Month: December 2015

23/12/2015

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.”

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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.

21/12/2015

New proposal published in RIO tackles problematic trial detection in ClinicalTrials.gov

Clinical trials are crucial in determining the effectiveness of treatments and directly influence practical and policy decisions. However, their results could be even detrimental to real-life patients if data is fabricated or subject to errors. While it is about 2% of all researchers that admit to having manipulated their data, a new Dutch Fulbright project proposal, published via the innovative Research Ideas & Outcomes (RIO) Journal, suggests new methods to tackle these issues and to apply them to results reported in the ClinicalTrials.gov database.

Decisions based on bad data, both clinical and policy ones made by medical doctors and governmental institutions, respectively, can pose direct risks on treated patients and the population in general. Such was the case of beta-blockers, for instance, used to be prescribed to cardiac patients in order to decrease perioperative mortality. However, a subsequent meta-analysis detected erroneous data in the related clinical trials. Moreover, it turned out that beta-blockers actually increase the risk of mortality.

The new Dutch Fulbright proposal led by Chris HJ Hartgerink, Tilburg University, Netherlands, and Dr. Stephen L George, Duke University, United States, proposes new additional statistical methods for erroneous data detection to provide an additional quality control filter for clinical trial results reported in the ClinicalTrials.gov database.

Unfortunately, misleading data is not simply the product of bad practice, but could also result from human error or inadequate data handling. It is not even clear enough how often such mistakes or manipulations occur and have occurred in reality, let alone their prevalence in any science in particular. What is beyond doubt, however, is that additional methods and procedures of detecting bad data are needed in order to minimize the risk of bad decisions being taken when health and wellbeing are at stake.

“Detecting problematic data is a niche field with few experts around the world, despite its importance,” further explains Chris HJ Hartgerink. “Systematic application remains absent and this project hopes to push this field into this area. New estimates of how prevalent problematic data are welcome, because we currently rely on self-report measures, which suffer from human bias.”

Recently submitted to Fulbright, the 6-month project proposal has now been made open-access by the authors with RIO Journal, an innovative platform publishing all outputs of the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles.

“A grant proposal is a research output like any other but is only rewarded when it results in funding,” says Chris HJ Hartgerink. “We know that many good proposals are rejected and consequently not rewarded. Publishing the grant proposal shows the output, makes it rewardable and can help improve it by post-publication peer review.”

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Original Source:

Hartgerink CHJ, George SL (2015) Problematic trial detection in ClinicalTrials.gov. Research Ideas and Outcomes 1: e7462. doi: 10.3897/rio.1.e7462

Additional Information:

The Research Ideas and Outcomes (RIO) Journal publishes all outputs of the research cycle, including: 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. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.

18/12/2015

Austrian Science Fund grant proposal goes public with RIO Journal

Controlled manipulation of matter on the scale of atoms is the topic of a new cutting edge Austrian Science Fund (FWF) project “Heteroatom quantum corrals and nanoplasmonics in graphene” (HeQuCoG), led by Finnish-born physicist Toma Susi. The project is the first to openly publish its proposal via the innovative platform of the Research Ideas & Outcomes (RIO) Journal, designed to uncover the entire research cycle.

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. 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.

RIO offers one of the most transparent, open and public peer-review processes, including pre-submission and post-publication peer-review options. The journal is designed to encourage collaboration between scientists within and across disciplines by making the entire research cycle open, and by mapping the social impact for its publications.

Dr. Susi, based at the University of Vienna in Austria, shares why he chose to make his research accessible to peers and the wider public from the proposal stage. “I must be honest: it was an instinctively scary prospect to publish a grant proposal, even a funded one. However, once I carefully weighed the potential pros and cons and discussed the idea with my close peers, I concluded that those fears most likely were unfounded. Moreover, there really can be no doubt that science as a whole would benefit if this became common practice.”

The aim of the HeQuCoG project is to create atomically precise structures consisting of silicon and phosphorus atoms embedded in the lattice of graphene using a combination of ion implantation, first principles modeling and electron microscopy. The expected outcome is a systematic demonstration of atomic-level material design and the creation of freestanding “quantum corral” structures for the first time.

“We are happy to have such an exciting and ambitious project as one of the first to publish its proposal in RIO. This goes to show that the platform is an ideal hub for forward-thinking young researchers wishing to take science to a new level of collaboration and real-world impact” comments Prof. Lyubomir Penev, co-founder of RIO.

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Original source:

Susi T (2015) Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG). Research Ideas and Outcomes 1: e7479. doi: 10.3897/rio.1.e7479

Additional information:

The Austrian Science Fund FWF is devoted to the support of the ongoing development of Austrian science and basic research at a high international level. In this way, the FWF makes a significant contribution to cultural development, to the advancement of a knowledge-based society, and to the creation of value and wealth in Austria and abroad.