Help us make Science more Open with GENERA

posted in: Updates | 14

We at Biology Fortified have a long-standing commitment to making science more accessible to the public. Whether it is through detailed and thoughtful posts on the Biofortified Blog, resource pages describing plant biotechnology traits and listing companies that make them, or chronicling the adventures of our blog mascot through photographs, we’re reaching more people than ever before. But one resource we have been talking about for a long time is ready to become so much more, but we need your help to do it. I’m talking about the GENetic Engineering Risk Atlas (GENERA) which aims to catalog every peer-reviewed study on genetically engineered crops, covering the safety of consuming them, to growing them in the environment, and to whether or not the traits work as described, and more.

The Need for GENERA

Today, various Open Science Champions of Change will be honored at the White House, and thanks to everyone’s help with nominating us, Anastasia and Frank N. Foode will at least be attending, maybe more. This initiative is intended to encourage projects that increase the ability of the public to access, understand, and even work with the science of one field or another. In the debate over genetically engineered crops and their relative risks, many claims are made based on a few cherry-picked studies, and sometimes the claim is there there are only a few studies to cherry-pick. We assembled a list, which has already reached 600 studies, and people are taking notice.

Our list of studies has been talked about in many places recently, from the CATO forum, to the Food Dialogues at the BIO convention in Chicago, to internet forums, blog posts, and twitter debates. Clearly, there is interest in this project, and a demand for better, more comprehensive access to the science. But right now it is still just a list of references, and not conducive to helping people find more information easily. Our goal is to turn this list into a searchable database, and there have been various challenges along the way, but in the next couple months those challenges are melting away.

Finding the time to devote to reading, categorizing, and rating hundreds of studies is a daunting task. Programming our website to display and search all these studies in an attractive format presented another barrier. But last fall, we were awarded a grant from the American Society of Plant Biologists to pay a programmer to make it work, artists to make it look good, and readers to analyze the studies. All ready to go, right? Almost.

The Perfect System

One of the challenges that we have faced with a project of this magnitude is how to maintain a database of hundreds to potentially thousands of studies that will allow us to get all the citation information for each study, categorize and rate them, and keep this information associated with the PDF files themselves. And importantly – it had to be web-based to allow for collaboration between many people. Our first plan was to do this with a Google spreadsheet, however what it gained in terms of accessibility and collaboration, it lost when it came to keeping the research papers themselves attached to their details.

We needed a citation manager that could do this for us. After a long search, we came across a nifty program called Qiqqa. It would allow us to import PDF files, scan them for citation information, and tag them for organizational purposes. It also has a really good system for online collaboration. All we needed to make sure was that it could export this information into a spreadsheet, which it did. However, it only exported some information about each study – not all of it. Rather than move on, this Spring we contacted Qiqqa directly with our concerns.

Within days, Qiqqa responded, figured out a solution, and released a new version of their program that would do exactly what we needed! Now we could enter any citation information we wanted, and indeed, design our own format that includes every attribute we want to collect about each study – and then have it all go straight into a spreadsheet so we can make a database out of it. We can do the entire project within Qiqqa and keep track of all this research indefinitely. All from one change from a responsive company. We feel very fortunate to have found Qiqqa, and now we can get this project really rolling.

How You Can Help

There are several ways you can help us out, and all of them are easy. If you are scrapped for time, you can just click on the Qiqqa links above – just once. It will actually help us increase our storage space with Qiqqa – just once per person is fine!

Second, if you do have time, we could use some help with some of the basic steps of building this database. Each step is easy to do, and you can help out as little or as much as you want. These include:

  • Finding PDF files for studies in our GENERA list and loading them in (drag and drop!)
  • Entering the basic citation information (Authors, title, abstract, etc) for each study
  • Looking through the references of entered studies to look for studies we haven’t found yet
  • Searching the literature, websites, to find more studies
Frank doesn’t want just one prize, he wants them all!

You can do any one of these things, and they are all helpful. If you have university access to scientific journals, then that would make finding PDFs easy. If you don’t have access, you could find open access papers, or, enter the information from studies or search their references. You could even pair up with someone else and each does one step in the chain. We can help arrange that.

We’ve got a nifty tagging system worked out so that everyone’s work doesn’t get duplicated, and we can keep track of how much everyone has contributed. It also means that we can offer some fabulous prizes for people who contribute, like books and bumper stickers, and jars of Honey from my bees. That’s right, July’s community contest will be all about GENERA, but this time everyone can win – not just one or two people! We’ll put up the prize scale on a special page soon, so you busy bees can get some honey! We’re going to give credit where credit is due (and if we publish a paper on this project, you might find your name in there as well).

You might wonder, do I need to be a scientist to help out? No, anyone can! We’re taking the guesswork out of this project for all our contributors. Once each study has been entered into our system, and its references checked, we’ll handle the rest, such as categorizing the study and rating its outcome. You do not need to worry about interpreting the research, which is the hard part, just help us get the papers in the system! If you helped out with our google spreadsheet before, you can easily put the work you did there into Qiqqa – it is not lost!

If you are interested to help us enter even just a few studies, here’s how to get started. Register for Qiqqa with this link, and send us an email through our contact form, letting us know that you want to help. If you are a newcomer, tell us a bit about yourself and your background, that way we can suggest ways that you can most effectively help out! Next week we will hold an orientation to show volunteers how to enter in a study, and to make things more fun we can also arrange hangouts to shoot the breeze while we put them in. Open Science can be fun and social too.

“Oh, I just saw this two weeks/months/years later and I would still like to help out”

No problem! Click links, sign up, and drop us a note, and you can join in anytime. Even when all 600 studies in our current list have been entered, rated, and uploaded to our site, the job will never really be done. Studies come out all the time, to the tune of 50 or more per year, so there will always be the need for help.

The world desperately needs resources like this to improve everyone’s access to science. I hope you can be a part of this!

Follow Karl Haro von Mogel:

Karl earned his Ph.D. in Plant Breeding and Plant Genetics at UW-Madison, with a minor in Life Science Communication. His dissertation was on both the genetics of sweet corn and plant genetics outreach. He recently moved back to his home state of California. His favorite produce might just be squash.