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Jun
10

The sound of silence – is the chemistry database discussion being avoided?

I had no idea that picking up comments from one blog and suggesting what we need to do in the chemistry database world would see  little if any response from the actual parties responsible or the journal involved. I think we have done a public service by pointing out limitations in this database (even if I have not personally curated a molecule) and raising the issue which it seems the NIH and publishers want to avoid. It is important that initiatives engage the community. Its arrogant to think that scientists are not going to check the integrity of what is put out and thankfully this country still allows freedom of speech.

By reporting in blogs over the past month we have seen a disclaimer added on the download site and indications that future versions will offer some corrections. Encouraging. Did any other journal or other scientific news outlet pick up on this. NO. It reached other blogs. But to date Science Translational Medicine has not clarified the status of this database as being preliminary rather than comprehensive or definitive, since it was first published on the 27th of April. I repeat the end of their abstract

“We report here the creation of a definitive, complete, and nonredundant list of all approved molecular entities as a freely available electronic resource and a physical collection of small molecules amenable to high-throughput screening.”

There is no mechanism to publish a letter to this journal and raise the issue. It seems to me most people want this issue kept pretty silent, its like a dirty little secret in the database world and the publishing world is complicit. Oh and I guess people are afraid if they criticize the NIH they can forget about getting grants. I guess we’ll have to see what happens.

1 comment

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  1. Antony Williams, ChemConnector says:

    I am happy to see the disclaimer at least. Based on responsiveness on Twitter to comments I know there is great concern about the data quality now. This good to see. Considering the enormous amounts of traffic to my blog posts about this (>10-15X above usual) I am quite surprised that so many people are looking (lurking) and not commenting. This example is a true example of the challenges that exist in public domain databases. I discussed this issue yesterday at the PharmScifair meeting here in Prague (slides are here: http://www.slideshare.net/AntonyWilliams/integrating-and-curating-internet-based-chemistry-resources-to-serve-life-scientists) and tried to educate the attendees in regards to question everything as well as “we are in this together”. The “crowd” that will help clean up these data issues will be SMALL based on my experiences. I’d love to hear from the NPC Browser hosts how many people in the community (non-NCGC) have curated data so far. I’d love to hear its dozens. I will continue to do my part…it’s important. But I am interested in what other people think…and will they help?

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