Archive for September, 2008

Free Pathway Culture

Friday, September 19th, 2008

According to this book by Lawrence Lessig, Free Culture, we are currently living in a permission culture. In our society you are required to ask permission before you copy, publish or derive from a work that was created by somebody else. If you don’t, you risk an expensive lawsuit.

But artists and inovators influence eachother. They always have. Especially in science progress comes from sharing results and building on top of the results of others. For scientists, permission culture is a nightmare.

The book is mostly about music and movies, but in the world of biological pathway databases the issues are the same. There are hundreds of collections of pathways available, but many of them are locked down. You can use a commercial pathway database to analyze and interpret your high-throughput experimental data, but you are not free to copy those pathways, extend them, derive from them, and publish the results on WikiPathways. This is understandable, after all, the makers of these commercial packages probably spent a lot of time and money on the creation of their high-quality, curated databases.

But imagine what we could do if all this information were free? Then suddenly everybody can contribute. You will never have to worry about legal details, what you can do and what you can’t do. Instead of many small databases, none of which are perfect, we can compile all free pathway information in the world into a single magnificent resource.

I think we have an opportunity here to set a standard for future generations, to set this content free once and for all. We have decided long ago that WikiPathways content will be available under a creative commons license. Our goal is to maximize the long term usefulness of the information collected in WikiPathways. The rules of the creative commons license are plain and simple. The only obligation you have is to attribute the pathway author(s), other than that you are free.

WikiPathways: Convergence

Friday, September 12th, 2008

Our recent article about WikiPathways in PLOS Biology has received an overwhelming response (mostly positive). Alex has already listed most of the responses

Most responses are positive, but some (understandably) express concern that WikiPathways is now one of the many new scientific wiki’s springing into existence. People are worried that all these different wiki’s will be terribly confusing and none will achieve critical mass without some sort of convergence. But I’m positive. Clearly, WikiPathways is an experiment, as we explain in Big Data: WikiOmics. All these wiki’s are experiments, no doubt some will fail but others will be succesful and make a real contribution to the march of progress.

The title of that article reminded me of something. There really used to be a site called WikiOmics, a wiki devoted to bioinformatics. It was a very interesting project, but I haven’t heard from them in a while. It turns out that the content of this wiki has now been folded into the hugely succesful and popular OpenWetWare.

As you can see the convergence is already happening.