Upgrade StorageChemical structure search in Zotero
As a chemist, many of the references I organize with zotero actually come along with a graphical abstract, often a typical reaction equation. Organic Letters [1] is an example for this. Searching literature references via structure/equation of chemical equation is common technique in commercial databases like Reaxys.
So far, I "partially solved" the problem of retrieve the interesting literature references by converting a typical drawing of a chemical structure into a short string ASCII characters according to the definition of smiles [2]. But this is of limited use only. It were more comfortable if I could notice reactions of my interest in a searchable way via a GUI instead. Maybe even allowing to search for similar (sub)structures I taught zotero.
Provided zotero uses JavaScript, and that there are editors based on JavaScript like ChemDoodle Webcomponents [3], why can't there be a plugin bridging the two worlds together?
[1] http://pubs.acs.org/toc/orlef7/current
[2] http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
[3] http://web.chemdoodle.com/
So far, I "partially solved" the problem of retrieve the interesting literature references by converting a typical drawing of a chemical structure into a short string ASCII characters according to the definition of smiles [2]. But this is of limited use only. It were more comfortable if I could notice reactions of my interest in a searchable way via a GUI instead. Maybe even allowing to search for similar (sub)structures I taught zotero.
Provided zotero uses JavaScript, and that there are editors based on JavaScript like ChemDoodle Webcomponents [3], why can't there be a plugin bridging the two worlds together?
[1] http://pubs.acs.org/toc/orlef7/current
[2] http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system
[3] http://web.chemdoodle.com/
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In my opinion there are several non-trivial questions that would need to be addressed in order to achieve this goal:
- finding a suitable molecular structure engine that is both light-weight and open enough to interact with Zotero's Javascript architecture (the ones I know are either closed-source black boxes, or add-ons for industrial-strength databases, or Just Not Mature Enough (TM));
- developing the interfaces allowing the retrieval of structures from external sources or from manual entries;
- creating the bridge itself.
ChemDoodle is indeed interesting. But the web components do not really deal with structure storage as far as I know. The non-free (but cheap) desktop program offers a way to search for structures in files on your hard drive, but I fear that the performance will drop sharply as the number of files to scan increases: there is no indexing so the program browses your directory or directories every time you start a new search. Besides that, I am not aware of an API one could use to connect the program with Zotero (or anything else). I'd be glad if someone proves me wrong, of course :-)