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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.

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

Can we make research more efficient through increased openness?

- July 16, 2014 in #openscience, Sessions

The following is a guest post by Daniel Mietchen. Researchers spend a lot of their time thinking about how to test assumptions or hypotheses and how to separate different effects that jointly influence some observation or measurements. In their famous experiment in the late 1890s, for instance, Michaelson and Morley took great care to measure […]

10,000 #OpenScience Tweets

- March 20, 2014 in #openscience, media, research, social media, social networks, tools, Twitter

We have collected 10,000+ tweets using the #openscience hashtag on Twitter, and invite volunteers to help analyse the data. The twelve most-retweeted tweets are embedded below. Happily, just over 4,600 accounts have participated in the Open Science community with its eponymous hashtag, in this span. The 10,000 tweets have accrued over ten weeks. Our own @openscience on Twitter has tweeted most, over 600 times at the hashtag, as well as having received the most retweets and @ mentions, over 8,000 in these 10,000. We have modified the vis which came with the data via the satisfying TAGS effort shared by Martin Hawksey. We added looks at the numbers of mentions and of mentions per tweets for top tweeters, and rankings of top tweets for the past ten weeks to Martin’s default views. We will continue collecting tweets, but do note that in another month or so, we will reach Google Docs limits e.g. on numbers of cells. We will use additional sheets, so links to all data will have changed, just how depending on when you are reading this post. Ask us @openscience on Twitter.

Help wanted

More could be done; won’t you help? Leave a reply below or ping us @openscience on Twitter if you need edit access to the sheet itself but we would like to see data and analyses in other tools as well. Our work to this point is only to get something started.

Top #openscience tweets of the past ten weeks

            The above list is not dynamic. The data collected and displayed here, however are dynamic and refresh themselves hourly. Not all tweets which are about Open Science include the #openscience hashtag. In a perfectly semantic world, they would and when they can, they really should. It has helped to form a community among the 4,600+ accounts participating in these ten weeks and many others in recent years. A couple reasons the hashtag might not be used in a relevant tweet include the character limit on tweets and lack of awareness of hashtags or of the term Open Science. We take our organising and leadership role seriously at @openscience on Twitter, an account shared by many in the community. We have a simple policy that all our tweets should be related to Open Science. Even at our account, not all our tweets include the #openscience hashtag, particularly as we discuss related concerns such as Citizen Science or Open Access. An example tweet from the time frame considered here, related to Open Science but not hashtagged as such is below. In this case, the limit on tweet length and the topic led to including #openaccess, not #openscience:   The most retweeted, Open Science related tweet of all time, so far as we know, did not use the #openscience hashtag but was lovely. From the Lord of Dance and Prince of Swimwear: