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.

###

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.

All Pensoft journals indexed in Transpose to support transparency in journal policies

All open-access, peer-reviewed academic titles of Pensoft‘s, as well as those using the white-label publishing solution provided by the scholarly publishing platform ARPHA, have their journal policy data fed into the Transpose database, in order to increase their discoverability and transparency.

Thanks to the recent integration with the community-sourced initiative Transpose, details about each journal’s approach to peer review, co-review and preprint publication can be easily accessed, navigated and compared through a user-friendly interface. Visitors can also query the data by journal title, publisher, ISSN or DOI, and apply several filters.

Having estimated that almost 1/3 of the top-cited journals across disciplines do not provide clearly basic information about their editorial policies, including whether they operate blind peer review or not, the team behind Transpose launched the forward-thinking community-sourced initiative with the aim to advance practices in academia and increase awareness and transparency amongst authors, editors and many other stakeholder groups. To highlight the essentiality of free and easy access to editorial policies for a wide range of actors, Transpose have published user testimonials on their website coming from various points of view, including early researchers, supervisors, project investigators, funders, publishing staff, and others.


Recent integration of the scholarly publishing platform ARPHA and Transpose results in the editorial policies of all ARPHA-hosted journals being fed into the associated database. Thus, various stakeholders from across the academic landscape are provided with an easy access to details about the peer review, co-review and preprint policies at each journal via a user-friendly interface.

Pensoft and ARPHA’s founder and CEO Prof. Lyubomir Penev says:

“Having been Open Science advocates from the very beginning, at Pensoft and ARPHA, we have always supported our clients and users in being as transparent as possible. Favourite examples are the open-science journal Research Ideas and Outcomes (RIO), welcoming continuously updatable publications from across the whole research cycle, and Rethinking Ecology, launched to voice innovative and even bold ideas for the purposes of taking swift actions towards the conservation of the environment. The former operates public pre- and post-publication peer review to support efficient collaboration in research, while the latter relies on double-blind peer reviews, in order to encourage researchers of various experience and background to share their inventive ideas in ecology. Obviously, journal policies are and should be crucial when it comes to picking a specific journal over another regardless of the perspective. This is why I am certain that joining Transpose is doing good for all ARPHA-hosted journals, as well as the academic community.”

ASAPbio‘s Executive Director and member of the team behind Transpose, Dr Jessica Polka adds:

“We’re thrilled to incorporate data from Pensoft into Transpose. Making policy information clear and easy to find ensures that authors and reviewers can work with journals that best align with their values — and that scholarly work can be fairly interpreted by everyone, including general readers.”

###

Additional information:

About Transpose:

Transpose is an initiative to build a database of journal policies. It focuses on three areas: open peer review, co-reviewing, and detailed pre-printing policies. It welcomes contributions from anyone, but seeks verification from journals and publishers. The goal of Transpose is to foster new practices while increasing awareness among authors, editors, and other stakeholders, and we seek to provide resources to assist journals in setting, sharing, and clarifying their policies.

Plazi and the Biodiversity Literature Repository (BLR) awarded EUR 1.1 million from Arcadia Fund to grant free access to biodiversity data

Plazi has received a grant of EUR 1.1 million from Arcadia – the charitable fund of Lisbet Rausing and Peter Baldwin – to liberate data, such as taxonomic treatments and images, trapped in scholarly biodiversity publications.

The project will expand the existing corpus of the Biodiversity Literature Repository (BLR), a joint venture of Plazi and Pensoft, hosted on Zenodo at CERN. The project aims to add hundreds of thousands of figures and taxonomic treatments extracted from publications, and further develop and hone the tools to search through the corpus.

The BLR is an open science community platform to make the data contained in scholarly publications findable, accessible, interoperable and reusable (FAIR). BLR is hosted on Zenodo, the open science repository at CERN, and maintained by the Switzerland-based Plazi association and the open access publisher Pensoft.

In its short existence, BLR has already grown to a considerate size: 35,000+ articles have been added, and extracted from 600+ journals. From these articles, more than 180,000 images have also been extracted and uploaded to BLR, and 225,000+ sub-article components, including biological names, taxonomic treatments or equivalent defined blocks of text have been deposited at Plazi’s TreatmentBank. Additionally, over a million bibliographic references have been extracted and added to Refbank.

The articles, images and all other sub-article elements are fully FAIR compliant and citable. In case an article is behind a paywall, a user can still access its underlying metadata, the link to the original article, and use the DOI assigned to it by BLR for persistent citation.

“Generally speaking, scientific illustrations and taxonomic treatments, such as species descriptions, are one of the best kept ‘secrets’ in science as they are neither indexed, nor are they citable or accessible. At best, they are implicitly referenced,” said Donat Agosti, president of Plazi. “Meanwhile, their value is undisputed, as shown by the huge effort to create them in standard, comparative ways. From day one, our project has been an eye-opener and a catalyst for the open science scene,” he concluded.

Though the target scientific domain is biodiversity, the Plazi workflow and tools are open source and can be applied to other domains – being a catalyst is one of the project’s goals.

While access to biodiversity images has already proven useful to scientists, but also inspirational to artists, for example, the people behind Plazi are certain that such a well-documented, machine-readable interface is sure to lead to many more innovative uses.

To promote BLR’s approach to make these important data accessible, Plazi seeks collaborations with the community and publishers, to remove hurdles in liberating the data contained in scholarly publications and make them FAIR.

The robust legal aspects of the project are a core basis of BLR’s operation. By extracting the non-copyrightable elements from the publications and making them findable, accessible and re-usable for free, the initiative drives the move beyond the PDF and HTML formats to structured data.

###

To participate in the project or for further questions, please contact Donat Agosti, President at Plazi at info@plazi.org

 

Additional information:

About Plazi:

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end, Plazi maintains TreatmentBank, a digital taxonomic literature repository to enable archiving of taxonomic treatments; develops and maintains TaxPub, an extension of the National Library of Medicine / National Center for Biotechnology Informatics Journal Article Tag Suite for taxonomic treatments; is co-founder of the Biodiversity Literature Repository at Zenodo, participates in the development of new models for publishing taxonomic treatments in order to maximize interoperability with other relevant cyberinfrastructure components such as name servers and biodiversity resources; and advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data. Plazi is a major contributor to the Global Biodiversity Information Facility.

About Arcadia Fund:

Arcadia is a charitable fund of Lisbet Rausing and Peter Baldwin. It supports charities and scholarly institutions that preserve cultural heritage and the environment. Arcadia also supports projects that promote open access and all of its awards are granted on the condition that any materials produced are made available for free online. Since 2002, Arcadia has awarded more than $500 million to projects around the world.

ScienceOpen indexes >1,000 articles from ARPHA-hosted journals RIO & Check List in a trial

Two scholarly journals published on ARPHA – Research Ideas and Outcomes (RIO Journal) and Check List – now have their articles freely available via the community-focused search and discovery platform ScienceOpen.

This new trial between the two high-tech innovators and Open Science proponents presents an important step forward to making research publications not only easier to find and access, but also more inviting to fellow scientists seeking new collaborations and platforms for voicing their ideas and expertise.

Currently, there are 168 and 948 article records fed to ScienceOpen straight from RIO and Check List respectively.

While the articles’ underlying data, such as author names, citations, keywords, journals and more, are automatically harvested and analyzed by ScienceOpen, so that research items can be easily interlinked, readers are encouraged to further provide context to the research items. The user-friendly intuitive interface invites them to add their comments, recommendations or open post-publication peer reviews, and even create their own topical collections regardless of affiliations and journals.

To make sure users land on the most relevant articles in what feels like the blink of an eye compared to traditional methods, ScienceOpen also accommodates an advanced multi-layer search engine relying on a total of 20 smart filters and six sorting parameters.

“We have long worked closely with ScienceOpen, as it only makes sense given our shared vision for the future of academia, so the present trial project happened very naturally,” says Prof. Lyubomir Penev, founder and CEO of ARPHA and its developer – scholarly publisher and technology provider Pensoft. “Nowadays, we are well aware that scientific findings are of little merit if ‘living’ in a vacuum. Therefore, we need research articles to be as discoverable as possible, and, no less importantly, to be open to feedback and further work.”

“We are thrilled to add this new content to the ScienceOpen as we have both strong researcher communities in zoology and in scholarly communications within our broadly interdisciplinary content. The ARPHA platform is a natural fit to deliver rich metadata to our discovery services and we are very much looking forward to working with their team,” says Stephanie Dawson, CEO of ScienceOpen.

 

About ScienceOpen:

ScienceOpen is an independent start-up company based in Berlin and Boston, which explores new ways to open up information for the scholarly community. It provides a freely accessible search and discovery platform that puts research in context. Smart filters, topical collections and expert input from the academic community help users to find the most relevant articles in their field and beyond.

The Biodiversity Literature Repository passes the 200,000-items milestone

The achievement is a result of an automated information-extraction workflow developed by Plazi, Pensoft and Zenodo/CERN

Everyday a large number of biodiversity data are uploaded to the free and open Biodiversity Literature Repository (BLR), a joint venture of Plazi and Pensoft, hosted on Zenodo/CERN.

The automated workflow, successfully digitizing scientific literature from start to finish, assures that articles and their sub-article elements, from illustrations to taxonomic treatments, metadata, images, figures, and supplementary files are given a persistent digital object identifier (e.g. DOIs) of their own, cross-referenced, and then uploaded to the repository. The BLR makes these data discoverable, accessible, reusable and citable by any scientist from anywhere in the world.

164542

The organizations behind this project are Plazi, a non-profit dedicated to supporting and promoting persistent and openly accessible digital taxonomic literature, and Pensoft, a scholarly publisher and publishing technology provider.

The start of 2018 marked a new milestone for BLR as the number of the deposits crossed 200,000, with an average of six links to related entities, including the link to the source publication, added to each deposit. The deposits in the BLR represent 63% of the total deposits in Zenodo.

To make sure that the extracted data remain open and accessible to all, Plazi, Pensoft and Zenodo stand firmly for the distribution of research data under unrestricted access by using waivers, such as CC0 or PDDL.

“The Plazi workflow allows, for the first time, access to, citing and reusing the hidden data in scientific publications, and thus opening up scientific literature in an unprecedented way,” says Donat Agosti, president of Plazi.

Last year, a paper focusing on unrestricted access to images comprising biodiversity data within research articles and its advantages was published by a team from Plazi in Pensoft’s open science RIO Journal.

###

Additional information:

About Pensoft:

Pensoft is an independent academic publishing company, well-known worldwide for its innovations in the field of semantic publishing, as well as for its cutting-edge publishing tools and workflows. In 2013, Pensoft launched the first ever end to end XML-based authoring, reviewing and publishing workflow, as demonstrated by the Pensoft Writing Tool (PWT) and the Biodiversity Data Journal (BDJ), now upgraded to the ARPHA Publishing Platform. Flagship titles include: Research Ideas and Outcomes (RIO), One Ecosystem, ZooKeys, Biodiversity Data Journal, PhytoKeys, MycoKeys, and more.

About Plazi:

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end, Plazi maintains TreatmentBank, a digital taxonomic literature repository to enable archiving of taxonomic treatments; develops and maintains TaxPub, an extension of the National Library of Medicine / National Center for Biotechnology Informatics Journal Article Tag Suite for taxonomic treatments; participates in the development of new models for publishing taxonomic treatments in order to maximize interoperability with other relevant cyberinfrastructure components such as name servers and biodiversity resources; and advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data.

About Zenodo:

Zenodo is an OpenAIRE project, in the vanguard of the open access and open data movements in Europe. It was commissioned by the EC to support their nascent Open Data policy by providing a catch-all repository for EC funded research. CERN, an OpenAIRE partner and pioneer in open source, open access and open data, provided this capability and Zenodo was launched in May 2013.

In support of its research programme CERN has developed tools for Big Data management and extended Digital Library capabilities for Open Data. Through Zenodo these Big Science tools can be effectively shared with the long-tail of research.

Pensoft journals integrated with Catalogue of Life to help list the species of the world

While not every taxonomic study is conducted with a nature conservation idea in mind, most ecological initiatives need to be backed by exhaustive taxonomic research. There simply isn’t a way to assess a species’ distributional range, migratory patterns or ecological trends without knowing what this species actually is and where it is coming from.

In order to facilitate taxonomic and other studies, and lay the foundations for effective biodiversity conservation in a time where habitat loss and species extinction are already part of our everyday life, the global organisation Catalogue of Life (CoL) works together with major programmes, including GBIFEncyclopedia of Life and the IUCN Red List, to collate the names of all species on the planet set in the context of a taxonomic hierarchy and their distribution.

Recently, the scholarly publisher and technological provider Pensoft has implemented a new integration with CoL, so that it joins in the effort to encourage authors publishing global taxonomic review in any of the publisher’s journals to upload their taxonomic contributions to the database.

Whenever authors submit a manuscript containing a world revision or checklist of a taxon to a Pensoft journal, they are offered the possibility to upload their datasets in CoL-compliant format, so that they can contribute to CoL, gain more visibility and credit for their work, and support future research and conservation initiatives.

Once the authors upload the dataset, Pensoft will automatically notify CoL about the new contribution, so that the organisation can further process the knowledge and contact the authors, if necessary.

In addition, CoL will also consider for indexing global taxonomic checklists, which have already been published by Pensoft.

It is noteworthy to mention that unlike an automated search engine, CoL does not simply gather the uploaded data and store them. All databases in CoL are thoroughly reviewed by experts in the relevant field and comply with a set of explicit instructions.

“Needless to say that the Species 2000 / Catalogue of Life community is very happy with this collaboration,” says Dr. Peter Schalk, Executive Secretary.

“It is essential that all kinds of data and information sharing initiatives in the realm of taxonomy and biodiversity science get connected, in order to provide integrated quality services to the users in and outside of our community. The players in this field carry responsibility to forge partnerships and collaborations that create added value for science and society and are mutually reinforcing for the participants. Our collaboration is a fine example how this can be achieved,” he adds.

“With our extensive experience in biodiversity research, at Pensoft we have already taken various steps to encourage and support data sharing practices,” says Prof. Lyubomir Penev, Pensoft’s founder and CEO. To better serve this purpose, last year, we even published a set of guidelines and strategies for scholarly publishing of biodiversity data as recommended by our own experience. Furthermore, at our Biodiversity Data Journal, we have not only made the publication of open data mandatory, but we were also the first to implement integrated narrative and data publication within a single paper.”

“It only makes sense to collaborate with organisations, such as Catalogue of Life, to make sure that all these global indexers are up-to-date and serve the world’s good in preserving our wonderful biodiversity,” he concludes.

New partnership between Pensoft and BEXIS 2 encourages Data Paper publications

Following the new partnership between the German open source platform BEXIS 2 and the academic publisher Pensoft, scientists are now able to publish data papers in three of the most innovative Pensoft journals: Biodiversity Data Journal (BDJ)One Ecosystem and Metabarcoding and Metagenomics (MBMG), using EML data packs from BEXIS 2.

In order to encourage and facilitate high-quality data publication, the collaboration allows for researchers to easily store, analyse and manage their data via BEXIS 2, before sharing it with the scientific community in a creditable format.

The newly implemented workflow requires researchers to first download their data from the free open source BEXIS 2 software and, then, upload the data pack on Pensoft’s ARPHA Journal Publishing Platform where the data can be further elaborated to comply to the established Data Paper standards. Within the software, they can work freely on these data.

Having selected a journal and a data paper article template, a single click at an ‘Import a manuscript’ button transfers the data into a manuscript in ARPHA Authoring Tool. Within the collaborative writing tool, the data owner can invite co-authors and peers to help him/her finalise the paper.

Once submitted to a journal, the article undergoes a peer review and data auditing and, if accepted for publication, is published to take advantage of all perks available at any Pensoft journal, including easy discoverability and increased citability.

“I am delighted to have this new partnership between Pensoft and BEXIS 2 announced,” says Pensoft’s founder and CEO Prof. Lyubomir Penev.

“I believe that workflows like ours do inspire scientists to, firstly, refine their data to the best possible quality, and, secondly, make them available to the world, so that these data can benefit the society much faster and more efficiently through collaborative efforts and constructive feedback.”

“With scientists becoming more and more eager to publish research data in data journals like Pensoft’s BDJ, it is important to provide comprehensive and easy workflows for the transition of data from a data management platform like BEXIS 2 to the repository of the data journal without losing or re-entering any information. So we are absolutely delighted that a first version of such data publication workflow is now available to users of BEXIS 2.” says Prof. Birgitta König-Ries, Principle Investigator of BEXIS 2.

The collaboration between Pensoft and BEXIS 2 is set to strengthen in the next few months, when a new import workflow is expected to provide an alternative way to publish datasets.

In 2015, Pensoft launched similar workflows for DataONE, the Global Biodiversity Information Facility (GBIF) and the Long Term Ecological Research Network (LTER).

###

Additional information:

About BEXIS 2:

BEXIS 2 is a free and open source software supporting researchers in managing their data throughout the entire data lifecycle from data collection, documentation, processing, analyzing, to sharing and publishing research data.

BEXIS 2 is a modular scalable platform suitable for working groups and collaborative project consortia with up to several hundred researchers. It has been designed to meet the requirements of researchers in the field of biodiversity, but it is generic enough to serve other communities as well.

BEXIS 2 is developed at Friedrich-Schiller-University Jena together with partners from Max-Planck Institute of Biogeochemistry Jena, Technical University Munich and GWDG Göttingen. The development is funded by the German Science Foundation (DFG).