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Tuesday, August 02, 2011

ToxBank and SEURAT-1

Update: these are my personal experiences, and do not reflect that of other people and/or organizations.

The first half year of the ToxBank EU FP7 project (co-founded by Colipa; I think I am legally required to mention them, and I am happy to do so either case) I am working on (50%) has giving me mixed feelings. ToxBank has a great team of people (and great names in the other cluster project too!), and I am quite happy about the results we made. What results, you may ask. Well, indeed: they exist, and nice results too! It's just that they are not so visible.

That is the part I am less happy about: legalities. It took months for the consortium agreement to get finalized, and then there is a cluster agreement for the whole of SEURAT-1. Information is monopolized, and there is a general scare to accidentally release information which others may claim IP. It slows us down; it inhibits new collaborations and thus serendipity. Naive and idealistic as I am, I say this is bad for science.

But, the community is positive about Open nowadays, one achievement of the gold Open Access journals, I guess, and we hosted a workshop on Open Data recently too, which was well attended. People realize that openly sharing data has a role in science (see also this post).

Anyway, the goals are great of SEURAT-1. There now is an official website, and I am pretty sure I am not disclosing any trade secrets. SEURAT (Safety Evaluation Ultimately Replacing Animal Testing) has as ambitious goal to make animal testing obsolete. The ultimately is there to reflect this will not happen any time soon, but at least we die trying (this is also why there is a -1 in the name... there may be follow projects, as outlined in the Vision and Strategy). Of course, that following up makes Open Source and Open Data important, in my personal opinion. Fortunately, more and more people share that opinion. I hope my direct and/or indirect contributions to ToxBank can set an example.

The title of the -1 project is "Towards the replacement of in vivo repeated dose systematic toxicity testing". So, that will be more or less the focus of the ToxBank data warehouse. The types of data will be very diverse, and includes many areas of the omics space, including my favorite: metabolomics. To allow a systems toxicology approach, a short list of test compounds will be established. As part of ToxBank we have set up a Semantic Web system, allowing these compounds to be part of the Linked Data network. However, here comes the legal stuff again, and the wiki is not generally accessible; only to SEURAT-1 member (more precisely: will be very soon).

And that makes it impossible for me to start call in the community to run that favorite tools against these compounds. For example, to calculate solubilities in various solvents. That is information useful to our compound evaluation, and would contribute to the SEURAT-1 project! But I cannot do that right now :(

But, we're just 6 months into the five year project. I think we'll see a lot of firework later! The hurdles may slow us down, they will not mean we will not reach what we want.