Monday, June 09, 2008

Open Access and WikiProfessional

One of the first WikiProfessional instances is WikiProteins. An article in Genome Biology describes it in great detail. The lead author of that article, Barend Mons, reacts to the post by Euan Adie on Nature’s Nascent blog (“WikiProteins is a croc”, later changed to “WikiProteins – a more critical look”). Because it is important to understand the open access nature of the WikiProfessional project, I am reproducing Barend's reaction to the blog entry in its entirety here.

Jan Velterop
Although the rather sour blog by Euan is quite an exception in the overall positive reactions we receive on the beta site of WikiProteins, I feel that a matter-of-fact reaction from the lead author of the article in Genome Biology that announced it is warranted. It goes hereby.

First of all on Authorship: Jimmy [Wales] was instrumental in making the initial contacts between me and Gerard Meijssen who was then working on WiktionaryZ, now Omegawiki. He also gave invaluable advice on several aspects of the system and he therefore deserves as much of an authorship acknowledgement as the average senior author/professor who ‘conceived of the study’. See also Gerard Meijssens’ Blog about that.

On the interface etc., we all know this is beta and we struggled for a long time to make it as ‘good’ as it is. Obviously a flat file is easier than managing a relational database and therefore the interface can never be ‘really easy’. I agree with Peter Jan [one of the commentators on the Nascent blog entry] that constructive criticism would have been more useful.

Criticism on the commercial nature (as it were) of a company on a blog made available by another commercial company – one that makes money on others’ scientific contributions for as long as we have been studying nature – is a bit peculiar as well. With the involvement of Amos Bairoch, Michael Ashburner , Mark Musen, Abel Packer, Roberto Pacheco, Matt Cockerill and many others in this process, not to mention Jan Velterop’s reputation, it seems to me that the OA nature of the projects is sufficiently safeguarded. With my personal background in malaria, working for 15 years with colleagues in developing countries, I also built a public track record in pushing free access to information for developing countries.

The content in WikiProfessional applications is completely freely available under the Creative Commons Attribution license (we are working on making author credits more clearly visible). The Knowlets are indeed proprietary as we create added value and apply algorithms that by themselves now have taken several million dollars to develop. It has proven exceedingly difficult to get sufficient public funding for this project, which has been carefully internationally discussed and prepared for several years. Bill Melton and Al Berkeley are to be highly commended for taking the risk to fund the vision.

Also the Knowlet space is in Open Access for non-commercial use. I sincerely hope that seasoned investors like Bill and Al would be more imaginative than trying to monetize this site – and the others still to come – by ads only.

On potential fear of competition: let me tell everyone up-front that the authors on the paper have every intention to connect all information on important concepts via WikiProfessional, not trying to put it behind any barrier or to compete with anyone. Some may see us as a competitor to IHOP or Wikipedia pages on biomedical concepts for instance, which is not true, as you will soon see.

We are planning to add locally maintained databases on genes such as to the appropriate concept page in WikiProteins much more prominently placed than today (now an indirect link via SwissProt data), but also locally-maintained databases on single gene mutations such as the growing number of Leiden Open Variation Databases (LOVD’s). We have a project starting to map all concepts in WikiProfessional, including all biomedical concept pages, to the corresponding pages in Wikipedia and other emerging wiki’s. People who find the WikiProfessional interface too difficult will be soon able to contribute to their own wiki of choice and their contributions will be seen in WikiProfessional anyway.

We collectively ‘own’ the basic data and anyone is free to ‘add value’ to these and make that ‘added value’ freely available to all or just for public not-for-profit use. Knewco is just one of the companies that derives value from the data and has decided to make the added value available to the scientific community for free.
I cannot wait until Nature will be Open Access as well, at least as far as the scientific articles are concerned. Then it will be easier to make full use of Nature content for the benefit of the scientific community.

One more point on equity and access: the collaboration with our Brazilian colleagues, with whom I co-developed and signed the Salvador Declaration on Open Access, referred to in the supplementary data of the Genome Biology paper, will soon result in crossing the language barrier to Spanish and Portuguese. The record for my beloved ‘malaria’ in Omegawiki will show you our ambition on in how many languages we would like to support the indexing on-the-fly. For Free.

I hope these further explanations take away at least the worst of Euans fears. I see in today’s version of the blog that he did not only change the original title of the contribution, but I also saw a more balanced reaction to Peter-Jan Roes.

However, Euan, if you still feel that some of your comments were justified and not yet properly addressed, please substantiate your claims and in the process it is highly appreciated if you give some constructive criticism. You would really help the community – and us – by doing that. Let’s keep discussing this project to make it better.