I have been off air for a week part of which is because we have been concentrating on crystallography. The next few posts will cover various aspects of this subject – but there are many which are general enough that readers interested in Open Access, repositories, etc will hopefully find something useful. There are at least the following themes.
- Nick Day is finishing writing up his thesis, part of which has been the compilation of CrystalEye to provide material for his thesis. I’ll blog about some of this but the headline messages are (a) that CrystalEye is a research tool (b) without the Open Data on publishers’ sites and COD we couldn’t have done the work (c) the fundamental architecture of CML has allowed Nick and Joe Townsend to develop high-throughput computational chemical crystallography – we have done over 20,000 calculations.
- Jim Downing has put in considerable work to create a subset of CrystalEye for Chemspider who now wish use to review their site:“The Unilever School at Cambridge, via Nick Day’s work, has generated CrystalEye and, after many conversations, we were provided the data source and have it on ChemSpider now. We are awaiting constructive feedback from Nick and Peter Murray-Rust regarding our implementation of their data on our site.” I have stressed several times that Nick is writing his thesis and has no time to review commercial sites – however I will do so sometime in the next few posts
- SimBioSys, and others have blogged about the availability of data from the CCDC (post). This raises some extremely serious points about the closing of data meant to be public.
- As part of our ongoing collaboration with the IUCr – International Union of Crystallography we have a summer student working on authoring tools and we are very grateful for this (CrystalEye was catalysed by an IUCr-sponsored student – the original project was highly overambitious, but Nick was able to build on it for his own work. We also have two other students sponsored by the department to build and populate a Departmental Crystallographic Repository – again more on that later.
Peter: Regarding “Jim Downing has put in considerable work to create a subset of CrystalEye for Chemspider who now wish use to review their site:” and “I have stressed several times that Nick is writing his thesis and has no time to review commercial sites – however I will do so sometime in the next few posts”.
Thanks to Jim for the considerable work, and I have already acknowledged it in an email to all of you.
It would be good to receive your feedback on the deposition of CrystalEye onto ChemSpider but you are under no obligation to do so. But, I would think that since ChemSpider is the first site other than CrystalEye itself (I believe this to be true) to host your data I thought you might want to look at it. If not that’s fine too.
Your modus operandi in regards to ChemSpider is to not provide direct feedback to us regarding any issues but rather to blog about any issues. My earlier email regarding providing feedback was a request to provide feedback directly to us on any obvious issues so we could resolve them. I understand your preference is to simply blog about them so I will monitor your site for the comments instead. I look forward to your comments.
To Nick- good luck with the thesis and apologies if the request to check out CrystalEye on ChemSpider was a distraction. I believe one of the outcomes of CrystalEye is Open Data that could proliferate to other sites ESPECIALLY now that Jim has done the hard work to create the dataset for download. I would hope that having your work more highly exposed would be good for you and you would have more bragging rights in your thesis in regards to your contribution to the domain of crystallography and Open Data since over 5000 people per day frequenting ChemSpider could end up over on CrystalEye as a result of the connection. I think this is good for the project personally. I look forward to seeing the data shown up on PubChem, eMolecules and other sites shortly.
Either way, of “referred sites” driving traffic to ChemSpider what is interesting to observe is that http://wwmm.ch.cam.ac.uk is now in the top 10 of referring sites so the benefit is mutual. Thanks!