Tag: open access

Posted on

The first microbial supertree from figure-mining thousands of papers

While recent reports reveal the existence of more than 114,000,000 documents of published scientific literature, finding a way to improve the access to this knowledge and efficiently synthesise it becomes an increasingly pressing issue.

Seeking to address the problem through their PLUTo workflow, British scientists Ross Mounce and Peter Murray-Rust, University of Cambridge and Matthew Wills, University of Bath perform the world’s first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Their results are published in the open science journal Research Ideas and Outcomes (RIO).

For their study, the researchers picked the International Journal of Systematics and Evolutionary Microbiology (IJSEM) – the sole repository hosting all new validly described prokaryote taxa and, therefore, an excellent choice against which to test systems for the automated and semi-automated synthesis of published phylogenies. According to the authors, IJSEM publishes a greater number of phylogenetic tree figure images a year than any other journal.

An eleven-year span of articles dating back to January, 2003 was systematically downloaded so that all image files of phylogenetic tree figures could be extracted for analysis. Computer vision techniques then allowed for the automatic conversion of the images back into re-usable, computable, phylogenetic data and used for a formal supertree synthesis of all the evidence.

During their research, the scientists had to overcome various challenges posed by copyrights formally covering almost all of the documents they needed to mine for the purpose of their work. At this point, they faced quite a paradox – while easy access and re-use of data published in scientific literature is generally supported and strongly promoted, common copyright practices make it difficult for a scientist to be confident when incorporating previously compiled data into their own work. The authors discuss recent changes to UK copyright law that have allowed for their work to see the light of day. As a result, they provide their output as facts, and assign them to the public domain by using the CC0 waiver of Creative Commons, to enable worry-free re-use by anyone.

“We are now at the stage where no individual has the time to read even just the titles of all published papers, let alone the abstracts,” comment the authors.

“We believe that machines are now essential to enable us to make sense of the stream of published science, and this paper addresses several of the key problems inherent in doing this.”

“We have deliberately selected a subsection of the literature (limited to one journal) to reduce the volume, velocity and variety, concentrating primarily on validity. We ask whether high-throughput machine extraction of data from the semistructured scientific literature is possible and valuable.”  

 

Original source:

Mounce R, Murray-Rust P, Wills M (2017) A machine-compiled microbial supertree from figure-mining thousands of papers. Research Ideas and Outcomes 3: e13589. https://doi.org/10.3897/rio.3.e13589

 

Additional information:

The research has been funded by the BBSRC (grant BB/K015702/1 awarded to MAW and supporting RM).

Posted on

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.

###

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

Posted on

Publishing grant proposals, presubmission

There are a lot of really interesting works being published over at Research Ideas and Outcomes (RIO).  If you aren’t already following the updates you can do so via RSS, Twitter, or via email (scroll to the bottom for sign-up).

In this post I’m going to discuss why Chad Hammond’s contribution is so remarkable and why it could represent an exciting model for a more transparent and more immediate future of scholarly communications.

Version1

 

 

 

So, what’s special?

Well, to state the obvious first: it’s a grant proposal, not a research article. RIO Journal has published quite a lot of research proposals now, it’s becoming a real strength of the journal. But that’s not the really interesting thing about it. The really cool thing is that Chad published this grant proposal with RIO before it was submitted it to the funder (Canadian Institutes of Health Research) for evaluation.

You’ll see the publication date of Version 1 of the work is 24th March 2016. Pleasingly, after publication in RIO Chad’s proposal was evaluated by CIHR and awarded research funding. Chad received news of this in late April:

…and the story gets even better from here because thanks to RIO’s unique technology called ARPHA, Chad was able to re-import his published article back into editing mode, to update the proposal to acknowledge that it had been funded:

This proposal was submitted to and received funding from the annual Canadian Institutes of Health Research (CIHR) competition for postdoctoral fellowships.

The updated proposal was then checked by the editorial team and republished as an updated version of the original proposal: Version 2, making-use of CrossMark technology to formally link the two versions and to make sure readers are always made aware if a newer version of the work exists. Chad’s updated proposal now has a little ‘Funded’ button appended to it (see below), to indicate that this proposal has been successfully funded. We hope to see many more such successfully funded proposals published at RIO.

Title and metadata

 

 

 

With permission given, Chad was also able to supply some of the reviewer comments passed to him from CIHR reviewers as supplementary data to the updated Version 2 proposal. These will undoubtedly provide invaluable insight into reviewing processes for many.

Finally, for funders and publishing-tech geeks: you should really take note of the lovely machine-readable XML-formatted version of Chad’s proposal. Pensoft has machine-readable XML output as standard, not just PDF and HTML. Funding agencies around the world would do well to think closely about the value of having XML-formatted machine-readable grant proposal submissions. There’s serious value to this and I think it’s something we’ll see more of in the future. Pensoft is actively looking to work with funders to develop further these ideas and approaches for genuinelyadding-value to scholarly communications.
RIO is truly an innovative journal don’t you think?

References

Version 1:
Hammond C (2016) Widening the circle of care: An arts-based, participatory dialogue with stakeholders on cancer care for First Nations, Inuit,and Métis peoples in Ontario, Canada. Research Ideas and Outcomes 2: e8615. doi: 10.3897/rio.2.e8615

Version 2:
Hammond C (2016) Widening the circle of care: An arts-based, participatory dialogue with stakeholders on cancer care for First Nations, Inuit, and Métis peoples in Ontario, Canada. Research Ideas and Outcomes 2: e9115. doi: 10.3897/rio.2.e9115

 

This blog post was originally published on Ross Mounce’s blog.

Posted on

Sharing biodiversity data: Best tools and practices via the EU-funded project EU BON

Due to the exponential growth of biodiversity information in recent years, the questions of how to mobilize such vast amounts of data has become more tangible than ever. Best practices for data sharing, data publishing, and involvement of scientific and citizen communities in data generation are the main topic of a recent report by the EU FP7 project Building the European Biodiversity Observation Network (EU BON), published in the innovative Research Ideas & Outcomes (RIO) journal.

The report “Data sharing tools for Biodiversity Observation Networks” provides conceptual and practical advice for implementation of the available data sharing and data publishing tools. A detailed description of tools, their pros and cons, is followed by recommendations on their deployment and enhancement to guide biodiversity data managers in their choices.

“We believe publishing this report in RIO makes a lot of sense given the journal’s innovative concept of publishing unconventional research outcomes such as project reports. This feature provides projects like EU BON with the chance to showcase their results effectively and timely. The report provides a useful practical guide for biodiversity data managers and RIO gives the project an opportunity to share findings with anyone who will make use of such information”, explains Prof. Lyubomir Penev, Managing Director of Pensoft and partner in EU BON.

The new report is the second EU BON contribution featured in a dedicated project outcomes collection in RIO. Together with the data policy recommendations it provides a comprehensive set of resources for the use of biodiversity data managers and users.

“We did our biodiversity data sharing tools comparison from the perspective of the needs of the biodiversity observation community with an eye on the development of a unified user interface to this data – the European Biodiversity Portal (EBP)”, add the authors.

The scientists have identified two main challenges standing in front of the biodiversity data community. On the one hand, there is a variety of tools but none can as stand alone, satisfy all the requirements of the wide variety of data providers. On the other hand, gaps in data coverage and quality demand more effort in data mobilization.

Envisaged information flows between EU BON and LTER Europe, showing the complexity of sharing biodiversity data (from the 3rd EU BON Stakeholder Roundtable, Granada on 9-11 December 2015).
Envisaged information flows between EU BON and LTER Europe, showing the complexity of sharing biodiversity data (from the 3rd EU BON Stakeholder Roundtable, Granada on 9-11 December 2015).

“For the time being a combination of tools combined in a new work-flow, makes the most sense for EU BON to mobilize biodiversity data,” comment the report authors on their findings. “There is more research to be done and tools to be developed, but for the future there is one firm conclusion and it is that the choice of tools should be defined by the needs of those observing biodiversity – the end user community in the broadest sense – from volunteer scientists to decision makers.”

###

Original Source:

Smirnova L, Mergen P, Groom Q, De Wever A, Penev L, Stoev P, Pe’er I, Runnel V, Camacho A, Vincent T, Agosti D, Arvanitidis C, Bonet F, Saarenmaa H (2016) Data sharing tools adopted by the European Biodiversity Observation Network Project. Research Ideas and Outcomes 2: e9390. doi: 10.3897/rio.2.e9390

 

About EU BON:

EU BON stands for “Building the European Biodiversity Observation Network” and is a European research project, financed by the 7th EU framework programme for research and development (FP7). EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU.

 

 

Posted on

50th publication in RIO Journal: Report of the first FORCE11 Scholarly Commons workshop

What if scholars, librarians, archivists, publishers and funders could restart scholarly communication all over? This was the slogan of the first FORCE11 Scholarly Commons Working Group (SCWG) workshop, which took place in February. Advocating for an open, sustainable, fair and creditable future that is technology- and business-enabled, not -led, FORCE11’s SCWG committee published a Workshop Report in the open access journal Research Ideas and Outcomes (RIO), becoming the anniversary 50th publication in the innovative research publishing platform.

The community of FORCE11, comprising scholars, librarians, archivists, publishers and research funders from around the globe, was born at the FORC Workshop held in Dagstuhl, Germany in August 2011. Ever since, the community have been working and striving together towards a change in modern scholarly communication through the effective use of information technology. Their aim has always been to facilitate the change to improved knowledge creation and sharing.

In 2016, the Scholarly Commons Working group within FORCE11 conducts two workshops in order to find the answers to the question how scholarly communication would have looked now, had it not been for the 350 years of traditional practices. They also focus on the implications of modern technology and modes of communications that could help bring the right change about.

“Too often, scholars are unaware of the origins of current practices and accept the status quo because ‘that’s how it’s done’,” the authors point out. “But what if we could start over? What if we had computers, Internet, search engines and social media, but no legacy of journals, articles, books, review systems etc.?”

The first workshop, held between 25th and 27th February in Madrid, Spain, was titled “What if we could start over?”. The second one is planned for later this year under the slogan “Putting the pieces together.”

During the three-day workshop, the fifty participants, representing experts, early career researchers and new voices from across disciplines and countries, engaged in various activities. In order to”diverge and then converge”, the participants were encouraged through a number of enjoyable tasks to freely think outside the box, assuming that the current system of scholarly communication, based on a paper-based reward system, never existed.116566

“Given today’s technology and the amount of money currently in the system, how would you design a system of scholarly communications (“The Scholarly Commons”), the goal of which is to maximize the accessibility and impact of scholarly works,” they were asked. “By putting us in an alternate reality with a clear charge, we sidestepped issues that often engulf such discussions: why do we publish and who do we publish for.”

At the end of the workshop, the group’s principles were ordered under five subheadings, namely:

  • Open and sustainable
  • Fair
  • Credit for all endeavors
  • Technology- and business-enabled, not -led
  • Governance and funding

The attendees’ ideas, visions and suggested principles were also captured in a live and interactive visualization, consisting of the participants’ virtual post-it notes, also available through Trello.

In the spirit of the workshop itself, the report is now formally published in the form of a new scholarly communication artifact. Workshop Report is only one of the various innovative research publication types, provided by the open access journal Research Ideas and Outcomes(RIO), whose aim is to acknowledge and disseminate all quality and valuable research outputs from across all stages of the research cycle.

###

Original source:

Kramer B, Bosman J, Ignac M, Kral C, Kalleinen T, Koskinen P, Bruno I, Buckland A, Callaghan S, Champieux R, Chapman C, Hagstrom S, Martone M, Murphy F, O’Donnell D (2016) Defining the Scholarly Commons – Reimagining Research Communication. Report of Force11 SCWG Workshop, Madrid, Spain, February 25-27, 2016. Research Ideas and Outcomes 2: e9340. doi: 10.3897/rio.2.e9340

Posted on

Open-source collaborative platform to collect content from over 350 institutions’ archives

With the technical and financial capacity of any currently existing single institution failing to answer the needs for a platform efficiently archiving the web, a team of American researchers have come up with an innovative solution, submitted to the U.S. Institute of Museum and Library Services (IMLS) and published in the open-access journal Research Ideas and Outcomes (RIO).

They propose a lightweight, open-source collaborative collection development platform, called Cobweb, to support the creation of comprehensive web archives by coordinating the independent activities of the web archiving community. Through sharing the responsibility with various institutions, the aggregator service is to provide a large amount of continuously updated content at greater speed with less effort.

In their proposal, the authors from the California Digital Library, the UCLA Library, and Harvard Library, give an example with the fast-developing news event of the Arab Spring, observed to unfold online simultaneously via news reports, videos, blogs, and social media.

“Recognizing the importance of recording this event, a curator immediately creates a new Cobweb project and issues an open call for nominations of relevant web sites,” explain the researchers. “Scholars, subject area specialists, interested members of the public, and event participants themselves quickly respond, contributing to a site list that is more comprehensive than could be created by any curator or institution.”

“Archiving institutions review the site list and publicly claim responsibility for capturing portions of it that are consistent with local collection development policies and technical capacities.”

Unlike already existing tools supporting some level of collaborative collecting, the proposed Cobweb service will form a single integrated system.

“As a centralized catalog of aggregated collection and seed-level descriptive metadata, Cobweb will enable a range of desirable collaborative, coordinated, and complementary collecting activities,” elaborate the authors. “Cobweb will leverage existing tools and sources of archival information, exploiting, for example, the APIs being developed for Archive-It to retrieve holdings information for over 3,500 collections from 350 institutions.”

If funded, the platform will be hosted by the California Digital Library and initialized with collection metadata from the partners and other stakeholder groups. While the project is planned to take a year, halfway through the partners will share a release with the global web archiving community at the April 2017 IIPC General Assembly to gather feedback and discuss ongoing sustainability. They also plan to organize public webinars and workshops focused on creating an engaged user community.

###

Original source:

Abrams S, Goethals A, Klein M, Lack R (2016) Cobweb: A Collaborative Collection Development Platform for Web Archiving. Research Ideas and Outcomes 2: e8760. doi: 10.3897/rio.2.e8760

Posted on

Roadmap: Global research data management advisory platform combines DMPTool and DMPonline

Roadmap, a global data management advisory platform that links data management plans (DMPs) to other components of the research lifecycle is a new open science initiative from partners at the University of California Curation Center (UC3) of the California Digital Library (CDL), USA, and the Digital Curation Centre (DCC), United Kingdom.

Both organizations sponsor and maintain such platforms, the DMPTool and DMPonline respectively. They allow researchers from around the world to create their data management plans in less time by employing ready-to-use templates with specific guidance tailored to address the requirements of specific funding agencies in the USA and the UK.

Recently, the proliferation of data sharing policies throughout the world has produced increasing demand for data management planning support from both organizations. Therefore, it makes sense for the CDL and DCC to consolidate efforts and move beyond a focus on national researchers and funders to extend their global outreach through Roadmap, a new open-source platform for data management planning. Their proposal was submitted to the Open Science Prize contest and is now published in the open access journal Research Ideas and Outcomes (RIO).

While the two teams have been working together unofficially and engaging in international initiatives, a formal partnership would signal to the global research community that there is one place to create DMPs and find advisory information.

“Research data management (RDM) that enables open science is now acknowledged as a global challenge: research is global, policies are becoming global, and thus the need is global,” explain the authors. “Open science has a global agenda, and by making DMPs true infrastructure in a global open access community we will elevate research and open data for reuse.”

roadmap still

In their joint project, the two organizations will combine their experience along with all existing functionality from their tools regarding the DMP use case into a single technical platform.

“New work on our respective systems is already underway to enable internationalization, integrate with other organizations and technical platforms, and encourage greater openness with DMPs,” they explain. “By joining forces, the Roadmap system will consolidate these efforts and move beyond a narrow focus on specific funders in specific countries, and even beyond institutional boundaries, to create a framework for engaging with disciplinary communities directly.”

To facilitate data sharing, reuse, and discoverability, Roadmap will be integrated with a number of platforms such as the Open Science Framework, SHARE, the Crossref/Datacite DOI Event Tracking system and Zenodo, among others. “Linking systems and research outputs across the web increases the chances that data will be discovered, accessed, and (re)used,” note the authors.

The team’s plan for enhanced openness includes encouraging authors to share their newly created data management plans by setting their privacy on “public” by default. They also intend to assign digital object identifiers (DOIs) to all plans, thus making them citable and motivating their authors to make them openly accessible. As part of this initiative, five researchers have just published their DMPs, created with the DMPTool, in Research Ideas and Outcomes (RIO).

“We see greater potential for the DMP as a dynamic checklist for pre- and post-award reporting; a manifest of research products that can be linked with published outputs; and a record of data, from primary through processing stages, that could be passed to repositories,” state the authors. “The DMP will therefore not only support the management of the data but boost its discoverability and reuse.”

###

Original source:

Simms S, Jones S, Ashley K, Ribeiro M, Chodacki J, Abrams S, Strong M (2016) Roadmap: A Research Data Management Advisory Platform. Research Ideas and Outcomes 2: e8649. doi: 10.3897/rio.2.e8649

Posted on

Making the most out of biological observations data

Creating and maintaining a biodiversity data collection has been a much-needed worldwide exercise for years, yet there is no single standard on how to do this. This has led to a myriad of datasets often incompatible with each other. To make the most out of biodiversity data and to ensure that its use for environmental monitoring and conservation is both easy and legal, the FP7-funded EU project Building the European Biodiversity Observation Network (EU BON) published recommendations that provide consistent Europe-wide Data Publishing Guidelines and Recommendations in the EU BON Biodiversity Portal.

The report “Data Policy Recommendations for Biodiversity Data. EU BON Project Report” featured in the Research Ideas & Outcomes (RIO) journal, is the first contribution in a pioneering comprehensive project outputs compilation taking advantage of RIO’s unique option to publish collections of project results.

Biodiversity data and information provide important knowledge for many biological, geological, and environmental research disciplines. Additionally, they are crucial for the development of strong environmental policies and the management of natural resources. Information management systems can bring together a wealth of information and a legacy of over 260 years of biological observations which are now dispersed in a myriad of different documents, institutions, and locations.

EU BON aims to build a comprehensive “European Biodiversity Portal” that will incorporate currently scattered Europe-wide biodiversity data, while at the same time helping to realize a substantial part of the worldwide Group on Earth Observations Biodiversity Observation Network (GEO BON). To achieve this ambitious plan, EU BON identifies the strong need for a coherent and consistent data policy in Europe to increase interoperability of data and make its re-use both easy and legal.

“Biodiversity data and information should not be treated as commercial goods, but as a common resource for the whole human society. The EU BON data sharing agreement is an important step in this direction,” comments the lead author of the report Dr. Willi Egloff from Plazi, Switzerland.

In its report, the EU BON project analysis available single recommendations and guidelines on different topics. On this basis, the report provides structured guidelines for legislators, researchers, data aggregators, funding agencies and publishers to be taken into consideration towards providing standardized, easy-to-find, re-shareable and re-usable biodiversity data.

“We are extremely happy that EU BON is among the first to take advantage of our project outputs collections option in RIO. The first report they are publishing with us deals with issues of opening up data, and digitizing and collecting scientific knowledge, all close to RIO’s mission to open up the research process and promote open science,” says Prof. Lyubomir Penev, Founder and Publisher of RIO.

###

Original Source:

Egloff W, Agosti D, Patterson D, Hoffmann A, Mietchen D, Kishor P, Penev L (2016) Data Policy Recommendations for Biodiversity Data. EU BON Project Report. Research Ideas and Outcomes2: e8458. doi: 10.3897/rio.2.e8458

 

About EU BON:

EU BON stands for “Building the European Biodiversity Observation Network” and is a European research project, financed by the 7th EU framework programme for research and development (FP7). EU BON seeks ways to better integrate biodiversity information and implement into policy and decision-making of biodiversity monitoring and management in the EU.

Posted on

One place for all scholarly literature: An Open Science Prize proposal

Openly accessible scholarly literature is referred to as “the fabric and the substance of Open Science” in the present small grant proposal, submitted to the Open Science Prize contest and published in the Research Ideas and Outcomes (RIO) open access journal. However, the scholarly literature is currently quite chaotically dispersed across thousands of different websites and disconnected from its context.

To tackle this issue, authors Marcin Wojnarski, Paperity, Poland, and Debra Hanken Kurtz, DuraSpace, USA, build on the existing prototype Paperity, the first open access aggregator of scholarly journals. Their suggestion is the first global universal catalog of open access scientific literature. It is to bring together all publications by automatically harvesting both “gold” and “green” ones.

Called Paperity Central, it is to also incorporate many helpful functionalities and features, such as a wiki-type one, meant to allow for registered users to manually improve, curate and extend the catalog in a collaborative, community-controlled way.

“Manual curation will be particularly important for “green” metadata, which frequently contain missing or incorrect information; and for cataloguing those publications that are inaccessible for automatic harvesting, like the articles posted on author homepages only,” further explain the authors.

To improve on its ancestor, the planned catalog is to seamlessly add “green” publications from across repositories to the already available articles indexed from gold and hybrid journals. Paperity Central is to derive its initial part of “green” content from DSpace, the most popular repository platform worldwide, developed and stewarded by DuraSpace, and powering over 1,500 academic repositories around the world.

All items available from Paperity Central are to be assigned with globally unique permanent identifiers, thus reconnecting them to their primary source of origin. Moreover, all different types of Open Science resources related to a publication, such as author profiles, institutions, funders, grants, datasets, protocols, reviews, cited/citing works, are to be semantically linked in order to assure none of them is disconnected from its context.

Furthermore, the catalog is to perform deduplication of each entry in the same systematic and consistent way. Then, these corrections and expansions are to be transferred back to the source repositories in a feedback loop via open application programming interfaces (APIs). However, being developed from a scratch, its code will possess many distinct features setting it apart from existing wiki-type platforms, such as Wikipedia, for example.

“Every entry will consist of structured data, unlike Wikipedia pages which are basically text documents,” explain the scientists. “The catalog itself will possess internal structure, with every item being assigned to higher-level objects: journals, repositories, collections – unlike Wikipedia, where the corpus is a flat list of articles.”

In order to guarantee the correctness of the catalog, Paperity Central is to be fully transparent, meaning the history of changes is to be made public. Meanwhile, edits are to be moderated by peers, preferably journal editors or institutional repository admins overlooking the items assigned to their collections.

In their proposal, the authors note that the present development plan is only the first phase of their project. They outline the areas where the catalog is planned to be further enhanced in future. Among others, these include involvement of more repositories and platforms, fully developed custom APIs and expansion on the scholarly output types to be included in the catalog.

“If we are serious about opening up the system of scientific research, we must plant it on the foundation of open literature and make sure that this literature is properly organized and maintained: accessible for all in one central location, easily discoverable, available within its full context, annotated and semantically linked with related objects,” explain the scientists.

“Assume we want to find all articles on Zika published in 2015,” they exemplify. “We can find some of them today using services like Google Scholar or PubMed Central, but how do we know that no other exist? Or that we have not missed any important piece of literature? With the existing tools, which have incomplete and undefined coverage, we do not know and will never know for sure.”

In the spirit of their principles of openness, the authors assure that once funded, Paperity Central will be releasing its code as open source under an open license.

###

Original source:

Wojnarski M, Hanken Kurtz D (2016) Paperity Central: An Open Catalog of All Scholarly Literature. Research Ideas and Outcomes 2: e8462. doi: 10.3897/rio.2.e8462

Posted on

Counting days and tweets: What’s happened to RIO Journal so far?

So, here we are, counting days and Twitter impressions since Research Ideas & Outcomes (or, RIO for short) our new open access journal was officially announced on 1st September 2015. As much as we were excited to take this long-prepared and anticipated stand in the spotlight, we are still holding our breath ahead of the big event – the launch itself, scheduled for November 2015.

In the meantime, when not busy welcoming our very first subject editors, we have our ear to the ground, so that we can make sure to provide everyone with the best services and insight. The truth is, we don’t only value attention, we deeply appreciate your opinion and respect your needs and concerns.

So, here below we provide a short summary of the eventful first week of RIO Journal:

It all started on 1st September on Twitter. Among the constantly growing list of our first followers, there were a lot of welcoming retweets, sounding just as excited as we were:

Then, the time came for the world media to give its verdict:

This week sees the birth of a new type of scientific journal, one that will publish not only study results and data, but also research ideas and proposals. It’s called Research Ideas and Outcomes (RIO).
/The Scientist, 3rd September/

With so many science journals already in existence, it is rare for a new title to draw attention. But researchers and publishing experts are taking notice of Research Ideas and Outcomes, or RIO, an open-access journal that launched on 1 September.
/Nature, 3rd September/

Understandably, the hottest discussion points were RIO’s initiatives:

> To present openly the whole process of the research cycle especially including research proposals
> To publish such ideas regardless of them being eventually approved or rejected for funding
> To apply a transparent, public, and open peer-review policy

Stephen Curry, a structural biologist at Imperial College London shared on Twitter that in his opinion RIO is “bringing a new sense of transparency and collaboration to research”, while he voiced his strong support for preprint publications and open feedback in his Guardian blog. “Preprints can help to refocus attention where it matters – on the work itself, not where it is published. In so doing, they have the potential to revitalize the scientific enterprise”, his column reads.

“I like the idea of getting “publishing-credit” for my research proposals and other research output. Roughly speaking for every proposal I write, I write one paper less”, points out computational chemist at the University of Copenhagen Jan Jansen on explaining why he accepted the invitation to become one of RIO’s subject editors.

At the end of the day, some of RIO’s innovations couldn’t escape being challenged by some criticisms. A librarian and known extreme critic of open access journals, Jeffrey Beall questioned the freedom given to RIO’s authors to make their own choice of reviewers.

One of the RIO’s own subject editors, Ivo Grigorov, a marine scientist at the Technical University of Denmark also raised his concerns on the matter. Yet, he and our ever growing list of editors and advisory board are sticking with us:

In his turn, Ross Mounce, a postdoc at the Natural History Museum, London and a founding editor of RIO, explained how the new open access journal seeks to improve the “immensely wasteful” traditional research process in his piece on the popular LSE Impact blog.

Ross also gave a podcast interview for Beta Pleated Chic, he spoke in detail about the whole list of innovative tools and strategies.

If you know of any other press mentions or blogs about RIO Journal, please don’t hesitate to forward them to us on Twitter @RIOJournal.