Collaborative book idea - is there a reason not to do things like this on Wikipedia? - Matthew Todd from Bookmarklet

Commented at the blog post: "Mitch, love the idea, and this even seems practical if you can get uptake. I just wanted to back Mat up a little and disagree with your motivations for avoiding Wikipedia. YMMV. Firstly Wikipedia may not be authoritative with your department head but it is the first palce many students go. Getting this kind of stuff right in Wikipedia would be a really valuable step forward. Secondly - you can still produce the book and still credit people with authorship - just grab the articles you want after the authoring process - adjust if necessary (possibly by getting main authors to re-write or standardise format) and then publish. You'd have to make the book CC-BY but if you put it up on a publishing on demand website so people can have physical copies then I think you'd actually get a reasonable number of sales. People still get the credit for having their articles included in the book, therefore get their authorship etc. The validation comes from the specific community editing and - Cameron Neylon

validating the articles that are _chosen_ for the book. Third - the fabled weirdness of editors on Wikipedia isn’t as bad as most think. And there are quite a few people who would be sympathetic to this project who are real chemists with significant influence within the WP community. And you’ve got a whole website already built for you ready to go - no need to set up yet another website. Finally, using an existing service that does the job and then reaggregating, editing, and selecting material to re-present in a new form is working the way the web does best. It connects all the information up together - which in the end is what we all want. - Cameron Neylon

I checked a few of the initial entries... looks good. However, it also very much looks like hamburger to me... :( Eg.. http://name.howtochem.com/hell-vo... has no links for the chemical, image drawings of the reactions... Come on! We're not in the 1980's anymore! I like MItch idea, but the implementation really needs some sanity checking... - Egon Willighagen

maybe I misunderstood the scope but there are some very high quality free online organic textbooks now available http://chem242.wikispaces.com/resourc... - Jean-Claude Bradley

Egon, kind of what I was trying to say in my comment - but yes making those specific comments might help. I think they're still stuck in the book concept. - Cameron Neylon

Cameron, yes, really a waste the effort... :( - Egon Willighagen

Also note the copyright license. Asking people to contribute for a vague promise of beer is probably not ideal if they're signing over all rights to their work. - Cameron Neylon

but it is still at an early stage - perhaps they can be persuaded to open it up - and at least cross post to Wikipedia? - Cameron Neylon

Jean-Claude is there a curated listing of named reactions already available online? This kind of catalogue seems to me something that the collaborative web could do well, and better than a static book. - Cameron Neylon

I wonder if this is the thing Mitch was refering to in the discussion on 'where can I host my data'... - Egon Willighagen

Egon - compare the entry you linked to to the Wikipedia article already written... http://en.wikipedia.org/wiki... - Matthew Todd

There is probably an argument for having infoboxes for named reactions on WP I would guess. For that matter is there any good way of displaying mechanism on the web? Individual images of molecules linked back to a resource, but how do you do the arrows? - Cameron Neylon

not a chemist, but just popping in to add: http://en.wikibooks.org/wiki... - Joe Dunckley

Applaud his motivation, but it could be the EOL of chemistry if he's not careful. Of course wiki (or similar) is the way to go. Someone talk him down! - Neil Saunders

Trying to be positive and negative at the same time in the comments at http://www.chemistry-blog.com/2009... Not sure how well that is coming across but we'll see. - Cameron Neylon

re: current comment on blog is there a way of getting a substructure into one of these picture generation services? Does the SMILES/InChi of a substructure even make sense? More generally is it possible to help Mitch make this into what it could be? - Cameron Neylon

Depicting substructure is not a big problem - Rajarshi Guha

But can we link to e.g. something sensible in Chemspider or rdf.openmolecules.net that makes sense of what the substructure is? Trying to think about how you would ideally link up the components of a mechanism - Cameron Neylon

FYI, enzyme reaction mechanisms are stored in CML in MACiE http://www.ebi.ac.uk/thornto... - Noel O'Boyle

uh, lots of improvements required, I will comment on the blog - joergkurtwegner

@Cameron - what do you mean linking by substructure? If a substructure is a well formed SMILES such linking should not be a problem, whereas if it is a more general query (i.e., SMARTS) such linking would be possibl but quite intensive (slow). How exactly it would be done is open to debate - I expect such linking into ChemSpider would be easier than into a RDF DB - Rajarshi Guha

I'm trying to think generally about what this named reaction page would like if possibly marked up. So how do you describe the concept "generic amine and generic caboxylic acid with reagent:coupling agent gives generic amide". From the user perspective you want to draw each reagent, drop it into place, and have each one go and get some sensible descriptors for itself. - Cameron Neylon

Describing the reaction can be done using reaction SMARTS - that's the (relatively) easy part. The problem arises when linking a generic description into a DB - how many results do you pull? And if the query is SMARTS, it will be, in general, slow. On the other hand, if you're just looking for hits against specific reagent, that can be done very fast. So I suppose the question is how general/specific are the goals? - Rajarshi Guha

Organic chemists will always want to search generally, with implies variation in the structures. All the named reactions have specific things occurring with functional groups, but the rest of the molecule is whatever. I've been thinking for a while we need "Inchis for mechanisms" or somesuch. - Matthew Todd

Cameron - good point about mechanism. I guess it would be nice to mark up intermediates/transition states (though the value of a static image is still immense if the mechanism is drawn correctly). Variations in arrow drawing cause some ambiguity - not so easy to represent with an atom connection table? - Matthew Todd

Like Noel said... I think CMLReact is at least one of the computer representations which handle electron movement... BTW, they did great things with *animating* these reaction mechanisms... - Egon Willighagen

I'll try a wiki concept in tandem but with a different topic. Here is a link: http://www.chemistry-blog.com/2009... - Mitch

Hi Mitch! I hope I was not too nasty... I was really looking forward to what you came up with... what I've seen so far was not matching my expectations... - Egon Willighagen

OK, Egon, will look at CMLReact. Need executive summary of capabilities since this had *completely* passed me by. Is 10.1021/ci0502698 still the right starting point? - Matthew Todd

Need input ->: http://www.chemistry-blog.com/2009... - Mitch

Posted at http://blog.openwetware.org/science... and comments on the blog post back at http://www.chemistry-blog.com/2009... - Cameron Neylon