Tag: open research

Posted on

Open Science environment Unicorn allows researchers and decision makers to work together

Given that the most important societal needs require multidiscipli­nary collaboration between researchers and decision makers, a suitable environment has to be provided in the first place. A proposal, prepared by a Finnish consortium and published in the open access journal Research Ideas and Outcomes, suggests a new, open virtual work and modeling platform to support evidence-based decision making in a number of areas, while also abiding by the principles of openness, criticism and reuse.

The Finnish consortium, led by Prof. Pekka Neittaanmäki, University of Jyväskylä, and bringing together Timo Huttula and Janne Ropponen, Finnish Environment Institute, Juha Karvanen and Tero Tuovinen, University of Jyväskylä, Tom Frisk, Pirkanmaa Centre for Economic Development, Transport and the Environment, Jouni Tuomisto, National Institute for Health and Welfare, and Antti Simola, VATT Institute for Economic Research, acknowledge that, “it is not enough that experts push data to politicians.”

“There must be practices for mutual communication: experts must answer policy questions in a defendable and useful way; decision makers must more clearly explain their views using evidence; and there must be ICT tools to support this exchange,” the authors explain. “The focus is on end-users.”

Unicorn is to combine shared practices, tools, data, working environments and concerted actions in order to aggregate open information from multiple databases, and create tools for efficient policy studies.

The consor­­tium have already developed and tested prototypes of such practices and tools in several projects, and insist that they are now ready to apply their experience and knowledge on a larger scale. They are also certain that open data and models are deservedly the “mega trend” nowadays.

“Unicorn directs this trend to paths that are the most beneficial for societal decision making by providing quick, reliable and efficient decision support,” they say.

“Significant saving of resources will be mani­fested with improved data collection, analyses and modeling. Also, the quality and amount of assessments that can be done to support work.”

“The major challenges related to evidence-based decision making actually are about changing the practices of researchers and dec­­ision makers,” according to the authors. Therefore, they see their project as a demonstration of the needed shifts.

Although the approach is applicable in all areas, the researchers are to initially implement them in environment, human health, and regional economy, “as they are com­plex and chal­lenging enough to offer a good test bed for general development.”

Having already been submitted to the Strategic Funds of Academy of Finland in 2015, the Unicorn environment proposal has been rejected due to overambitiousness and low commercial potential. However, the authors are confident that the Unicorn environment along with its growing community of developers can, in fact, meet a great success. They are currently looking for further funding suggestions and forming new consortiums.

###

Original source:

Neittaanmäki P, Huttula T, Karvanen J, Frisk T, Tuomisto J, Simola A, Tuovinen T, Ropponen J (2016) Unicorn-Open science for assessing environmental state, human health and regional economy. Research Ideas and Outcomes 2: e9232. doi: 10.3897/rio.2.e9232

Posted on

Open neuroscience: Collaborative Neuroimaging Lab finalist for the Open Science Prize

Despite the abundance of digital neuroimaging data, shared thanks to all funding, data collection, and processing efforts, but also the goodwill of thousands of participants, its analysis is still falling behind. As a result, the insight into both mental disorders and cognition is compromised.

The Open Neuroimaging Laboratory framework, promises a collaborative and transparent platform to optimise both the quantity and quality of this invaluable brain data, ultimately gaining a greater insight into both mental disorders and cognition.

The project was submitted for the Open Science Prize competition by Katja Heuer, Max Planck Institute for Human Cognitive and Brain Sciences, Germany, Dr Satrajit S. Ghosh, Massachusetts Institute of Technology (MIT), USA, Amy Robinson Sterling, EyeWire, USA, and Dr Roberto Toro, Institut Pasteur, France. Amongst 96 submissions from all around the globe, it was chosen as one of six teams to compete in the second and final phase of the Prize.

Simply having access and being able to download brain magnetic resonance imaging (MRI) data is not enough to reap all potential benefits. In order for it to be turned into insight and knowledge, it needs to also be queried, pre-processed and analysed, which requires a substantial amount of human curation, visual quality assessment and manual editing. With research being rather patchy, a lot of efforts are currently redundant and unreliable.

On the other hand, the Open Neuroimaging Laboratory aims to aggregate annotated brain imaging data from across various resources, thus improving its searchability and potential for reuse. It is to also develop a tool that will facilitate and encourage the creation of distributed teams of researchers to collaborate together in the analysis of this open data in real time.

“Our project will help transform the massive amount of static brain MRI data readily available online into living matter for collaborative analysis,” explain the researchers.

“We will allow a larger number of researchers to have access to this data by lowering the barriers that prevent their analysis: no data will have to be downloaded or stored, no software will have to be installed, and it will be possible to recruit a large, distributed, group of collaborators online.”

“By working together in a distributed and collaborative way, sharing our work and our analyses, we should improve transparency, statistical power and reproducibility,” they elaborate. “Our aim is to provide to everyone the means to share effort, learn from each other, and improve quality of and trust in scientific output.”Untitled

Having already developed a functional prototype of the BrainBox web application, which provides an interactive online space for collaborative data analyses and discussions, the team will now turn it into a first version with an improved user experience, stability and documentation. Planned for the Open Science Prize Phase 2 are furthering the type of analyses and exploring the development of interfaces for database-wise statistical analyses.

In the spirit of the competition, the scientists have decided to release their code open source on GitHub to facilitate bug fixes, extension and maintainability.

###

Original source:

Heuer K, Ghosh S, Robinson Sterling A, Toro R (2016) Open Neuroimaging Laboratory.Research Ideas and Outcomes 2: e9113. doi: 10.3897/rio.2.e9113

Posted on

Data sharing pilot to report and reflect on data policy challenges via 8 case studies

This week, FORCE2016 is taking place in Portland, USA. The FORCE11 yearly conference is devoted to the utilisation of technological and open science advancements towards a new-age scholarship founded on easily accessible, organised and reproducible research data.

As a practical contribution to the scholarly discourse on new modes of communicating knowledge, Prof. Cameron Neylon, Centre for Culture and Technology, Curtin University, Australia, and collaborators are to publish a series of outputs and outcomes resulting from their ongoing data sharing pilot project in the open access journal Research Ideas and Outcomes (RIO).

Starting with their Grant Proposal, submitted and accepted for funding by the Canadian International Development Research Centre (IDRC), over the course of sixteen months, ending in December 2016, they are to openly publish the project outputs starting with the grant proposal.

The project will collaborate with 8 volunteering IDRC grantees to develop Data Management Plans, and then support and track their development. The project expects to submit literature reviews, Data Management Plans, case studies and a final research article with RIO. These will report and reflect on the lessons they will have learnt concerning open data policies in the specific context of development research. Thus, the project is to provide advice on refining the open research data policy guidelines.

“The general objective of this project is to develop a model open research data policy and implementation guidelines for development research funders to enable greater access to development research data,” sum up the authors.

“Very little work has been done examining open data policies in the context of development research specifically,” they elaborate. “This project will serve to inform open access to research data policies of development research funders through pilot testing open data management plan guidelines with a set of IDRC grantees.”

The researchers agree that data constitutes a primary form of research output and that it is necessary for research funders to address the issue of open research data in their open access policies. They note that not only should data be publicly accessible and free for re-use, but they need to be “technically open”, which means “available for no more than the cost of reproduction, and in machine-readable and bulk form.” At the same time, research in a development context raises complex issues of what data can be shared, how, and by whom.

“The significance of primary data gathered in research projects across domains is its high potential for not only academic re-use, but its value beyond academic purposes, particularly for governments, SME, and civil society,” they add. “More importantly, the availability of these data provides an ideal opportunity to test the key premise underlying open research data — that when it is made publicly accessible in easily reusable formats, it can foster new knowledge and discovery, and encourage collaboration among researchers and organizations.”

However, such openness is also calling for extra diligence and responsibility while sharing, handling and re-using the research data. This is particularly the case in development research, where challenging ethical issues come to the fore. The authors point out the issues, raised by such practice, to be, among others, realistic and cost-effective strategies for funded researchers to collect, manage, and store the various types of data resulting from their research, as well as ethical issues such as privacy and rights over the collected data.

###

Original source:

Neylon C, Chan L (2016) Exploring the opportunities and challenges of implementing open research strategies within development institutions. Research Ideas and Outcomes 2: e8880. doi: 10.3897/rio.2.e8880

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

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

Openly published Open Science Prize Grant Proposal builds on ContentMine and Hypothes.is to bridge scientists and facts

Public health emergencies such as the currently spreading Zika disease might be successfully necessitating open access for the available biomedical researches and their underlying data, yet filtering the right information, so that it lands in the hands of the right people, is what holds up professionals to bring the adequate measures about.

Submitted to the Open Science Prize contest, the present grant proposal, prepared with the joint efforts of scientists affiliated with Hypothes.is, ContentMine, University of Cambridge, Cottage Labs LLP and Imperial College of London, suggests a new scholarly assistant system, called amanuens.is, based on the existing ContentMine and Hypothes.is prototypes. Its aim is to combine machines and humans, so that mining critically important facts and making them available to the world can be made not only significantly faster, but also less costly. Through their publication in the open access journal Research Ideas and Outcomes (RIO), the scientists, who are also well-known open access and open data proponents, are looking for further support, feedback and collaborations.

While Hypothes.is is a mixture of software and communities, which together annotate the available literature, ContentMine are building an open source pipeline to extract facts from scientific documents, thus making the literature review process cheaper, more rigorous, continuous and transparent. The role of amanuens.is is meant to bring these two systems together.

As a result, Hypothes.is is to display ContentMine facts as annotations on the online document, therefore increasing their visibility. In turn, the large Hypothes.is community, comprising users ranging from devoted and experienced Wikipedia editors to dedicated citizen scientists, would be able to provide manually their own annotations, which could be then fed back into the ContentMine facts store.

“Facts are important – but science is performed by people – so ContentMine are partnering with Hypothes.is to bring communities together around facts in the scholarly literature,” sums up Dr Peter Murray-Rust. “Through combining machines and humans in a tight, iterating, loop, amanuens.is will be able to mine critically important facts and make them available to the world.”

In their proposal, the authors give a hypothetical, yet foreseeable example with a Hypothes.is community, centered around research and discussions regarding a bacterium, already proven to restrain some mosquitoes from transmitting various viruses, and its potential use against Zika. There, amanuens.is downloads all open access papers on Zika from a multitude of sources within 3 minutes. In a matter of a couple of seconds a total of 123 files are downloaded. Then, amanuens.is delivers a data table of the extracted data, including species, human genes, DNA primers and top word frequencies.

Within the community and thanks to the literature, made available via ContentMine, the users would be able to collaborate and build on the existing research outcomes. As a result, it could take only fifteen minutes and a brief proposal to mobilise the related scholarly resources and test for Zika resistance in infected with the virus mosquitoes.

“Finding facts to finding people took 15 minutes and this is how modern collaborative science should work,” Prof Peter Murray-Rust says about the given example. “The people then create knowledge from the facts. The knowledge creates communities. The communities explore science- and people-based solutions.”

In conclusion, the proposal states that similarly to the content and software provided by ContentMine and Hypothes.is, the outputs produced by amanuens.is will also be openly available. All of its data and annotations are to be public domain under a CC0 waiver.

###

Original source:

Martone M, Murray-Rust P, Molloy J, Arrow T, MacGillivray M, Kittel C, Kasberger S, Steel G, Oppenheim C, Ranganathan A, Tennant J, Udell J (2016) ContentMine/Hypothes.is Proposal.Research Ideas and Outcomes 2: e8424. doi: 10.3897/rio.2.e8424

Posted on

An Open Science plan: Wikidata for Research

Wikidata is to databases what Wikipedia is to encyclopedias – the free version that anyone can edit. Both aim to share “the sum of all human knowledge” across the world in a multitude of languages, and while Wikidata is younger and has a smaller community, it attracts the collaboration of more than 16,000 volunteer contributors globally each month (up from 14,000 a year ago).

Meanwhile, recent years have witnessed a constantly increasing demand and support for Open Access and Open Science across professional research communities and citizen scientists. Therefore, a Horizon 2020 project plan was put together by a team of six European partners led by the Museum für Naturkunde Berlin to integrate research workflows with Wikidata into a new virtual research environment (VRE) for Open Science, called Wiki4R. The plan combined approaches to make Wikidata useful for researchers both across disciplines and for several specific use cases, e.g. chemistry.

The cross-disciplinary aspects included standard ways for handling scholarly references in Wikidata and for asking questions of Wikidata, whereas the chemical part focused on how to describe Wikidata entries for chemical topics like molecules, solvents or reactions and pathways, how to link this information to scholarly databases and publications, and how to ask chemical questions of Wikidata. These technical parts of the proposal were complemented by parts on how to bring Wikidata together with citizen science projects, on what the value proposition of openness is for institutions, and on training activities.

The grant proposal was submitted in January and ultimately rejected, but its drafters believe it contains a range of ideas that may still be worth pursuing. In fact, efforts to handle scholarly references through Wikidata are ongoing, and Wikidata can now be queried for things like a list of countries ordered by the number of their cities with a female mayor.

“The idea of a closer integration between Wikidata and research workflows is not itself rejected, and we believe that it is useful for both the research and Wikimedia communities to continue to explore the opportunities here, to pilot them and to keep talking to funders and other stakeholders about the value that such infrastructure would provide to society, so they can consider making the necessary resources available,” comments Dr. Daniel Mietchen, who spearheaded the effort.

In order to stimulate such activities, the Wiki4R proposal is among the first ones published via the new open-access journal Research Ideas & Outcomes (RIO). The innovative platform accepts submissions of scholarly works from the entire research life-cycle, including research ideas and proposals that are deemed to be valuable to scholarly research and its future.

“Our proposal focuses on the needs of open science and empowering researchers to work together across disciplines in an open environment,” explains Dr. Daniel Mietchen. “The concept of open science is central to this proposal. Open science is highly inclusive, inviting collaboration from professional peers as well as other interested parties, including citizen scientists. It is also open with respect to the process, providing access to research as it unfolds, allowing anyone to engage with it right away.”

###

Original source:

Mietchen D, Hagedorn G, Willighagen E, Rico M, Gómez-Pérez A, Aibar E, Rafes K, Germain C, Dunning A, Pintscher L, Kinzler D (2015) Enabling Open Science: Wikidata for Research (Wiki4R). Research Ideas and Outcomes 1: e7573. doi: 10.3897/rio.1.e7573

 

Additional Information:

The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.

The journal harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research outputs than those traditionally made public: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform offering one of the most transparent, open and public peer-review processes.