Tag: publishing

Strategic collaboration agreement signed between ScienceOpen and Pensoft

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination.

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination. The new cooperation will focus on the unified indexation, the integration of Pensoft’s ARPHA Platform content into ScienceOpen and the utilization of novel streams of scientific communication for the published materials.

Pensoft is an independent academic publishing company, well known worldwide for bringing novelty through its cutting-edge publishing tools and for its commitment to open access practices. In 2013, Pensoft launched the first ever, end-to-end, XML-based, authoring, reviewing and publishing workflow, now upgraded to the ARPHA Publishing Platform. As of today, ARPHA hosts over 50 open access, peer-reviewed scholarly journals: the whole Pensoft portfolio in addition to titles owned by learned societies, university presses and research institutions.

As part of the strategic collaboration, all Pensoft content and journals hosted on ARPHA are indexed in the ScienceOpen’s research and discovery environment, which puts them into thematic context of over 60 million articles and books. In addition, thousands of articles across more than 20 journals were integrated into a “Pensoft Biodiversity” Collection. Combined this way, the content benefits from the special infrastructure of ScienceOpen Collections, which supports thematic groups of articles and books equipped with a unique landing page, a built-in search engine and an overview of the featured content. The Collections can be reviewed, recommended and shared by users, which facilitates academic debate and increases the discoverability of the research.

The Pensoft Biodiversity collection is available from: https://www.scienceopen.com/collection/PensoftBiodiversity

“It is certainly great news and a much-anticipated milestone for Pensoft, ARPHA and our long-year partners and supporters from ScienceOpen to have brought our collaboration to a new level by indexing the whole ARPHA-hosted content at ScienceOpen,” comments Pensoft’s and ARPHA’s CEO and founder Prof. Lyubomir Penev. “Most of all, the integration between ARPHA and ScienceOpen at an infrastructural level means that we will be able to offer this incredible service and increased visibility to newcoming journals right away. On the other hand, by streaming fresh and valuable publicly accessible content to the ScienceOpen database, these journals will be further adding to the growth of science in the open.”

Stephanie Dawson, CEO of ScienceOpen says, “I am particularly excited to add new high-quality, open access biodiversity content from Pensoft Publishers to the ScienceOpen discovery environment as we have a very active community of researchers on ScienceOpen creating and sharing Collections in this field. We are looking forward to working with Pensoft’s innovative journals to support their open science goals.”

The collaboration reflects not only the commitment of both Pensoft and ScienceOpen to new methods of knowledge dissemination, but also the joint mission to champion open science through innovation. The two companies will cooperate at a strategic level in order to increase the international outreach of their content and services, and to make them even more accessible to the broad community.

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About ScienceOpen:

From promotional collections to Open Access hosting and full publishing packages, ScienceOpen provides next-generation services to academic publishers embedded in an interactive discovery platform. ScienceOpen was founded in 2013 in Berlin and Boston by Alexander Grossmann and Tibor Tscheke to accelerate research communication.

How to import occurrence records into manuscripts from GBIF, BOLD, iDigBio and PlutoF

On October 20, 2015, we published a blog post about the novel functionalities in ARPHA that allows streamlined import of specimen or occurrence records into taxonomic manuscripts.

Recently, this process was reflected in the “Tips and Tricks” section of the ARPHA authoring tool. Here, we’ll list the individual workflows:

Based on our earlier post, we will now go through our latest updates and highlight the new features that have been added since then.

Repositories and data indexing platforms, such as GBIF, BOLD systems, iDigBio, or PlutoF, hold, among other types of data, specimen or occurrence records. It is now possible to directly import specimen or occurrence records into ARPHA taxonomic manuscripts from these platforms [see Fig. 1]. We’ll refer to specimen or occurrence records as simply occurrence records for the rest of this post.

Import_specimen_workflow_
[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 GBIF, BOLD systems, iDigBio, or PlutoF, 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 in the ARPHA Writing Tool. To import records, the author needs to:

  1. Locate an occurrence record or records in one of the supported data portals;
  2. Note the ID(s) of the records that ought to be imported into the manuscript (see Tips and Tricks for screenshots);
  3. Enter the ID(s) of the occurrence record(s) in a form that is to be seen in the “Materials” section of the species treatment;
  4. Select 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.

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. We have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found on 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. 2].

Figure-61-01
[Fig. 2] Edit materials
In this example, type or paste the UUID (b9ff7774-4a5d-47af-a2ea-bdf3ecc78885), select the iDigBio source 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. 3].

taxon-treatments- 3
[Fig. 3] Materials after they have been imported
This workflow can be used for a number of purposes. An interesting future application is the rapid re-description of species, but even more exciting is the description of new species from BIN’s. BIN’s (Barcode Identification Numbers) delimit Operational Taxonomic Units (OTU’s), created algorithmically at BOLD Systems. If a taxonomist decides that an OTU is indeed a new species, then he/she can import all the type information associated with that OTU for the purposes of describing it as a new species.

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, iDigBio and PlutoF. 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. 642241.