Month: July 2016

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Guiding EU researchers along the ‘last mile’ to Open Digital Science

Striving to address societal challenges in sectors including Health, Energy and the Environment, the European Union is developing the European Open Science Cloud, a complete socio-technical environment, including robust e-infrastructures capable of providing data and computational solutions where publicly funded research data are Findable, Accessible, Interoperable and Re-usable (FAIR).

Since 2007 The European Commission (EC) has invested more than €740 million in e-infrastructures through Horizon 2020 (the European Union Research and Innovation programme 2014-2020) and FP7 (the European Union’s Seventh Framework Programme for Research and Technological Development). They want to see this exploited in full.

Many research communities are, however, struggling to benefit from this investment. The authors call for greater emphasis on Virtual Research Environments (VREs) as the only way for researchers to capitalise on EC advances in networking and high performance computing. The authors characterise this as a “last mile” problem, a term borrowed from telecommunications networks and once coined to emphasise the importance (and difficulty) of connecting the broader network to each customer’s home or office. Without the last mile of connectivity, a network won’t generate a cent of value.

Some concerns around the transition to Open Digital Science refer to attribution and quality assurance, as well as limited awareness of open science and its implications to research. However, most difficulties relate to many e-infrastructure services being too technical for most users, not providing easy-to-use interfaces and not easily integrated into the majority of day-to-day research practices.

Trustworthy and interoperable Virtual Research Environments (VREs) are layers of software that hide technical details and facilitate communication between scientists and computer infrastructures. They serve as friendly environments for the scientists to work with complicated computer infrastructures, while being able to use their own set of concepts, ways of doing things and working protocols.

Helping them to solve the difficulties noted above, VREs could guide the skeptical research communities along the ‘last mile’ towards Open Digital Science, according to an international team of scientists who have published their Policy Brief in the open access journal Research Ideas and Outcomes (RIO).

The authors state “These domain-specific solutions can support communities in gradually bridging technical and socio-cultural gaps between traditional and open digital science practice, better diffusing the benefits of European e-infrastructures”. They also recognise that “different e-infrastructure audiences require different approaches.”

“Intuitive user interface experience, seamless data ingestion, and collaboration capabilities are among the features that could empower users to better engage with provided services,” stress the authors.

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Original source:

Koureas D, Arvanitidis C, Belbin L, Berendsohn W, Damgaard C, Groom Q, Güntsch A, Hagedorn G, Hardisty A, Hobern D, Marcer A, Mietchen D, Morse D, Obst M, Penev L, Pettersson L, Sierra S, Smith V, Vos R (2016) Community engagement: The ‘last mile’ challenge for European research e-infrastructures. Research Ideas and Outcomes 2: e9933. doi: 10.3897/rio.2.e9933>

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Biodiversity data import from historical literature assessed in an EMODnet Workshop Report

While biodiversity loss is an undisputable issue concerning everyone on a global scale, data about species distribution and numbers through the centuries is crucial for adopting adequate and timely measures.

However, as abundant as this information currently is, large parts of the actual data are locked-up as scanned documents, or not digitized at all. Far from the machine-readable knowledge, this information is left effectively inaccessible. In particular, this is the case for data from marine systems.

This is how data managers who implement data archaeology and rescue activities, as well as external experts in data mobilization and data publication, were all brought together in Crete for the European Marine Observation and Data network (EMODnet) Workshop, which is now reported in the open access journal Research Ideas and Outcomes (RIO).

“In a time of global change and biodiversity loss, information on species occurrences over time is crucial for the calculation of ecological models and future predictions”, explain the authors. “But while data coverage is sufficient for many terrestrial areas and areas with high scientific activity, large gaps exist for other regions, especially concerning the marine systems.”

Aiming to fill both spatial and temporal gaps in European marine species occurrence data availability by implementing data archaeology and rescue activities, the workshop took place on 8th and 9th June in 2015 at the Hellenic Center for Marine Research Crete (HCMR), Heraklion Crete, Greece. There, the participants joined forces to assess possible mechanisms and guidelines to mobilize legacy biodiversity data.

Together, the attendees reviewed the current issues associated with manual extraction of occurrence data. They also used the occasion to test tools and mechanisms that could potentially support a semi-automated process of data extraction. Long-disputed in the scholarly communities matters surrounding data re-publication, such as openly accessible data and author attribution were also discussed. As a result, at the end of the event, a list of recommendations and conclusions was compiled, also openly available in the Workshop Report publication.

Ahead of the workshop, curators extracted legacy data to compile a list of old faunistic reports, based on certain criteria. While performing the task, they noted the time and the problems they encountered along the way. Thus, they set the starting point for the workshop, where participants would get the chance to practice data extraction themselves at the organised hands-on sessions.

“Legacy biodiversity literature contains a tremendous amount of data that are of high value for many contemporary research directions. This has been recognized by projects and institutions such as the Biodiversity Heritage Library (BHL), which have initiated mass digitization of century-old books, journals and other publications and are making them available in a digital format over the internet,” note the authors.

“However, the information remains locked up even in these scanned files, as they are available only as free text, not in a structured, machine-readable format”.

In conclusion, the participants at the European Marine Observation and Data network Workshop listed practical tips regarding in-house document scanning; suggested a reward scheme for data curators, pointing out that credit needs to be given to the people “who made these valuable data accessible again”; encouraged Data papers publication, for aligning with the “emerging success of open data”; and proposed the establishment of a data encoding schema. They also highlighted the need for academic institutions to increase their number of professional data manager permanent positions, while also providing quality training to long-term data experts.

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Original source:

Faulwetter S, Pafilis E, Fanini L, Bailly N, Agosti D, Arvanitidis C, Boicenco L, Capatano T, Claus S, Dekeyzer S, Georgiev T, Legaki A, Mavraki D, Oulas A, Papastefanou G, Penev L, Sautter G, Schigel D, Senderov V, Teaca A, Tsompanou M (2016) EMODnet Workshop on mechanisms and guidelines to mobilise historical data into biogeographic databases. Research Ideas and Outcomes 2: e9774. doi: 10.3897/rio.2.e9774

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How RIO Collections help showcase research project outputs

This text was originally featured on the OpenAIRE Blog. We thank OpenAIRE for allowing us to republish, the original post can be found here.

A recent SPARC Innovator award winner, Research Ideas and Outcomes (RIO) was built around the principles of open research in scholarly communications. Traditionally, a research project ends up with just a few articles published in scholarly journals after many years of work. But why communicate just research articles at the end of a cycle?

Research articles are just a small component of the research cycle. What about all the other project outputs – research ideas, grant proposals, methodologies, data, software, policy briefs and others? At RIO we want to publish the full research cycle, all in one place, with ‘Collections’, to encourage re-usability and effective open knowledge transfer.

Collections for Project Coordinators

RIO offers a wide range of publication types to cover the needs of each research project. Flexible article templates are tailored to provide an easy fit for project outcomes, including H2020, FP7, NSF, NIH, DFG, FWF and other Grant Proposals, Case Studies, Project Reports, Data Management Plans, Data Papers, Software Descriptions, Workshop Reports, Policy Briefs, Conference Presentations and Posters, and many more.

Collections can be opened for each project, where project results, including interim ones, are officially published in both human- (HTML, PDF) and machine-readable (JATS XML) formats, assigned a DOI, collected, archived, made discoverable, easily citable and openly available to everyone. To ensure longevity and compatibility with Horizon 2020 recommendations for open access, all RIO publications are also automatically archived in ZENODO (in both PDF and XML) on the very same day.

RIO is also integrated with OpenAIRE and the CrossRef’s Open Funders Registry meaning that authors can choose to tag both funders and projects in their articles. The workflow is highly-beneficial – automatically linking funders to publications via API, whilst at the same time directly adding RIO articles to project and funder output lists, browsable on OpenAIRE.

This comes packed with additional innovation, thanks to the ARPHA Journal Publishing Platform.

ARPHA (Authoring, Reviewing, Publishing, Hosting and Archiving), is the first ever online collaborative journal publishing platform that supports the full life cycle of a manuscript, from authoring through submission, peer review, publication, dissemination and updates, within a single online collaborative environment.

ARPHA includes a What-You-See-Is-What-You-Get (WYSIWYG) authoring tool. It allows authors to work collaboratively on a manuscript with their co-authors, and one can also invite external contributors, such as mentors, pre-submission reviewers, linguistic and copy editors.

The authoring tool is fully integrated in the publishing workflow so there is no need for a ‘typesetting’ stage or ‘page proofs’ – we have eliminated this inefficiency. What the authors see, is what the reviewers and editors see, and is what will be published. At other publishers, errors and delays are often introduced by the need for a typesetting process – we therefore offer a more efficient and timely system.

The platform lays the infrastructure for RIO’s transparent three-stage peer review: (1) author-organized,pre-submission, during the manuscript authoring process in ARPHA (2) community-sourced, post-publication, and (3) journal-organised, post-publication (optional), to ensure quality-controlled, efficient publication and dissemination.

Emphasis is put on the societal relevance of research by mapping research outputs to the United Nations’Sustainable Development Goals (SDGs) for each published output.

All this comes with an affordable pricing model, which offers tailored packages for projects and individual researcher needs. For individual publications an à la carte pricing model gives authors the opportunity to select only the publishing services they need, thus providing flexibility in the final price they pay.

An example Collection at RIO: the FP7-funded EU BON project

The large-scale FP7-funded EU BON project: Building the European Biodiversity Observation Network is one of the first to try out our Collections feature. The EU BON Collection at RIO is a great way for the project to showcase and link-up all the important published outputs in the same place, openly available in a variety of formats, at the click of a button.

EU BON collection

Be our next open research pilot!

If you are feeling inspired and see the potential of publishing more of your project results, RIO invites you to enquire about publishing a pilot Collection with us. We welcome suggestions from all fields of research, not just the sciences.

The journal will support a limited number of FREE project output Collections. Apply now to be one of the first fully open access research cycles!

Interested project co-ordinators can contact us at rio@riojournal.com outlining initial output proposals or a Collection of project outcomes they would like to publish in RIO.