Where Would Biomedical Research Be Without Open Data?


By Florence Chaverneff, PhD


Two major approaches in the study of neuroscience are electrophysiology, which consists in recording electrical activity of cells or cell populations and requires elaborate-looking equipment, and molecular biology, which requires…pipettes. Arguably, most biologists are thoroughly trained in either discipline, as they involve distinct skill sets, thinking process, abilities…My training is in cellular and molecular biology. An electrophysiologist friend of mine once told me (wording might be slightly inaccurate due to unconscious bias): “Molecular biology, that’s all about recipes! You follow the recipe, it works”, opposing it to none other than, you guessed it…electrophysiology. Unsurprisingly, electrophysiology, according to him, is soooo much trickier. Turns out, in practice, molecular biology is not all that straightforward.


Had my friend (being no more a wizard than the rest of us) ever actually had to use molecular biology to do his work, he most likely would have realized that it takes much more than following a recipe to obtain usable and reproducible data. The same holds for regular cooking, in that, carefully following recipes in a cookbook doesn’t turn one into Julia Child. That’s where biologists have understood that sharing tips for protocols used in molecular biology for example, can help the community (e.g. Protocol online). Making it freely accessible, providing feedback and a platform to interact. Well, this is sort of the concept of open data. What is open data? According to the Open Data Handbook, it is: “data that can be freely used, reused and redistributed by anyone – subject only, at most, to the requirement to attribute and share alike.” In biology, open databases are either started and maintained by institutions: e.g. UNIProt  by the Swiss Institute for Bioinformatics, Stanford’s SOURCE, or governmental organizations such as the National Center for Biotechnology Information provides the richest source of databases with for example Genbank, Epigenomics, EST and also Prodom. Which biologist, over the course of their career, has never had recourse to open access databases? Probably, very few. And we are all extremely grateful for them. And by open access, I mean, open access. As in, freely available online to anyone with an internet connection. Our work is not only facilitated by these databases, they have become an integral part of biomedical research.


The age of the internet has brought about a cultural shift. Sharing is not an attitude that’s associated with the mentality of the research community, where competing for funding, publications and jobs prevails. We compete, that’s who we are. But we are also learning to share information and resources, knowing our work will benefit from doing so. That’s who we have become. Thankfully. Understandably, the sheer existence of some of these databases is due to lack of manpower to analyze huge amounts of data (think big data), hence, the sharing. However, the majority of open databases addresses real needs and has, as sole purpose to benefit the entire community.


A parallel can be drawn between open access biological databases and the free online encyclopedia – Wikipedia. A few years ago, I caught a colleague of mine in his laboratory, working on the Wikipedia page of a topic related to his studies. At the time, I didn’t think much of it, being under the misconception that most information on this site was unverified, and that anyone could contribute, regardless of their expertise. My colleague corrected me, pointing to the fact that additions to the site go through a review process and require proper referencing. A while later, I heard a TED talk by Wikipedia co-founder, Jimmy Wales. In his talk, this open access pioneer describes the original concept of Wikipedia where “every person on the planet is given free access to the sum of all human knowledge […] written by thousands of volunteers around the world in many different languages […] managed by an all-volunteer staff”. Wikipedia, is the epitome of open access, particularly under Mr. Wales’ definition. Why is it, then, those individuals who do not get credit or monetary compensation, spend valuable time and effort contributing to such databases? What are their motivations? Are some people simply altruistic? Or does it provide some sort of ‘feel good’ effect? I would say, it’s as simple as that: they do it to benefit, at their level, mankind.