Authors should start by publishing a dataset comprised of data and metadata that meets GBIF’s stated data quality requirement. This effort will involve work on an installation of the GBIF Integrated Publishing Toolkit.

Only when the dataset is prepared should authors then turn to working on the manuscript text. The extended metadata you enter in the IPT while describing your dataset can be converted into manuscript with a single-click of a button in the ARPHA Writing Tool (see also Creation and Publication of Data Papers from Ecological Metadata Language (EML) Metadata. Authors can then complete, edit and submit manuscripts to BDJ for review.

Datasets with geographic coverage in European Russia west of the Ural mountains

In correspondence with the funding priorities of this programme, at least 80% of the records in a dataset should have coordinates that fall within the priority area of European Russia west of the Ural mountains. However, authors of the paper may be affiliated with institutions anywhere in the world.

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Data audit at Pensoft’s biodiversity journals

Data papers submitted to Biodiversity Data Journal, as well as all relevant biodiversity-themed journals in Pensoft’s portfolio, undergo a mandatory data auditing workflow before being passed down to a subject editor.

Learn more about the workflow here:
https://www.eurekalert.org/pub_releases/2019-10/pp-aif101819.php.

Book on plants in the Murmansk region (Russia) scores 4/19 correct insect identifications

A recently published book on some aspects of the ecology of woody introducents in the Murmansk oblast of Russia provides the information on 19 species of plant-damaging insects out of which only 4 species are identified correctly. Dr Mikhail V. Kozlov from the University of Turku provides correct identifications for the insects, illustrated in the book, in his paper, published in the open-access journal Arctic Environmental Research in order to prevent the spread of erroneous information across future publications and databases.

Insect fauna of the Murmansk region is relatively well-studied and that’s why any new faunistic records from this region immediately attract the attention of entomologists. Those findings are especially exciting when they extend the distribution range of certain species by 1,000 to 2,000 km towards the North Pole.

The published misidentifications of insect species can lead to a cascading effect of mistakes, because entomologists commonly use faunistic data published by colleagues decades and even centuries ago. That’s why it is very important to keep a track of such cases and provide correct identifications if possible, remarks the author.

“In particular, three moth species (Archips crataegana, A. podanaand Erannis defoliaria) reported in this book to occur around Kirovsk have not yet been found either in the Murmansk oblast or in the more southern Karelia. In neighbouring Finland, the northernmost records of these species are from locations some 1,000 km to the south of Kirovsk”,

Dr Kozlov shares his concerns.

The most striking examples of misidentification in the book are at the order level: a syrphid fly (Diptera) identified as a leafcutter bee (Hymenoptera), and a sawfly (Hymenoptera) identified as a psyllid (Hemiptera).


Leaf beetle Chrysomela lapponica, erroneously mentioned in the criticized book as a pest of bird cherry, shadbush and chokeberry, feeds in the Murmansk oblast only on willows.
Credit: Vitali Zverev
License: CC-BY 4.0

In conclusion, Dr Kozlov’s revision found that 15 out of the 19 species illustrated were incorrectly identified. Thus, the leaf damage associated with certain insect species, considered in the book, also becomes very questionable.

“The misidentification of pest species can easily result in incorrect pest management and face unnecessary costs, while publication of incorrect data distorts our knowledge of the distribution and biology of insects. Therefore, insect identification for scientific, educational or pest management purposes should always be performed by professionals or by volunteers and students who have specific training for this
purpose”,

concludes Dr Mikhail V. Kozlov.

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Original source:
Kozlov MV (2019) Insects identified by unqualified scientists: multiple “new” records from the Murmansk oblast of Russia are dismissed as false. Arctic Environmental Research 19(4): 153-158. https://doi.org/10.3897/issn2541-8416.2019.19.4.153 

The biodiversity data journal Check List joins Pensoft and ARPHA

The well-reputed and established journal Check List is the latest biodiversity-themed title to join scholarly publisher Pensoft’s peer-reviewed and open access family. Its first issue in collaboration with Pensoft is now published on the journal’s new website.

Check List is an online open access journal launched in 2005 in Brazil. It publishes distribution summaries, annotated lists of species and notes on the geographic distribution of all taxa. The journal stands for the idea that maintaining records of the range of a species is the very first step towards undertaking effective actions for its conservation. Furthermore, its team believes that publishing such data provides the baseline for biodiversity preservation as a whole.

The move sees Check List migrating to the Pensoft-developed journal publishing platform ARPHA (abbreviation for Authoring, Reviewing, Publishing, Hosting and Archiving) to provide its authors, editors and users with a brand new look and feel along with a whole set of high-tech perks.

While the all-new sleek interface is evident at first visit of the Check List‘s new website, there is much more under the surface. The partnership with Pensoft and ARPHA means that Check List will enjoy fast-track and convenient publishing. The manuscripts will be taken care for from the authoring stage, through reviewing and dissemination – all the way to archiving. The papers will be published in three formats (PDF, XML, HTML) and full of semantic enhancements.

Recognising the importance of easy and efficient publication of accessible data in the spirit of both biodiversity conservation and open science, ARPHA allows for data to be published as supplementary files along with the article, or through internationally recognised repositories, such as GBIFGenbankBarcode of LifeDryad, and others.

“It is fantastic to have Check List join the world’s leading and most technologically advanced biodiversity publisher,” comments Check List Editor-in-Chief Marcus Guidoti.

“At Pensoft, we are happy to once again share and apply our long-year experience and know-how in scholarly publishing and biodiversity data handling,” says Prof. Lyubomir Penev, the founder and Managing Director of Pensoft. “I am certain that this collaboration will advance the technological and publishing label of Check List to the benefit of the scientific community”

Check List is the second scholarly journal of South American origin to join Pensoft’s growing portfolio, after another highly regarded Brazilian-born academic title – Zoologia – moved to ARPHA earlier this year.

Import of Specimen or Occurrence Records Into Taxonomic Manuscripts

Repositories and data indexing platforms, such as GBIFBOLD systems, or iDigBio hold documented specimen or occurrence records along with their record ID’s. In order to streamline the authoring process, save taxonomists’ time, and provide a workflow for peer-review and quality checks of raw occurrence data, the ARPHA team has introduced an innovative feature that makes it possible to easily import specimen occurrence records into a taxonomic manuscript (see Fig. 1).

For the remainder of this post we will refer to specimen data as occurrence records, since an occurrence can be both an observation in the wild, or a museum specimen.

Figure1

Fig. 1: Workflow for directly importing occurrence records into a taxonomic manuscript.

Until now, when users of the ARPHA writing tool wanted to include occurrence records as materials in a manuscript, they would have had to format the occurrences as an Excel sheet that is uploaded to the Biodiversity Data Journal, or enter the data manually. While the “upload from Excel” approach significantly simplifies the process of importing materials, it still requires a transposition step – the data which is stored in a database needs to be reformatted to the specific Excel format. With the introduction of the new import feature, occurrence data that is stored at GBIFBOLD systems, or iDigBio, can be directly inserted into the manuscript by simply entering a relevant record identifier.

The functionality shows up when one creates a new “Taxon treatment” in a taxonomic manuscript prepared in the ARPHA Writing Tool. The import functions as follows:

  1. the author locates an occurrence record or records in one of the supported data portals;
  2. the author notes the ID(s) of the records that ought to be imported into the manuscript (see Fig. 2, 3, and 4 for examples);
  3. the author enters the ID(s) of the occurrence records in a form that is to be seen in the materials section of the species treatment, selects a particular database from a list, and then simply clicks ‘Add’ to import the occurrence directly into the manuscript.

In the case of BOLD Systems, the author may also select a given Barcode Identification Number (BIN; for a treatment of BIN’s read below), which then pulls all occurrences in the corresponding BIN (see Fig. 5).

Figure 2       Figure 3

Fig. 2: (Left) An occurrence record in iDigBio. The UUID is highlighted; Fig. 3: (Right) An occurrence record in GBIF. The GBIF ID and the Occurrence ID is highlighted. (Click on images to enlarge)

Figure 4       Figure 5

Fig. 4: (Left) An occurrence record in BOLD Systems. The record ID is highlighted.; Fig. 5:  (Right) All occurrence records corresponding to a OTU. The BIN is highlighted. (Click on images to enlarge)

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. Let’s assume we have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found in iDigBio. What we need to do is to locate the ID of the occurrence record in the iDigBio webpage. In the case of iDigBio, the ARPHA system supports import via a Universally Unique Identifier (UUID). We have already created a treatment for S. capillifolium and clicked on the pencil to edit materials (Fig. 6). When we scroll all the way down in the pop-up window, we see the form which is displayed in the middle of Fig. 1.

Figure 6

Fig. 6: Edit materials.

From here, the following actions are possible:

  • insert (an) occurrence record(s) from iDigBio by specifying their UUID’s (universally unique identifier) (Fig.2);
  • insert (an) occurrence record(s) from GBIF by entering their GBIF ID’s (Fig.3);
  • insert (an) occurrence record(s) from GBIF by entering their occurrence ID’s (note that unfortunately not all GBIF records have an occurrence ID, which is to be understood as some sort of universal identifier) (Fig. 3);
  • insert (an) occurrence record(s) from BOLD by entering their record ID’s (Fig. 4);
  • insert a set of occurrence records from BOLD belonging to a BIN (barcode index number) (Fig. 5).

In this example, select the fifth option (iDigBio) and type or paste the UUID b9ff7774-4a5d-47af-a2ea-bdf3ecc78885 and click Add. This will pull the occurrence record for S. capillifolium from iDigBio and insert it as a material in the current paper (Fig. 6). The same workflow applies also to the aforementioned GBIF and BOLD portals.

Figure 7

Fig. 7: Materials after they have been imported.

This workflow can be used for a number of purposes but one of its most exciting future applications is the rapid re-description of Linnaean species, or new morphological descriptions of species together with DNA barcode sequences (a barcode is a taxon-specific highly conserved gene that provides enough inter-species variation for statistical classification to take place) using the  Barcode Identification Numbers (BIN’s) underlying an Operational Taxonomic Units (OTU). If a taxonomist is convinced that a species hypothesis corresponding to OTU defined algorithmically at  BOLD systems clearly presents a new species, then he/she can import all specimen records associated with that OTU via inserting that OTU’s BIN ID in the respective fields.

Having imported the specimen occurrence records, the author needs to define one specimen as holotype of the news species, other as paratypes, and so on. The author can also edit the records in the ARPHA tool, delete some, or add new ones, etc.

Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can easily be downloaded from the article text into structured data by anyone who needs the data for reuse.

Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD and iDigBio. Taxonomists are used to publish only records of specimens they or their co-authors have personally studied. In a sense, the workflow will serve as a “cleaning filter” for portions of data that are passed through the publishing process. Thereafter, the published records can be used to curate raw data at collections, e.g. put correct identifications, assign newly described species names to specimens belonging to the respective BIN and so on.

Additional Information:

The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4(Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.