Welcome to Open Chemistry Web Posted by: will in ProjectAs the latest addition to ChemSpider’s services, ChemRefer is specialised in text-indexing and it is now focused (and soon to be integrated with the main ChemSpider search) on providing access to chemistry related information and building a structure centric community for chemists. I originally created the ChemRefer service to allow chemists to have a search engine to perform text-based searches of freely accessible chemistry articles. When I saw what ChemSpider was trying to achieve I joined their advisory group to assist their efforts. With time it was clear that a closer relationship would benefit both parties. Now, ChemRefer and ChemSpider are merged together and we have an opportunity to produce a FREE search engine which will allow users to input structural and textual queries into one search interface. Any ideas, comments on any sources you would like us to index or any features you would wish this service to have are most welcome. This blog is a parallel blog to the ChemSpider Blog and ChemSpider News so that we can discuss the ins and outs of text indexing of the chemistry literature. At a time when there is a great deal of openly available literature and data in this arena, it is time there was an openly available service with the cheminformatics and text indexing capabilities to search this effectively. We want to play a role in making that happen. We look forward to dialoguing with you. Please add Open Chemistry Web to your Blog Reader…PMR: There is nothing Open about this. Even the blog is not Open (it does not carry a CC licence). The services may be free, and they may be useful, but they are not Open. The text that they index may indeed be Open Access in its own right (and probably is because otherwise the publishers will sue them) but this is no especial credit to Chemrefer. We also index Open resources but we make our results Open. Chemrefer could disappear tomorrow. Only if the data, and the source code are made Openly available under licence can they be called Open.
Chemspider and “Open Chemistry Web”
Recently the Chemspider company has announced an “Open Chemistry Web” which in my opinion misuses the word “Open”. Before I start I’ll review my relationships and attitude to Chemspider and Chemspiderman to try to clear the air. Chemspider.com and its associates are commercial organization which have aggregated a large number of chemical connection tables and have started by calculating their properties and extracting literature references which they make freely accessible but not Open. The freedom is for an unspecified timescale and you cannot download significant amounts of the data and you cannot re-use it without permission. Initially I was concerned about the complete lack of quality in these calculations and said so – I believe there has been some improvement in quality but I do not check and do not intend to do so. I do not follow Chemspider regularly but they appear to have added the ability for anyone to add annotations and curation. I have serious concerns about the lack of thought given to metadata and I do not expect Chemspider to be able to scale or to compete against modern approaches. Chemspider also encourages Uploading Spectra Onto ChemSpider. These spectra by default all belong to Chemspider. They are not Open. If you can convince the world at large to donate IPR to you for free, you deserve some form of congratulations for sheer bravado. Note that even if you upload data and metadata you are not allowed to download it (there is a limit of 100 structures). We have ca. 250,000 calculations on molecules and 130,000 crystal structures which Chemspider have suggested we upload to them. I’m not yet sure why we should do this. Chemrefer appears to allow searching of Open chemistry articles by keyword. Unexceptional, but why shouldn’t we simply use Pubchem? AFAIK it will index all these journals. The IPR model of Chemspider seems clear. No data, metadata and author contributions are Open. That allows them, at some stage in the future to close some or all of the site and to charge for data and services and – like eMolecules and their tie-up with Wiley (Wiley and eMolecules: unacceptable; an explanation would be welcome) – I predict this will happen within 5 years (unless Chemspider fails to survive in its current form). So all the authors who are contributing metadata are, in effect, donating IP to Chemspider. I have no moral objection to this – it just seems retrograde when we have Open collections of molecules such as PubChem and our own crystalEye. But a number of my friends in the Open Chemistry area are on the Chemspider advisory board, so I must be missing something. Perhaps they can show how donating IP to a commercial closed company advances the cause of Open Chemistry. And I applaud Chemspiderman’s efforts to clean up chemistry. Sometimes this gets muddled with the association with a commercial organisation based on possessing chemical IP so sometimes my messages have been less than generous and I apologized. I am not anti-capitalist – I do not attack companies per se. But I do attack people who use the word “Open” incorrectly and to promote themselves. I have done this when publishers come up with “Open Access” offerings which appear to be less than satisfactory ( see “open access products” at Nature obscures the debate, Why Open Access metrics are necessary) and for which the community has to pay. “Open” is now used by commercial organisations in the same way as “healthy” – please feel good about us and our activities as we use the word “Open”. We know it’s meaningless, but it makes us look good. Well, it isn’t meaningless. A number of people are trying carefully to describe what is meant by Open access, Open Data, Open source and Open Services. And when others use it to mean something less, I take exception. If nothing else it makes our job much harder. So: