Since you have a node which uses ChemSpider to convert InChI keys into structures, is it possible you can incorporate into this the conversion of CAS Registry Numbers into structures (which is supported on the ChemSpider website).
This is an unmet need in KNIME and would be great if this can be implemented. There are often many times we get lists of Registry Numbers and can be a real pain to get all the structures for them.
There are a few other nice to haves, although less essential;
- Support for converting Synonyms and Trade Names into structures too.
- Support for retrieving Chemical Vendor information. This can be really useful for checking if chemicals are commercially available. Ideally, this would from a structure input into the node. Again this is an unmet need in KNIME and would open up a whole new avenue in KNIME of reagent searching.
- Property search such as Mw, melting point, boiling point, and density.
that sounds like a job for the Generic Webservice Client node. The node can consume ChemSpider's webservice (http://www.chemspider.com/blog/how-to-use-chemspider-webservices-from-knime.html) and ultimately convert, e.g., CAS numbers to structures. There is also a IntrinsicPropertiesSearch operation, which allows you to search by a selection of physical properties.
The webservice client works rather well and does what you are looking for. I have attached a screenshot for reference. Please let me know if that does the trick for you. (http://www.ebi.ac.uk/~beisken/knime/chemspider.png)
Thanks for the reply and details on how to do this, but oh my, this is rather complicated. There is no way I could persuade fellow chemists to follow this protocol if they wish to use ChemSpider, its took me over half an hour working this out, downloading the zip, extracting it, and then spent some time working out why it wouldn't analyse it, only to realise that the "file:/" prefix needs adding, the "\"'s changed to "/", and then that directories with a space in are not acceptable.
Also a token is then needed which is only free for academic users, and since I work in industry, I had to give up at this point.
Thank you anyway for the instructions, hopefully others will find these useful.
unfortunately I don't believe Chemspider offers a "free", that is untokenized, identifier search. I looked at their website and most of the more interesting searches require a token. If, however, you find a simple, direct way to convert CAS to structural information, I would be more than happy to implement that option.
Is there a way to implement the Chemical Identifier Resolver? I also convert CAS to structure and would be useful if it could be performed in KNIME without needing a token.
it's already there. "Talete" is a plug-in that contains a single node: The Chemical Identity Resolver!
You can find the plug-in in the community section under the name "CIR KNIME integration".
Just tried it on a CAS to InChI case and it worked well.
Awesome, thanks for the link!