Scientists lead the push for open data sharing

Scientists lead the push for open data sharing
Cameron Neylon in the lab recording research electronically

Biologist Cameron Neylon describes a community that is changing the way scientists communicate by making their data publicly available on the web

Research Information: April/May 2009

Scientists are notorious for keeping their work under lock and key. An enormous body of scientific knowledge remains unavailable to those who need it most, existing only in the minds of individual researchers and their notebooks. However, some scientists like myself are pioneering an online ‘open notebook science’ approach to make scientific communication more efficient and to make research results more readily available.

A traditionally-published scientific paper focuses on what the authors think the results mean. It often doesn’t include the actual data, and rarely includes details of analysis and experimental procedures that could assist other scientists. For example: How many times was this actually tried before it worked? How important is the timing? What does the raw data look like? These details can be crucial to re-using published results, but they are rarely found in papers.

Worse still, much research is never published. Many experiments fail, give negative results, or provide information that ‘doesn’t fit’ into the final publication. This information is nearly impossible to publish in scientific journals but can be incredibly valuable to researchers deciding between different approaches or methods.

A central facility like the ISIS Pulsed Neutron Source at the Rutherford Appleton Laboratory in the UK needs to support its community. By making our work public we are helping the researchers who use our facility. In the ISIS Biomolecular Sciences group, we aim to make our research records and the data available on the web as soon as possible. The open notebook approach is not currently a standard ISIS policy for data access but our group is exploring the approaches that could work at a large research centre like ISIS. Our aim is simply to make more of this information available to those who want and need it.

Open notebook science in practice

At ISIS we are using the open notebook science approach to study the structure and function of a class of proteins found in biological membranes. The research aims to determine how these molecules, similar to those involved in transmitting nerve signals in humans, change shape when they bind to specific targets. Membrane proteins are notoriously difficult to obtain structural information on. Our aim is to develop and improve methods, using ISIS facilities, which can be shared with other researchers interested in membrane proteins. Using the small-angle scattering instruments at ISIS we aim to determine low-resolution structures of these important molecules.

Biology experiments like this involve considerable trial and error and generate large volumes of data. In most projects much of this data is discarded, and methods are often not described in detail, although these may be useful for other research. By capturing and recording our data and placing it in the public domain, we provide a foundation that can save other scientists valuable time and money.

Cameron Neylon is part of a community that aims to open up scientific data

Helping collaboration

This approach helps us to overcome the geographical distance between ISIS and some of our collaborators. By sharing our laboratory notebooks online we eliminate the time wasted physically transferring and gathering data from scientists involved in various projects.

It also helps when teams of scientists within ISIS are working on one project. By having data stored on a central, accessible website, scientists within the group can work more efficiently.

In addition, when people know that their work is going to be readily available for others to view, they’re likely to be more precise in their note taking. At the core of doing good science, is making a high-quality record of that research.

We try to provide detailed methodology online, in papers or in other online services that are linked back to specific examples in our lab notebooks. For instance, we have placed methods for labelling proteins on OpenWetWare, a service for sharing biological research protocols, with links to examples of these labelling reactions. People who find the online methods useful but want more detail can check volumes and amounts in our notebooks. At ISIS we are currently working through analysis of our small angle scattering data, and this will provide further examples for online protocols.

We don’t impose open notebooks on visiting scientists or where it would risk the disclosure of confidential information or a patent application being refused, but the tools are available and we look at the options for each project on a case-by-case basis.

ISIS from above

Adapting to a new approach

Traditionally, scientists have kept research close to their chests, fearing plagiarism from rivals or refusal from scientific journals to be published. In the scientific community, having a piece of research published is considered a “gold standard.” Some scientific journals won’t publish a paper if it has been pre-published in any form.

There’s a legitimate concern here, and open notebook science is not ideal for every scenario, especially if you want your work patented. However, in many cases freely-available data can greatly benefit the scientific community.

Scientists need to overcome this overlycautious mentality and realise the potential of freely-available data. Additionally, open notebook tools need to become more userfriendly. Currently, open notebooks are practical but not as user-friendly as we would like. It takes effort to make the researchers’ records available and the results are far from perfect.

The web makes it possible to share more with a wider audience. We need improved tools to do this, and many groups are working on building those. Currently, sharing requires an active choice and additional work. I believe that, in the future, when the tools mature, sharing will be a question of pressing a button. Researchers may choose to press that button when the results are formally published or as soon as the experiment is done. My belief is that the benefits of sharing immediately will encourage more (but by no means all) people to share all their work as it is recorded. In some cases, even industrial researchers may see benefits in taking an open notebook approach.

The ultimate aim is to continue to make science communication more effective and more efficient and to help scientists do what they do best – science!

Cameron Neylon is a senior scientist at the ISIS Pulsed Neutron Source. ISIS is a centre for research in physical and life sciences operated by the Science and Technology Facilities Council at the Rutherford Appleton Laboratory, Didcot, Oxfordshire, UK. ISIS supports an international community of more than 2,000 scientists who use neutrons and muons for research in physics, chemistry, materials science, geology, engineering and biology. Neylon uses neutron and X-ray scattering techniques to study biological structures.