Jun 5, 2014

Open Projects - Open Humans


This article is the second in a series highlighting open science projects around the community. You can read the interview this article was based on: edited for clarity, unedited.

While many researchers encounter no privacy-based barriers to releasing data, those working with human participants, such as doctors, psychologists, and geneticists, have a difficult problem to surmount. How do they reconcile their desire to share data, allowing their analyses and conclusions to be verified, with the need to protect participant privacy? It's a dilemma we've talked about before on the blog (see: Open Data and IRBs, Privacy and Open Data). A new project, Open Humans, seeks to resolve the issue by finding patients who are willing - even eager - to share their personal data.

Open Humans, which recently won a $500,000 grant from the Knight Foundation, grew out of the Personal Genome Project. Founded in 2005 by Harvard genetics professor George Church, the Personal Genome Project sought to solve a problem that many genetics researchers had yet to recognize. "At the time people didn't really see genomes as inherently identifiable," Madeleine Price Ball explains. Ball is co-founder of OpenHumans, Senior Research Scientist at PersonalGenomes.org, and Director of Research at the Harvard Personal Genome Project. She quotes from 1000 Genomes' informed consent form: "'Because of these measures, it will be very hard for anyone who looks at any of the scientific databases to know which information came from you, or even that any information in the scientific databases came from you.'"

"So that's sort of the attitude scientists had towards genomes at the time. Also, the Genetic Information Nondiscrimination Act didn't exist yet. And there was GATTACA. Privacy was still this thing everyone thought they could have, and genomes were this thing people thought would be crazy to share in an identifiable manner. I think the scientific community had a bit of unconscious blindness, because they couldn't imagine an alternative."

Church found an initial ten participants - the list includes university professors, health care professionals, and Church himself. The IRB interviewed each of the participants to make sure they truly understood the project and, satisfied, allowed it to move forward. The Personal Genome Project now boasts over 3,400 participants, each of whom have passed an entrance exam showing that they understand what will happen to their data, and the risks involved. Most participants are enthusiastic about sharing. One participant described it as "donating my body to science, but I don't have to die first".

The Personal Genome Project's expansion hasn't been without growing pains. "We've started to try to collect data beyond genomes." Personal health information, including medical history, procedures, test results, prescriptions, has been provided by a subset of participants. "Every time one of these new studies was brought before the IRB they'd be like ‘what? that too?? I don't understand what are you doing???' It wasn't scaling, it was confusing, the PGP was trying to collect samples and sequence genomes and it was trying to let other groups collect samples and do other things."

Thus, Open Humans was born. "Open Humans is an abstraction that takes part of what the PGP was doing (the second part) and make it scalable," Ball explains. "It's a cohort of participants that demonstrate an interest in public data sharing, and it's researchers that promise to return data to participants."

Open Humans will start out with a number of participants and an array of public data sets, thanks to collaborating projects American Gut, Flu Near You, and of course, the Harvard Personal Genome Project. Participants share data and, in return, researchers promise to share results. What precisely "sharing results" means has yet to be determined. "We're just starting out and know that figuring out how this will work is a learning process," Ball explains. But she's already seen what can happen when participants are brought into the research process - and brought together:

"One of the participants made an online forum, another a Facebook group, and another maintains a LinkedIn group… before this happened it hadn't occurred to me that abandoning the privacy-assurance model of research could empower participants in this manner. Think about the typical study - each participant is isolated, they never see each other. Meeting each other could breach confidentiality! Here they can talk to each other and gasp complain about you. That's pretty empowering." Ball and her colleague Jason Bobe, Open Humans co-founder and Executive Director of PersonalGenomes.org, hope to see all sorts of collaborations between participants and researchers. Participants could help researchers refine and test protocols, catch errors, and even provide their own analyses.

Despite these dreams, Ball is keeping the project grounded. When asked whether Open Humans will require articles published using their datasets to be made open access, she replies that, "stacking up a bunch of ethical mandates can sometimes do more harm than good if it limits adoption". Asked about the effect of participant withdrawals on datasets and reproducibility, she responds, "I don't want to overthink it and implement things to protect researchers at the expense of participant autonomy based on just speculation." (It is mostly speculation. Less than 1% of Personal Genome Project users have withdrawn from the study, and none of the participants who've provided whole genome or exome data have done so.)

It's clear that Open Humans is focused on the road directly ahead. And what does that road look like? "Immediately, my biggest concern is building our staff. Now that we won funding, we need to hire a good programmer... so if you are or know someone that seems like a perfect fit for us, please pass along our hiring opportunities". She adds that anyone can join the project's mailing list to get updates and find out when Open Humans is open to new participants - and new researchers. "And just talk about us. Referring to us is an intangible but important aspect for helping promote awareness of participant-mediated data sharing as a participatory research method and as a method for creating open data."

In other words: start spreading the news. Participant mediated data isn't the only solution to privacy issues, but it's an enticing one - and the more people who embrace it, the better a solution it will be.

Jan 22, 2014

Open Projects - Wikipedia Project Medicine


This article is the first in a series highlighting open science projects around the community. You can read the interview this article was based on: edited for clarity, unedited.

Six years ago, Doctor James Heilman was working a night shift in the ER when he came across an error-ridden article on Wikipedia. Someone else might have used the article to dismiss the online encyclopedia, which was then less than half the size it is now. Instead, Heilman decided to improve the article. “I noticed an edit button and realized that I could fix it. Sort of got hooked from there. I’m still finding lots of articles that need a great deal of work before they reflect the best available medical evidence.”

Heilman, who goes by the username Jmh649 on Wikipedia, is now the president of the board of Wiki Project Med. A non-profit corporation created to promote medical content on Wikipedia, WPM contains over a dozen different initiatives aimed at adding and improving articles, building relationships with schools, journals and other medical organizations, and increasing access to research.

One of the initiatives closest to Heilman’s heart is the Translation Task Force, an effort to identify key medical articles and translate them into as many languages as they can. These articles cover common and potentially deadly medical circumstances, such as gastroenteritis (diarrhea), birth control, HIV/AIDS, and burns. With the help of Translators Without Borders, over 3 million words have been translated into about 60 languages. One of these languages is Yoruba, a West African language. Although Yoruba is spoken by nearly 30 million people, there are only a few editors working to translate medical articles into it.

“The first two billion people online by and large speak/understand at least one of the wealthy languages of the world. With more and more people getting online via cellphones that is not going to be true for the next 5 billion coming online. Many of them will find little that they can understand.” Wikipedia Zero, a program which provides users in some developing countries access to Wikipedia without mobile data charges, is increasing access to the site.

“People are, for better or worse, learning about life and death issues through Wikipedia. So we need to make sure that content is accurate, up to date, well-sourced, comprehensive, and accessible. For readers with no native medical literature, Wikipedia may well be the only option they have to learn about health and disease.”

That’s Jake Orlowitz (Ocaasi), WPM’s outreach coordinator. He and Heilman stress that there’s a lot of need for volunteer help, and not just with translating. Of the 80+ articles identified as key, only 31 are ready to be translated. The rest need citations verified, jargon simplified, content updated and restructured, and more.

In an effort to find more expert contributors, WPM has launched a number of initiatives to partner with medical schools and other research organizations. Orlowitz was recently a course ambassador to the UCSF medical school, where students edited Wikipedia articles for credit. He also set up a partnership with the Cochrane Collaboration a non-profit made up of over 30,000 volunteers, mostly medical professionals, who conduct reviews of medical interventions. “We arranged a donation of 100 full access accounts to The Cochrane Library, and we are currently coordinating a Wikipedian in Residence position with them. That person will teach dozens of Cochrane authors how to incorporate their findings into Wikipedia,” explains Orlowitz.

Those who are familiar with how Wikipedia is edited might balk at the thought of contributing. Won’t they be drawn in to “edit wars”, endless battles with people who don’t believe in evolution or who just enjoy conflict? “There are edit wars,” admits Heilman. “They are not that common though. 99% of articles can be easily edited without problems.”

Orlowitz elaborates on some of the problems that arise. “We have a lot of new editors who don't understand evidence quality.” The medical experts they recruit face a different set of challenges. “One difficulty many experts have is that they wish to reference their own primary sources. Or write about themselves. Both those are frowned upon. We also have some drug and device companies that edit articles in their area of business--we discourage this strongly and it's something we keep an eye on.”

And what about legitimate differences of opinion about as yet unsettled medical theories, facts and treatments?

“Wikipedia 'describes debates rather than engaging in them'. We don't take sides, we just summarize the evidence on all sides--in proportion to the quality and quantity of that evidence,” says Orlowitz. Heilman continues: “For example Cochrane reviews state it is unclear if the risk versus benefits of breast cancer screening are positive or negative. The USPSTF is supportive. We state both.” Wikipedia provides detailed guidelines for evaluating sources and dealing with conflicting evidence.

Another reason academics might hesitate before contributing is the poor reputation Wikipedia has in academic circles. Another initiative, the Wikipedia-journal collaboration, states: "One reason some academics express for not contributing to Wikipedia is that they are unable to get the recognition they require for their current professional position. A number of medical journals have agreed in principle to publishing high quality Wikipedia articles under authors' real names following formal peer review.” A pilot paper, adapted from the Wikipedia article on Dengue Fever, is to be published in the Journal of Open Medicine, with more publications hopefully to come.

The stigma against Wikipedia itself is also decreasing. “The usage stats for the lay public, medical students, junior physicians, and doctors, and pharmacists are just mindbogglingly high. It's in the range of 50-90%, even for clinical professionals. We hear a lot that doctors 'jog their memory' with Wikipedia, or use it as a starting point,” says Orlowitz. One 2013 study found that a third or more of general practitioners, specialists and medical professors had used Wikipedia, with over half of physicians in training accessing it. As more diverse kinds of scientific contributions begin to be recognized, Wikipedia edits may make their way onto CVs.

Open science activists may be disappointed to learn that Wikipedia doesn’t require or even prefer open access sources for its articles. “Our policy simply states that our primary concern is article content, and verifi_ability_. That standard is irrespective of how hard or easy it is to verify,” explains Orlowitz. Both Wikipedians personally support open access, and would welcome efforts to supplement closed access citations with open ones. “If there are multiple sources of equal quality that come to the same conclusions we support using the open source ones,” says Heilman. A new project, the Open Access Signalling project aims to help readers quickly distinguish what sources they’ll be able to access.

So what are the best ways for newcomers to get involved? Heilman stresses that editing articles remains one of the most important tasks of the project. This is especially true of people affiliated with universities. “Ironically, since these folks have access to high quality paywalled sources, one great thing they could do would be to update articles with them. We also could explore affiliating a Wikipedia editor with a university as a Visiting Scholar, so they'd have access to the library's catalogue to improve Wikipedia, in the spirit of research affiliates,” says Orlowitz.

Adds Heilman, “If there are institution who would be willing to donate library accounts to Wikipedia's we would appreciate it. This would require having the Wikipedian register in some manner with the university. There are also a number of us who may be willing / able to speak to Universities that wish to learn more about the place of Wikipedia in Medicine.” The two also speak at conferences and other events.

Wiki Project Med, like Wikipedia itself, is an open community - a “do-ocracy”, as Orlowitz calls it. If you’re interested in learning more, or in getting involved, you can check out their project page, which details their many initiatives, or reach out to Orlowitz or the project as a whole on Twitter (@JakeOrlowitz, @WikiProjectMed) or via email (jorlowitz@gmail.com, wikiprojectmed@gmail.com).