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Wednesday, 8 May 2013

Direct submissions of data to ChEMBL and the Open PHACTS project



Don’t we just love the fact that these days so much bioactivity data is freely available at no cost (to the end user)? I think we do. The more, the better. So, what would your answer be if someone asked you if you consider it to be a good idea if they would deposit some of their unpublished bioactivity data in ChEMBL? My guess is that you would be all in favour of this idea. 'Go for it', you might even say. On the other hand, if the same person would ask you what you think of the idea to deposit some of ‘your bioactivity data’ in ChEMBL the situation might be completely different.  

First and foremost you might respond that there is no such bioactivity data that you could share. Well let’s see about that later. What other barriers are there? If we cut to the chase then there is one consideration that (at least in my experience) comes up regularly and this is the question:  'What’s in it for me?' Did you ask yourself the same question? If you did and you were thinking about ‘instant gratification’ I haven’t got a lot to offer. Sorry, to disappoint you. However, since when is science about ‘instant gratification’? If we would all start to share the bioactivity data that we can share (and yes, there is data that we can share but don’t) instead of keeping it locked up in our databases or spreadsheets this would make a huge difference to all of us. So far the main and almost exclusive way of sharing bioactivity data is through publications but this is (at least in my view) far too limited. In order to start to change this (at least a little bit) the concept of ChEMBL supplementary bioactivity data has been introduced (as part of the efforts of the Open PHACTS project, http://www.openphacts.org).

Here is how it works: If you have unpublished bioactivity data that has been generated in an assay that can be found in ChEMBL (since the publication where the assay is described is also in ChEMBL), you can now deposit this data in ChEMBL (see http://dx.doi.org/10.6019/CHEMBL2094195 for an example). The obvious situation would be one where only a subset of the results have been reported in the publication but there are many more results (e.g. inactives). If you work in an industrial setting and might feel that you are not be in a position to release additional chemical structures you could think about depositing bioactivity data for compounds in (older) patents. Or you have reported bioactivity data in a poster. These are only examples and there are many more opportunities. In some cases we might explore new territory and the progress might be slow, but if we don’t try new things we are stuck with what we have. 'Do we really want this?' I hope the answer is no. So, let’s not focus on ‘instant gratification’ but help to grow the body of freely available bioactivity data by contributing to ChEMBL supplementary bioactivity data. If we could just give it a go it might make a difference. The concept might be quite restricted (e.g. the assay needs to be published) but we need to start somewhere. If you want to find out more about ChEMBL supplementary bioactivity data why not drop ChEMBL Help a line (chembl-help@ebi.ac.uk) and put ‘ChEMBL supplementary bioactivity data’ in the subject field. And don’t worry, you are not committing yourself by wanting to know more. 

ChEMBL, and the whole world of drug discoverers, is looking forward to hearing from you.  

Stefan Senger

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