Open Trials

Curated on Posted on by Stefaan Verhulst

“Open Knowledge today announced plans to develop Open Trials, an open, online database of information about the world’s clinical research trials funded by The Laura and John Arnold Foundation. The project, which is designed to increase transparency and improve access to research, will be directed by Dr. Ben Goldacre, an internationally known leader on clinical transparency.

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Open Trials will aggregate information from a wide variety of existing sources in order to provide a comprehensive picture of the data and documents related to all trials of medicines and other treatments around the world. Conducted in partnership with the Center for Open Science and supported by the Center’s Open Science Framework, the project will also track whether essential information about clinical trials is transparent and publicly accessible so as to improve understanding of whether specific treatments are effective and safe.

“There have been numerous positive statements about the need for greater transparency on information about clinical trials, over many years, but it has been almost impossible to track and audit exactly what is missing,” Dr. Goldacre, the project’s Chief Investigator and a Senior Clinical Research Fellow in the Centre for Evidence Based Medicine at the University of Oxford, explained. “This project aims to draw together everything that is known around each clinical trial. The end product will provide valuable information for patients, doctors, researchers, and policymakers—not just on individual trials, but also on how whole sectors, researchers, companies, and funders are performing. It will show who is failing to share information appropriately, who is doing well, and how standards can be improved.”

Patients, doctors, researchers, and policymakers use the evidence from clinical trials to make informed decisions about which treatments are best. But studies show that roughly half of all clinical trial results are not published, with positive results published twice as often as negative results. In addition, much of the important information about the methods and findings of clinical trials is only made available outside the normal indexes of academic journals….

Open Trials will help to automatically identify which trial results have not been disclosed by matching registry data on trials that have been conducted against documents containing trial results. This will facilitate routine public audit of undisclosed results. It will also improve discoverability of other documents around clinical trials, which will be indexed and, in some cases, hosted. Lastly, it will help improve recruitment for clinical trials by making information and commentary on ongoing trials more accessible….(More)”

A Process Model for Crowdsourcing Design: A Case Study in Citizen Science

Curated on Posted on by Stefaan Verhulst

Chapter by Kazjon Grace et al in Design Computing and Cognition ’14: “Crowdsourcing design has been applied in various areas of graphic design, software design, and product design. This paper draws on those experiences and research in diversity, creativity and motivation to present a process model for crowdsourcing experience design. Crowdsourcing experience design for volunteer online communities serves two purposes: to increase the motivation of participants by making them stakeholders in the success of the project, and to increase the creativity of the design by increasing the diversity of expertise beyond experts in experience design. Our process model for crowdsourcing design extends the meta-design architecture, where for online communities is designed to be iteratively re-designed by its users. We describe how our model has been deployed and adapted to a citizen science project where nature preserve visitors can participate in the design of a system called NatureNet. The major contribution of this paper is a model for crowdsourcing experience design and a case study of how we have deployed it for the design and development of NatureNet….(More)”

 

These researchers want to turn phones into earthquake detectors

Curated on Posted on by Stefaan Verhulst

Russell Brandom in TheVerge: “Early warning on earthquakes can help save lives, but many countries can’t afford them. That’s why scientists are turning to another location sensor already widespread in many countries: the smartphone. A single smartphone makes for a crappy earthquake sensor — but get enough of them reporting, and it won’t matter.

A new study, published today in Science Advances, says that the right network of cell phones might be able to substitute for modern seismograph arrays, providing a crucial early warning in the event of a quake. The study looks at historical earthquake data and modern smartphone hardware (based on the Nexus 5) and comes away with a map of how a smartphone-based earthquake detector might work. As it turns out, a phone’s GPS is more powerful than you might think.

A modern phone has almost everything you could want in an earthquake sensor

Early warning systems are designed to pick up the first tremors of an earthquake, projecting where the incoming quake is centered and how strong it’s likely to be. When they work, the systems are able to give citizens and first responders crucial time to prepare for the quake. There are already seismograph-based systems in place in California, Mexico, and Japan, but poorer countries often don’t have the means to implement and maintain them. This new method wouldn’t be as good as most scientific earthquake sensors, but those can cost tens of thousands of dollars each, making a smartphone-based sensor a lot cheaper. For countries that can’t afford a seismograph-based system (which includes much of the Southern Hemisphere), it could make a crucial difference in catching quakes early.

A modern phone has almost everything you could want in an earthquake sensor: specifically, a GPS-powered location sensor, an accelerometer, and multiple data connections. There are also a lot of them, even in poor countries, so a distributed system could count on getting data points from multiple angles….(More)”

The big medical data miss: challenges in establishing an open medical resource

Curated on Posted on by Stefaan Verhulst

Eric J. Topol in Nature: ” I call for an international open medical resource to provide a database for every individual’s genomic, metabolomic, microbiomic, epigenomic and clinical information. This resource is needed in order to facilitate genetic diagnoses and transform medical care.

“We are each, in effect, one-person clinical trials”

Laurie Becklund was a noted journalist who died in February 2015 at age 66 from breast cancer. Soon thereafter, the Los Angeles Times published her op-ed entitled “As I lay dying” (Ref. 1). She lamented, “We are each, in effect, one-person clinical trials. Yet the knowledge generated from those trials will die with us because there is no comprehensive database of metastatic breast cancer patients, their characteristics and what treatments did and didn’t help them”. She went on to assert that, in the era of big data, the lack of such a resource is “criminal”, and she is absolutely right….

Around the same time of this important op-ed, the MIT Technology Review published their issue entitled “10 Breakthrough Technologies 2015” and on the list was the “Internet of DNA” (Ref. 2). While we are often reminded that the world we live in is becoming the “Internet of Things”, I have not seen this terminology applied to DNA before. The article on the “Internet of DNA” decried, “the unfolding calamity in genomics is that a great deal of life-saving information, though already collected, is inaccessible”. It called for a global network of millions of genomes and cited theMatchmaker Exchange as a frontrunner. For this international initiative, a growing number of research and clinical teams have come together to pool and exchange phenotypic and genotypic data for individual patients with rare disorders, in order to share this information and assist in the molecular diagnosis of individuals with rare diseases….

an Internet of DNA — or what I have referred to as a massive, open, online medicine resource (MOOM) — would help to quickly identify the genetic cause of the disorder4 and, in the process of doing so, precious guidance for prevention, if necessary, would become available for such families who are currently left in the lurch as to their risk of suddenly dying.

So why aren’t such MOOMs being assembled? ….

There has also been much discussion related to privacy concerns that patients might be unwilling to participate in a massive medical information resource. However, multiple global consumer surveys have shown that more than 80% of individuals are ready to share their medical data provided that they are anonymized and their privacy maximally assured4. Indeed, just 24 hours into Apple’s ResearchKit initiative, a smartphone-based medical research programme, there were tens of thousand of patients with Parkinson disease, asthma or heart disease who had signed on. Some individuals are even willing to be “open source” — that is, to make their genetic and clinical data fully available with free access online, without any assurance of privacy. This willingness is seen by the participants in the recently launched Open Humans initiative. Along with the Personal Genome Project, Go Viral and American Gut have joined in this initiative. Still, studies suggest that most individuals would only agree to be medical research participants if their identities would not be attainable. Unfortunately, to date, little has been done to protect individual medical privacy, for which there are both promising new data protection technological approaches4 and the need for additional governmental legislation.

This leaves us with perhaps the major obstacle that is holding back the development of MOOMs — researchers. Even with big, team science research projects culling together hundreds of investigators and institutions throughout the world, such as the Global Alliance for Genomics and Health (GA4GH), the data obtained clinically are just as Laurie Becklund asserted in her op-ed — “one-person clinical trials” (Ref. 1). While undertaking the construction of a MOOM is a huge endeavour, there is little motivation for researchers to take on this task, as this currently offers no academic credit and has no funding source. But the transformative potential of MOOMs to improve medical care is extraordinary. Rather than having the knowledge die with each of us, the time has come to take down the walls of academic medical centres and health-care systems around the world, and create a global knowledge medical resource that leverages each individual’s information to help one another…(More)”

Americans’ Views on Open Government Data

Curated on Posted on by Stefaan Verhulst

John Horrigan and Lee Rainie at Pew Internet, Technology and Science: “Government reformers and advocates believe that two contemporary phenomena hold the potential to change how people engage with governments at all levels. The first is data. There is more of it than ever before and there are more effective tools for sharing it. This creates new service-delivery possibilities for government through use of data that government agencies themselves collect and generate. The second is public desire to make government more responsive, transparent and effective in serving citizens — an impulse driven by tight budgets and declining citizens’ trust in government.

The upshot has been the appearance of a variety of “open data” and “open government” initiatives throughout the United States that try to use data as a lever to improve government performance and encourage warmer citizens’ attitudes toward government.

This report is based on the first national survey that seeks to benchmark public sentiment about the government initiatives that use data to cultivate the public square. The survey, conducted by Pew Research Center in association with the John S. and James L. Knight Foundation, captures public views at the emergent moment when new technology tools and techniques are being used to disseminate and capitalize on government data and specifically looks at:

  • People’s level of awareness of government efforts to share data
  • Whether these efforts translate into people using data to track government performance
  • If people think government data initiatives have made, or have the potential to make, government perform better or improve accountability
  • The more routine kinds of government-citizen online interactions, such as renewing licenses or searching for the hours of public facilities.

The results cover all three levels of government in America — federal, state and local — and show that government data initiatives are in their early stages in the minds of most Americans. Generally, people are optimistic that these initiatives can make government more accountable; even though many are less sure open data will improve government performance. And government does touch people online, as evidenced by high levels of use of the internet for routine information applications. But most Americans have yet to delve too deeply into government data and its possibilities to closely monitor government performance.

Among the survey’s main findings:

As open data and open government initiatives get underway, most Americans are still largely engaged in “e-Gov 1.0” online activities, with far fewer attuned to “Data-Gov 2.0” initiatives that involve agencies sharing data online for public use….

Minorities of Americans say they pay a lot of attention to how governments share data with the public and relatively few say they are aware of examples where government has done a good (or bad) job sharing data. Less than one quarter use government data to monitor how government performs in several different domains….
Americans have mixed hopes about government data initiatives. People see the potential in these initiatives as a force to improve government accountability. However, the jury is still out for many Americans as to whether government data initiatives will improve government performance….
People’s baseline level of trust in government strongly shapes how they view the possible impact of open data and open government initiatives on how government functions…
Americans’ perspectives on trusting government are shaped strongly by partisan affiliation, which in turn makes a difference in attitudes about the impacts of government data initiatives…

Americans are for the most part comfortable with government sharing online data about their communities, although they sound cautionary notes when the data hits close to home…

Smartphone users have embraced information-gathering using mobile apps that rely on government data to function, but not many see a strong link between the underlying government data and economic value…

…(More)”

21st-Century Public Servants: Using Prizes and Challenges to Spur Innovation

Curated on Posted on by Stefaan Verhulst

Jenn Gustetic at the Open Government Initiative Blog: “Thousands of Federal employees across the government are using a variety of modern tools and techniques to deliver services more effectively and efficiently, and to solve problems that relate to the missions of their Agencies. These 21st-century public servants are accomplishing meaningful results by applying new tools and techniques to their programs and projects, such as prizes and challenges, citizen science and crowdsourcing, open data, and human-centered design.

Prizes and challenges have been a particularly popular tool at Federal agencies. With 397 prizes and challenges posted on challenge.gov since September 2010, there are hundreds of examples of the many different ways these tools can be designed for a variety of goals. For example:

  • NASA’s Mars Balance Mass Challenge: When NASA’s Curiosity rover pummeled through the Martian atmosphere and came to rest on the surface of Mars in 2012, about 300 kilograms of solid tungsten mass had to be jettisoned to ensure the spacecraft was in a safe orientation for landing. In an effort to seek creative concepts for small science and technology payloads that could potentially replace a portion of such jettisoned mass on future missions, NASA released the Mars Balance Mass Challenge. In only two months, over 200 concepts were submitted by over 2,100 individuals from 43 different countries for NASA to review. Proposed concepts ranged from small drones and 3D printers to radiation detectors and pre-positioning supplies for future human missions to the planet’s surface. NASA awarded the $20,000 prize to Ted Ground of Rising Star, Texas for his idea to use the jettisoned payload to investigate the Mars atmosphere in a way similar to how NASA uses sounding rockets to study Earth’s atmosphere. This was the first time Ted worked with NASA, and NASA was impressed by the novelty and elegance of his proposal: a proposal that NASA likely would not have received through a traditional contract or grant because individuals, as opposed to organizations, are generally not eligible to participate in those types of competitions.
  • National Institutes of Health (NIH) Breast Cancer Startup Challenge (BCSC): The primary goals of the BCSC were to accelerate the process of bringing emerging breast cancer technologies to market, and to stimulate the creation of start-up businesses around nine federally conceived and owned inventions, and one invention from an Avon Foundation for Women portfolio grantee.  While NIH has the capacity to enable collaborative research or to license technology to existing businesses, many technologies are at an early stage and are ideally suited for licensing by startup companies to further develop them into commercial products. This challenge established 11 new startups that have the potential to create new jobs and help promising NIH cancer inventions support the fight against breast cancer. The BCSC turned the traditional business plan competition model on its head to create a new channel to license inventions by crowdsourcing talent to create new startups.

These two examples of challenges are very different, in terms of their purpose and the process used to design and implement them. The success they have demonstrated shouldn’t be taken for granted. It takes access to resources (both information and people), mentoring, and practical experience to both understand how to identify opportunities for innovation tools, like prizes and challenges, to use them to achieve a desired outcome….

Last month, the Challenge.gov program at the General Services Administration (GSA), the Office of Personnel Management (OPM)’s Innovation Lab, the White House Office of Science and Technology Policy (OSTP), and a core team of Federal leaders in the prize-practitioner community began collaborating with the Federal Community of Practice for Challenges and Prizes to develop the other half of the open innovation toolkit, the prizes and challenges toolkit. In developing this toolkit, OSTP and GSA are thinking not only about the information and process resources that would be helpful to empower 21st-century public servants using these tools, but also how we help connect these people to one another to add another meaningful layer to the learning environment…..

Creating an inventory of skills and knowledge across the 600-person (and growing!) Federal community of practice in prizes and challenges will likely be an important resource in support of a useful toolkit. Prize design and implementation can involve tricky questions, such as:

  • Do I have the authority to conduct a prize or challenge?
  • How should I approach problem definition and prize design?
  • Can agencies own solutions that come out of challenges?
  • How should I engage the public in developing a prize concept or rules?
  • What types of incentives work best to motivate participation in challenges?
  • What legal requirements apply to my prize competition?
  • Can non-Federal employees be included as judges for my prizes?
  • How objective do the judging criteria need to be?
  • Can I partner to conduct a challenge? What’s the right agreement to use in a partnership?
  • Who can win prize money and who is eligible to compete? …(More)

Data Science and Ebola

Curated on Posted on by Stefaan Verhulst

Inaugural Lecture by Aske Plaat on the acceptance of the position of professor of Data Science at the Universiteit Leiden: “…Today, everybody and everything produces data. People produce large amounts of data in social networks and in commercial transactions. Medical, corporate, and government databases continue to grow. Ten years ago there were a billion Internet users. Now there are more than three billion, most of whom are mobile.1 Sensors continue to get cheaper and are increasingly connected, creating an Internet of Things. The next three billion users of the Internet will not all be human, and will generate a large amount of data. In every discipline, large, diverse, and rich data sets are emerging, from astrophysics, to the life sciences, to medicine, to the behavioral sciences, to finance and commerce, to the humanities and to the arts. In every discipline people want to organize, analyze, optimize and understand their data to answer questions and to deepen insights. The availability of so much data and the ability to interpret it are changing the way the world operates. The number of sciences using this approach is increasing. The science that is transforming this ocean of data into a sea of knowledge is called data science. In many sciences the impact on the research methodology is profound—some even call it a paradigm shift.

…I will address the question of why there is so much interest in data. I will answer this question by discussing one of the most visible recent challenges to public health of the moment, the 2014 Ebola outbreak in West Africa…(More)”

Citizen Science for Citizen Access to Law

Curated on Posted on by Stefaan Verhulst

Paper by Michael Curtotti, Wayne Weibel, Eric McCreath, Nicolas Ceynowa, Sara Frug, and Tom R Bruce: “This paper sits at the intersection of citizen access to law, legal informatics and plain language. The paper reports the results of a joint project of the Cornell University Legal Information Institute and the Australian National University which collected thousands of crowdsourced assessments of the readability of law through the Cornell LII site. The aim of the project is to enhance accuracy in the prediction of the readability of legal sentences. The study requested readers on legislative pages of the LII site to rate passages from the United States Code and the Code of Federal Regulations and other texts for readability and other characteristics. The research provides insight into who uses legal rules and how they do so. The study enables conclusions to be drawn as to the current readability of law and spread of readability among legal rules. The research is intended to enable the creation of a dataset of legal rules labelled by human judges as to readability. Such a dataset, in combination with machine learning, will assist in identifying factors in legal language which impede readability and access for citizens. As far as we are aware, this research is the largest ever study of readability and usability of legal language and the first research which has applied crowdsourcing to such an investigation. The research is an example of the possibilities open for enhancing access to law through engagement of end users in the online legal publishing environment for enhancement of legal accessibility and through collaboration between legal publishers and researchers….(More)”

White House Releases 150 Data Sets to Fight Climate Change

Curated on Posted on by Stefaan Verhulst

 at GovTech: “To support the president’s Climate Data Initiative, the White House revealed on Tuesday, April 7, a series of data projects and partnerships that includes more than 150 new open data sets, as well as commitments from Google, Microsoft and others to cultivate climate analysis.

The undertakings were released at a White House climate and health conference where John Holdren, director of the White House Office of Science and Technology Policy, pressed the need for greater data to compel decreases to greenhouse emissions.

“This is a science-based administration, a fact-based administration, and our climate policies have to be based on fact, have to be based on data, and we want to make those data available to everybody,” Holdren said.

The data initiative touches multiple agencies — including NASA, the Centers for Disease Control and Prevention, the National Institutes of Health and the Environmental Protection Agency — and is part of the White House proclamation of a new National Public Health Week, from April 6 to April 12, to spur national health solutions and awareness.

The 150-plus data sets are all connected to health, and are among the 560 climate-related data sets available on Data.gov, the U.S. government’s open data portal. Accompanying the release, the Department of Health and Human Services added a Health Care Facilities Toolkit on Toolkit.climate.gov, a site that delivers climate resilience techniques, strategies, case studies and tools for organizations attempting climate change initiatives.

Holdren was followed by White House Chief Data Scientist D.J. Patil, who moderated a tech industry panel with representatives from Google, Microsoft and GIS mapping software company Esri.

Google Earth Outreach Program Manager Allison Lieber confirmed that Google will continue to provide assistance with 10 million hours for high-performance computing for climate data projects — down from 50 million in 2014 — and the company will likewise provide climate data hosting on Google Earth….(More)”

Big Data, Little Data, No Data

Curated on Posted on by Stefaan Verhulst

New book by Christine L. Borgman: “Big Data” is on the covers of Science, Nature, the Economist, and Wired magazines, on the front pages of the Wall Street Journal and the New York Times. But despite the media hyperbole, as Christine Borgman points out in this examination of data and scholarly research, having the right data is usually better than having more data; little data can be just as valuable as big data. In many cases, there are no data—because relevant data don’t exist, cannot be found, or are not available. Moreover, data sharing is difficult, incentives to do so are minimal, and data practices vary widely across disciplines.

Borgman, an often-cited authority on scholarly communication, argues that data have no value or meaning in isolation; they exist within a knowledge infrastructure—an ecology of people, practices, technologies, institutions, material objects, and relationships. After laying out the premises of her investigation—six “provocations” meant to inspire discussion about the uses of data in scholarship—Borgman offers case studies of data practices in the sciences, the social sciences, and the humanities, and then considers the implications of her findings for scholarly practice and research policy. To manage and exploit data over the long term, Borgman argues, requires massive investment in knowledge infrastructures; at stake is the future of scholarship….(More)”