OPEN CHEMISTRY WEB

In a recent article in Chemistry World, the declining support for PhD and Postdocs was highlighted. The explanation given is that this is a result of “changes to the way research costs are calculated”.

Can’t argue with that, but it is also true that if PhD/Postdocs were all that valuable, industry would fund them regardless. The truth about chemistry degrees, at least in England, is that they are all about sticking to the recipe given out by the lecturer. “Experiments” consist of following a procedure to the letter. Whilst this is a valuable skill to have, these are not “experiments” at all. In fact they are anti-experiments because should you deviate from the plan given to you, your grades will fall. If you do not *think* or question a procedure, you will get straight As.

Given that it is the straight A students who are likely to go on and do Phds/postdocs, these qualities will persist at this level, and industry is right to be unimpressed by this, since they are all about the ability to think and innovate.

Vested interest: I only got a 2.2 so maybe I would say this

…. and it did. But not quite in the way that Cambridge had imagined. Over the last few weeks around 200,000 articles from contributing publishers have been added to ChemSpider’s literature search (as ChemRefer is now styled), though even this is not in the final form which we imagine.

Another 40,000 articles or so are following next week as this resource grows. The indexer is running hot 24 hours, seven days a week. Tens of thousands more articles will follow after that and on top of that we now have the capability to index text from image PDFs (many journal articles are still in this form) which that also opens up the possibility of users sending in scanned images of their data rich documents as a form of submission of chemical information to ChemSpider as well.

The main issue now is not having the time/resources to index everything we have permission for, we have still barely scratched the surface of Highwire for instance and adding updates from the resources we already index is not yet implemented properly. But, these are nice problems to have.

When we do have the critical mass of text journal articles indexed, the “cited in” feature can be implemented and we can open up the chemical names from the indexed content for downloading and curation by the ChemSpider community… and that’s when things get really interesting.

We are still on track, with just scant resources, to create a community curated cheminformatics-text search that we hope will eventually gain unstoppable momentum thanks to our community backing. Mozilla Firefox competes with Microsoft’s Internet Explorer because it has user and developer community backing and that is worth consideration as a role model for ChemSpider and the chemistry world as a whole.

The turn around that has occurred in terms of the interest in having published materials text indexed is highly significant in the long run since thousands of references will pour into ChemSpider structure records to enhance the usefulness of the database.

These, of course, will be free for anyone to download, so will make a material contribution to the openness of chemical data (which is what I want Open Chemistry Web to be all about) as opposed to talking about definitions/licenses/copyrights and other such distractions (as I see them) surrounding open access and open data.

Some of the richest sources of chemical information are research group websites. Some time ago, I indexed primary literature PDFs from many such websites into the legacy (now non-existent) ChemRefer index.

I then received this correspondence from a major publisher. I submitted it to Chilling Effects to see what the various legal ins and outs of all of this meant.

Please read the letter and then the rest of this post.

It is worth pointing out here that the publisher may well have been right, but there is no way to confirm this since I am not (and should not be) able to access author-publisher contracts.

In any case, the result was that I stopped linking to research group website PDFs (the “just in case” approach). Was that the best course of action?  Comments welcome.