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OpenTrialsFDA presents prototype as finalist for the Open Science Prize

- December 1, 2016 in #openscience, News, Open Science, Open Trials, opentrials, Press

For immediate release Open Knowledge International is thrilled to announce that the OpenTrialsFDA team is presenting its prototype today at the BD2K Open Data Science Symposium in Washington, DC as finalist for the Open Science Prize. The Open Science Prize is a global science competition to make both the outputs from science and the research process broadly accessible. From now until 6 January 2017, the public is asked to help select the most promising, innovative and impactful prototype from among the six finalists – of which one will receive the grand prize of $230,000. OpenTrialsFDA is a collaboration between Dr. Erick Turner (a psychiatrist-researcher and transparency advocate), Dr. Ben Goldacre (Senior Clinical Research Fellow in the Centre for Evidence Based Medicine at the University of Oxford) and the team behind OpenTrials at Open Knowledge International.   OpenTrialsFDA works on making clinical trial data from the FDA (the US Food and Drug Administration) more easily accessible and searchable. Until now, this information has been hidden in the user-unfriendly Drug Approval Packages that the FDA publishes via its dataportal Drugs@FDA. These are often just images of pages, so you cannot even search for a text phrase in them. OpenTrialsFDA scrapes all the relevant data and documents from the FDA documents, runs Optical Character Recognition across all documents, links this information to other clinical trial data, and now presents it through a new user-friendly web interface at fda.opentrials.net. otfda_prototype_search
Explore the OpenTrialsFDA search interface
Any user can type in a drug name, and see all the places where this drug is mentioned in an FDA document. Users can also access, search and present this information through the application programming interfaces (APIs) the team will produce. In addition, the information has been integrated into the OpenTrials database, so that the FDA reports are linked to reports from other sources, such as ClinicalTrials.gov, EU CTR, HRA, WHO ICTRP, and PubMed. The prototype will provide the academic research world with important information on clinical trials in general, improving the quality of research, and helping evidence-based treatment decisions to be properly informed. Interestingly, the FDA data is unbiased, compared to reports of clinical trials in academic journals. Dr. Erick Turner explains: “With journal articles everything takes place after a study has finished, but with FDA reviews, there is a protocol that is submitted to the FDA before the study has even started. So the FDA learns first of all that the study is to be done, which means it can’t be hidden later. Secondly it learns all the little details, methodological details about how the study is going to be done and how it is going to be analyzed, and that guards against outcome switching.”
Dr Ben Goldacre: “These FDA documents are hugely valuable, but at the moment they’re hardly ever used. That’s because – although they’re publicly accessible in the most literal sense of that phrase – they are almost impossible to search, and navigate. We are working to make this data accessible, so that it has the impact it deserves.”

Voting for the Open Science Prize finalists is possible through  http://event.capconcorp.com/wp/osp: more information on OpenTrialsFDA is available from fda.opentrials.net/about and from the team’s video below.   Editor’s notes Dr. Ben Goldacre
Ben is a doctor, academic, writer, and broadcaster, and currently a Senior Clinical Research Fellow in the Centre for Evidence Based Medicine at the University of Oxford. His blog is at www.badscience.net and he is @bengoldacre on twitter. Read more here. His academic and policy work is in epidemiology and evidence based medicine, where he works on various problems including variation in care, better uses of routinely collected electronic health data, access to clinical trial data, efficient trial design, and retracted papers. In policy work, he co-authored this influential Cabinet Office paper, advocating for randomised trials in government, and setting out mechanisms to drive this forwards. He is the co-founder of the AllTrials campaign. He engages with policy makers. Alongside this he also works in public engagement, writing and broadcasting for a general audience on problems in evidence based medicine. His books have sold over 600,000 copies.
Dr. Erick Turner
Dr. Erick Turner is a psychiatrist-researcher and transparency advocate. Following a clinical research fellowship at the NIH, he worked for the US Food and Drug Administration (FDA), acting as gatekeeper for new psychotropic drugs seeking to enter the US market. In 2004 he published a paper drawing researchers’ attention to the Drugs@FDA website as a valuable but underutilized source of unbiased clinical trial data. Dissatisfied with the continuing underutilization of Drugs@FDA, he published a paper in the BMJ in order to encourage wider use of this trove of clinical trial data.
Open Knowledge International
https://okfn.org   
Open Knowledge International is a global non-profit organisation focussing on realising open data’s value to society by helping civil society groups access and use data to take action on social problems. Open Knowledge International addresses this in three steps: 1) we show the value of open data for the work of civil society organizations; 2) we provide organisations with the tools and skills to effectively use open data; and 3) we make government information systems responsive to civil society.
Open Science Prize
https://www.openscienceprize.org/res/p/finalists/
The Open Science Prize  is a collaboration between the National Institutes of Health and the Wellcome Trust, with additional funding provided by the Howard Hughes Medical Institute of Chevy Chase, Maryland.  The Open Data Science Symposium will feature discussions with the leaders in big data, open science, and biomedical research while also showcasing the finalists of the Open Data Science Prize, a worldwide competition to harness the innovative power of open data.

OpenTrialsFDA presents prototype as finalist for the Open Science Prize

- December 1, 2016 in #openscience, News, Open Science, Open Trials, opentrials, Press

For immediate release Open Knowledge International is thrilled to announce that the OpenTrialsFDA team is presenting its prototype today at the BD2K Open Data Science Symposium in Washington, DC as finalist for the Open Science Prize. The Open Science Prize is a global science competition to make both the outputs from science and the research process broadly accessible. From now until 6 January 2017, the public is asked to help select the most promising, innovative and impactful prototype from among the six finalists – of which one will receive the grand prize of $230,000. OpenTrialsFDA is a collaboration between Dr. Erick Turner (a psychiatrist-researcher and transparency advocate), Dr. Ben Goldacre (Senior Clinical Research Fellow in the Centre for Evidence Based Medicine at the University of Oxford) and the team behind OpenTrials at Open Knowledge International.   OpenTrialsFDA works on making clinical trial data from the FDA (the US Food and Drug Administration) more easily accessible and searchable. Until now, this information has been hidden in the user-unfriendly Drug Approval Packages that the FDA publishes via its dataportal Drugs@FDA. These are often just images of pages, so you cannot even search for a text phrase in them. OpenTrialsFDA scrapes all the relevant data and documents from the FDA documents, runs Optical Character Recognition across all documents, links this information to other clinical trial data, and now presents it through a new user-friendly web interface at fda.opentrials.net. otfda_prototype_search
Explore the OpenTrialsFDA search interface
Any user can type in a drug name, and see all the places where this drug is mentioned in an FDA document. Users can also access, search and present this information through the application programming interfaces (APIs) the team will produce. In addition, the information has been integrated into the OpenTrials database, so that the FDA reports are linked to reports from other sources, such as ClinicalTrials.gov, EU CTR, HRA, WHO ICTRP, and PubMed. The prototype will provide the academic research world with important information on clinical trials in general, improving the quality of research, and helping evidence-based treatment decisions to be properly informed. Interestingly, the FDA data is unbiased, compared to reports of clinical trials in academic journals. Dr. Erick Turner explains: “With journal articles everything takes place after a study has finished, but with FDA reviews, there is a protocol that is submitted to the FDA before the study has even started. So the FDA learns first of all that the study is to be done, which means it can’t be hidden later. Secondly it learns all the little details, methodological details about how the study is going to be done and how it is going to be analyzed, and that guards against outcome switching.”
Dr Ben Goldacre: “These FDA documents are hugely valuable, but at the moment they’re hardly ever used. That’s because – although they’re publicly accessible in the most literal sense of that phrase – they are almost impossible to search, and navigate. We are working to make this data accessible, so that it has the impact it deserves.”

Voting for the Open Science Prize finalists is possible through  http://event.capconcorp.com/wp/osp: more information on OpenTrialsFDA is available from fda.opentrials.net/about and from the team’s video below.   Editor’s notes Dr. Ben Goldacre
Ben is a doctor, academic, writer, and broadcaster, and currently a Senior Clinical Research Fellow in the Centre for Evidence Based Medicine at the University of Oxford. His blog is at www.badscience.net and he is @bengoldacre on twitter. Read more here. His academic and policy work is in epidemiology and evidence based medicine, where he works on various problems including variation in care, better uses of routinely collected electronic health data, access to clinical trial data, efficient trial design, and retracted papers. In policy work, he co-authored this influential Cabinet Office paper, advocating for randomised trials in government, and setting out mechanisms to drive this forwards. He is the co-founder of the AllTrials campaign. He engages with policy makers. Alongside this he also works in public engagement, writing and broadcasting for a general audience on problems in evidence based medicine. His books have sold over 600,000 copies.
Dr. Erick Turner
Dr. Erick Turner is a psychiatrist-researcher and transparency advocate. Following a clinical research fellowship at the NIH, he worked for the US Food and Drug Administration (FDA), acting as gatekeeper for new psychotropic drugs seeking to enter the US market. In 2004 he published a paper drawing researchers’ attention to the Drugs@FDA website as a valuable but underutilized source of unbiased clinical trial data. Dissatisfied with the continuing underutilization of Drugs@FDA, he published a paper in the BMJ in order to encourage wider use of this trove of clinical trial data.
Open Knowledge International
https://okfn.org   
Open Knowledge International is a global non-profit organisation focussing on realising open data’s value to society by helping civil society groups access and use data to take action on social problems. Open Knowledge International addresses this in three steps: 1) we show the value of open data for the work of civil society organizations; 2) we provide organisations with the tools and skills to effectively use open data; and 3) we make government information systems responsive to civil society.
Open Science Prize
https://www.openscienceprize.org/res/p/finalists/
The Open Science Prize  is a collaboration between the National Institutes of Health and the Wellcome Trust, with additional funding provided by the Howard Hughes Medical Institute of Chevy Chase, Maryland.  The Open Data Science Symposium will feature discussions with the leaders in big data, open science, and biomedical research while also showcasing the finalists of the Open Data Science Prize, a worldwide competition to harness the innovative power of open data.

OpenTrials launch date + Hack Day

- August 25, 2016 in Events, Hackday, Open Trials, opentrials

Exciting news! OpenTrials, a project in which Open Knowledge is developing an open, online database of information about the world’s clinical research trials, will officially launch its beta on Monday 10th October 2016 at the World Health Summit in Berlin. After months of work behind-the-scenes meeting, planning, and developing, we’re all really excited about demoing OpenTrials to the world and announcing how to access and use the site! The launch will take place at the ‘Fostering Open Science in Global Health’ workshop, with OpenTrials being represented by our Community Manager, Ben Meghreblian. The workshop will be a great opportunity to talk about the role of open data, open science, and generally how being open can bring improvements in medicine and beyond!worldhealthsummit_logo As the workshop’s theme is public health emergencies, we’ll also be demoing Ebola Trials Tracker, another OpenTrials project showing how long it takes for the results of Ebola trials to be made available. If you’ll be attending the conference or the workshop, we’d love to meet you – please do get in touch and let us know.

Hack Day

If that wasn’t enough, we also have a confirmed date and location for the OpenTrials Hack Day – it will take place on Saturday 8th October at the German office of Wikimedia in Berlin. We’re inviting people from a range of backgrounds. So, if you’re developer, data scientist, health technologist, open data advocate, or otherwise interested in health, medicine, and clinical trials, come along and learn more about the data that powers OpenTrials, how it’s structured, and how to use our API to search the OpenTrials database or build applications using the data. On the day our technical lead and a domain expert will be on hand to explain the data and facilitate the day – we’re really looking forward to seeing what clever hacks and mini-projects you’ll create. For those of you who have already asked, we’ll be releasing documentation on the OpenTrials API and database soon, but meanwhile if you’re interested in the event you’ll find more details on the OpenTrials Eventbrite page, or you can register quickly below.
OpenTrials is funded by The Laura and John Arnold Foundation and directed by Dr. Ben Goldacre, an internationally known leader on clinical transparency. Contact: opentrials@okfn.org
Twitter: @opentrials

Update on OpenTrialsFDA: finalist for the Open Science Prize

- August 11, 2016 in #openscience, Open Science, Open Trials, opentrials

In May, the OpenTrialsFDA team (a collaboration between Erick Turner, Dr. Ben Goldacre and the  OpenTrials team at Open Knowledge) was selected as a finalist for the Open Science Prize. This global science competition is focused on making both the outputs from science and the research process broadly accessible to the public. Six finalists will present their final prototypes at an Open Science Prize Showcase in early December 2016, with the ultimate winner to be announced in late February or early March 2017. image01As the name suggests, OpenTrialsFDA is closely related to OpenTrials, a project funded by The Laura and John Arnold Foundation that is developing an open, online database of information about the world’s clinical research trials. OpenTrialsFDA will work on increasing access, discoverability and opportunities for re-use of a large volume of high quality information currently hidden in user-unfriendly Food and Drug Administration (FDA) drug approval packages (DAPs). The FDA publishes these DAPs as part of the general information on drugs via its data portal known as Drugs@FDA. These documents contain detailed information about the methods and results of clinical trials, and are unbiased, compared to reports of clinical trials in academic journals. This is because FDA reviewers require adherence to the outcomes and analytic methods prespecified in the original trial protocols, so, in contrast to most journal editors, they are unforgiving of practices such as post hoc switching of outcomes and changes to the planned statistical analyses. These review packages also often report on clinical trials that have never been published.
joined

A more complete picture: contrasting the journal version of antidepressant trials with the FDA information (image: Erick Turner, adapted from http://bit.ly/1XKLjzp

However, despite their high value, these FDA documents are notoriously difficult to access, aggregate, and search. The website itself is not easy to navigate, and much of the information is stored in PDFs or non-searchable image files for older drugs. As a consequence, they are rarely used by clinicians and researchers. OpenTrialsFDA will work on improving this situation, so that valuable information that is currently hidden away can be discovered, presented, and used to properly inform evidence-based treatment decisions. The team has started to scrape the FDA website, extracting the relevant information from the PDFs through a process of OCR (optical character recognition). A new OpenTrialsFDA interface will be developed to explore and discover the FDA data, with application programming interfaces (APIs) allowing third party platforms to access, search, and present the information, thus maximising discoverability, impact, and interoperability. In addition, the information will be integrated into the OpenTrials database, so that for any trial for which a match exists, users can see the corresponding FDA data. Future progress will be shared both through this blog and the OpenTrials blog: you can also sign up for the OpenTrials newsletter to receive regular updates and news. More information about the Open Science Prize and the other finalists is available from www.openscienceprize.org/res/p/finalists. Contact: opentrials@okfn.org
Twitter: @opentrials

Progress report: OpenTrials – linking clinical trial data

- July 15, 2016 in Featured Project, OKI Projects, Open Trials, opentrials

Since last year Open Knowledge has been developing OpenTrials, an open, online database linking the publicly available data and documents on all clinical trials conducted – something that has been talked about for many years but never created. The project is funded by The Laura and John Arnold Foundation and directed by Dr. Ben Goldacre, an internationally known leader on clinical trial transparency. Having an open and freely re-usable database of the world’s clinical trial data will increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data, and drive standards around open data in evidence-based medicine. The project is currently in its first phase (which runs until March 2017), where the focus is on building and populating the first prototype of the OpenTrials database, as well as raising awareness of the project in the community and getting user involvement and feedback. The progress that has been made so far was presented last month at the Evidence Live conference in Oxford, which brought together leaders across the world of Evidence Based Medicine, including researchers, doctors, and the pharmaceutical industry. This was an excellent opportunity to demonstrate the project and speak to both researchers who want to use the platform as well as people with a general enthusiasm for its impact on medicine. Around 40 people attended our talk which explained why OpenTrials is an important infrastructure project for medicine, covered some of the technical aspects of the platform, details of what data we’ve imported so far, and lastly a quick demo. If you’re feeling impatient, here are the slides from the talk, or scroll down for a summary. OpenTrials at Evidence Live

Ben Goldacre and Vitor Baptista present OpenTrials at Evidence Live 2016 (photo by benmeg / CC BY)

What we’ve imported into the OpenTrials database so far

  • 331,999 deduplicated trials, collected from nine clinical trial registries:
    • ANZCTR 11,645
    • ClinicalTrials.gov 205,422
    • EU CTR 35,159
    • GSK 4,131
    • ISRCTN 14,256
    • Pfizer 1,567
    • Takeda 1,142
    • UMIN 20,557
    • WHO ICTRP 298,688
Imported trials

Current functionality

  • Basic search (by keyword)
  • Searching for trials with publications
  • Uploading missing data/documents for a particular trial
  • Showing trials with discrepancies (e.g. target sample size)

What we’re importing next

Feedback and get involved

If you attended the talk and have any questions or feedback, please email us. And generally if you’re interested in contributing to OpenTrials, get in touch. Want to get early access to the data and be a user tester? Sign up and we’ll be in touch soon.  

Open Trials: Open Knowledge Announce Plans for Open, Online Database of Clinical Trials

- April 21, 2015 in Featured, Open Knowledge, Open Trials

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. logo-black-CMYK 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. “This project will help to shed light on both good and bad practices by the sponsors of clinical trials,” Stuart Buck, LJAF Vice President of Research Integrity, explained. “If those sponsors become more transparent about their successes and failures, medical science will advance more quickly, thus benefitting patients’ health.” “We are thrilled to partner with Open Knowledge on the use of the Open Science Framework (OSF) for this project. Open Trials is a great example of how the free, open source OSF infrastructure can be utilized by the community in different ways to increase transparency in scientific research,” Andrew Sallans, Center for Open Science Partnerships Lead, explained. 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. “This is an incredible opportunity to identify which trial results are being withheld,” Rufus Pollock, President and Founder of Open Knowledge, explained. “It is the perfect example of a project where opening up data and presenting it in a usable form will have a direct impact—it can literally save lives. We’re absolutely delighted to partner with Ben Goldacre, a leading expert and advocate in this space, as well as with the Center for Open Science and LJAF to conduct this groundbreaking work.” The first phase of the Open Trials project is scheduled for completion in March 2017. For project updates, please follow @opentrials on twitter or get in touch with us at opentrials@okfn.org. COS LJAF OpenKnowledge_LOGO_COLOUR_CMYK