Comments on: Providing Some Structured Support with ChemSpider’s Wikipedia Services

By: ChemSpider Blog » Blog Archive » German and Spanish Wikibox Support Added

Fri, 17 Apr 2009 13:40:44 +0000

[...] recently released ChemSpider’s WikiBox service. Then we made a call for support so we could release multilingual support. Our friends on the [...]

By: Antony Williams

Antony Williams — Mon, 13 Apr 2009 14:27:56 +0000

Bill..in regards to your comments about the CAS number linking out to CommonChemistry.Org and NOT finding Domoic Acid the reason is that not all Wikipedia articles are represented in CommonChemistry.org. There is a certain overlap but it is far from complete.

By: Antony Williams

Antony Williams — Mon, 13 Apr 2009 13:20:15 +0000

Bill – if you compare the PubChem structure with the Wikipedia structure they are the same. But check both with the ChemSPider structure and they are different. Welcome to the world of validating structures. Compare the systematic name on ChemSpider with that on PubChem and you will see a difference in the name and it will help you find the difference on the structure

PubChem name: (2S,3S,4S)-3-(carboxymethyl)-4-[(2Z,4E)….

ChemSpider name: (2S,3S,4S)-3-(carboxymethyl)-4-[(1Z,3E,5R)….

Also, checking the InChI on PubChem you’ll see in the stereo a “question mark”
InChI=1S/C15H21NO6c1-8(4-3-5-9(2)14(19)20)11-7-16-13(15(21)22)10(11)6-12(17)18/h3-5,9-11,13,16H,6-7H2,1-2H3,(H,17,18)(H,19,20)(H,21,22)/b5-3+,8-4-/t9?,10-,11+,13-/m0/s1

Now the question is whether undefined stereo for domoic acid is correct or not?

By: bill

bill — Mon, 13 Apr 2009 07:05:20 +0000

You mean, check the CS structure vs the one shown in Wikipedia right now? The PubChem link from the Wikipedia entry goes to a structure drawn the same way as the one in CS, but the Wikipedia one is different in two ways: it’s flipped vertically, and the two ring-associated carboxylic acid groups are shown in different relation to one another. Since I see no reason they can’t rotate freely, that seems to be just a drawing choice, and the two structures look the same to me.

What am I missing?

Something else I found… interesting, was to click the CAS number link on the Wikipedia entry. Good thing there’s a free alternative, no?

By: Martin Walker

Martin Walker — Mon, 13 Apr 2009 05:51:25 +0000

Just tested it on the sodium periodate page, and everything worked fine. I think this will be an excellent tool for us to use on Wikipedia. If the structures can be adjusted to ACS format, it’ll be perfect. MANY thanks!