Comments on: How Big is the Challenge of Curation and What is the Structure of Ginkgolide B http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html Building Community for Chemists Fri, 10 Feb 2012 11:07:05 +0000 hourly 1 http://wordpress.org/?v=3.1.2 By: David Barden http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-23218 David Barden Mon, 03 Mar 2008 17:01:43 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-23218 Antony - I am an organic chemist working on the RSC journal in which the published structure of ginkgolide B appeared, and am pretty sure that it is correct, having been written by a regular author of ours familiar with the literature on the ginkgolides. I think the problem might lie with the representation (and/or conversion to InChI) of the structures - even in the one structure you indicated as having "full stereochemistry", it seemed to me that 3 stereocentres were undefined, from a visual inspection of the structure. Apart from these stereocentres, the structure and InChI (generated myself) otherwise seem identical, so I'm not sure why the last part of the string in the ChemSpider entry is "20+" rather than "20-". The difficulty of visually comparing structures from different sources (rotation, reflection, etc), especially for complex molecules like this, would make the task of validation much more difficult. Antony – I am an organic chemist working on the RSC journal in which the published structure of ginkgolide B appeared, and am pretty sure that it is correct, having been written by a regular author of ours familiar with the literature on the ginkgolides. I think the problem might lie with the representation (and/or conversion to InChI) of the structures – even in the one structure you indicated as having “full stereochemistry”, it seemed to me that 3 stereocentres were undefined, from a visual inspection of the structure. Apart from these stereocentres, the structure and InChI (generated myself) otherwise seem identical, so I’m not sure why the last part of the string in the ChemSpider entry is “20+” rather than “20-”. The difficulty of visually comparing structures from different sources (rotation, reflection, etc), especially for complex molecules like this, would make the task of validation much more difficult.

]]> By: Antony Williams http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20112 Antony Williams Mon, 18 Feb 2008 04:51:58 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20112 Bear..I agree that the ginkgolides are a group. The challenge is that the name Ginkgolide B is associated with 6 structures. I cannot prove that this situation is one of a "changing structure" with time but rather an issue of drawing structure correctly. Again..I cannot validate this perception. I've done a search on ChemRefer now to find some structures: http://www.chemrefer.com/search.cgi?zoom_query=ginkgolide+B I need to now sketch these representations in and validate. Thanks for your comments! Bear..I agree that the ginkgolides are a group. The challenge is that the name Ginkgolide B is associated with 6 structures. I cannot prove that this situation is one of a “changing structure” with time but rather an issue of drawing structure correctly. Again..I cannot validate this perception. I’ve done a search on ChemRefer now to find some structures: http://www.chemrefer.com/search.cgi?zoom_query=ginkgolide+B

I need to now sketch these representations in and validate. Thanks for your comments!

]]> By: Antony Williams http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20111 Antony Williams Mon, 18 Feb 2008 04:32:20 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20111 Joerg...we CAN turn on "Notify Me" by default but I need more than one vote for that! Joerg…we CAN turn on “Notify Me” by default but I need more than one vote for that!

]]> By: Antony Williams http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20110 Antony Williams Mon, 18 Feb 2008 04:30:08 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20110 Joerg..you hit the nail on the head...so for Taxol: http://www.chemspider.com/Search.aspx?q=RCINICONZNJXQF FORTY-TWO structures! The extension of the InChI sounds interesting but I'm not sure how well that would go down with the InChI team etc. But let's see if anyone responds...it might fir well into the InChIKey resolver. Joerg..you hit the nail on the head…so for Taxol:
http://www.chemspider.com/Search.aspx?q=RCINICONZNJXQF

FORTY-TWO structures!

The extension of the InChI sounds interesting but I’m not sure how well that would go down with the InChI team etc. But let’s see if anyone responds…it might fir well into the InChIKey resolver.

]]> By: Antony Williams http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20109 Antony Williams Mon, 18 Feb 2008 04:22:00 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20109 Chris: You might be aware I've been working on Wikipedia (http://www.chemconnector.com/chemunicating/dedicating-christmas-time-to-the-cause-of-curating-wikipedia.html) I've been wondering about the wiki type approach. We hope to get our hands on Microsoft's Sharepoint shortly to add wiki capabilities... http://www.chemspider.com/blog/the-chemspider-team-chooses-our-future-platform-for-collaboration-microsoft-sharepoint.html Thanks for the very constructive feedback Chris...it is very much aligned with what we've been thinking and it's good to get it independently validated. Chris: You might be aware I’ve been working on Wikipedia (http://www.chemconnector.com/chemunicating/dedicating-christmas-time-to-the-cause-of-curating-wikipedia.html)
I’ve been wondering about the wiki type approach. We hope to get our hands on Microsoft’s Sharepoint shortly to add wiki capabilities… http://www.chemspider.com/blog/the-chemspider-team-chooses-our-future-platform-for-collaboration-microsoft-sharepoint.html

Thanks for the very constructive feedback Chris…it is very much aligned with what we’ve been thinking and it’s good to get it independently validated.

]]> By: Soaring Bear http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20108 Soaring Bear Mon, 18 Feb 2008 04:12:55 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20108 The various ginkgolides ought to be considered as a group rather than just the B variant. Add the bilobalides along with the ginkgolides since they share the biosynthetic path. These compounds are prominent enough that there's probably been enough labs evaluating the NMR spectra, and maybe crystal structures, that there is likely to be some consensus on the "true" stereochemistry. Contacting such people directly may be the best way to evaluate what is true on this. More broadly, we all keep in the back of our minds the occasional corrections of structures which keep us humble in being too sure of what the true structure of anything is, especially compounds that are less studied than the ginkgolides. The various ginkgolides ought to be considered as a group rather than just the B variant. Add the bilobalides along with the ginkgolides since they share the biosynthetic path. These compounds are prominent enough that there’s probably been enough labs evaluating the NMR spectra, and maybe crystal structures, that there is likely to be some consensus on the “true” stereochemistry. Contacting such people directly may be the best way to evaluate what is true on this.

More broadly, we all keep in the back of our minds the occasional corrections of structures which keep us humble in being too sure of what the true structure of anything is, especially compounds that are less studied than the ginkgolides.

]]> By: Joerg Kurt Wegner http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20017 Joerg Kurt Wegner Sun, 17 Feb 2008 18:22:08 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20017 Oh, forgot the "notify on followup comments', and can you turn this on by default ;-) Oh, forgot the “notify on followup comments’, and can you turn this on by default ;-)

]]> By: Joerg Kurt Wegner http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-20016 Joerg Kurt Wegner Sun, 17 Feb 2008 18:20:42 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-20016 1. Finding all structures? The first key of the InchiKey should do the trick, since it is covering topology without stereo information http://www.chemspider.com/Search.aspx?q=SQOJOAFXDQDRGF 2. @Chris: I love this approach ! Keeps all information and points to the good one. @Tony: It should be made very clear on the page that the whole page is deprecated, and not only a few entries needs curation. Beside, this is one of those examples where the ChemSpider-InChIKey (CIK) might get enriched with 'curated' tag, all the others , e.g. SQOJOAFXDQDRGF-UHFFFAOYAY-C(urrent) SQOJOAFXDQDRGF-TWOSMEHPBO-D(eprecated) SQOJOAFXDQDRGF-KRNPTNFHBW-D(eprecated) and so on... Further expert/user tags might be possible, e.g. W(rong), N(eeds help/discussion) Especially the N(eeds help/discussion) is a great Wikipedia feature, because people can look at a special page which structures needs emergency discussion/curation. 1. Finding all structures? The first key of the InchiKey should do the trick, since it is covering topology without stereo information
http://www.chemspider.com/Search.aspx?q=SQOJOAFXDQDRGF

2. @Chris: I love this approach ! Keeps all information and points to the good one.
@Tony: It should be made very clear on the page that the whole page is deprecated, and not only a few entries needs curation.
Beside, this is one of those examples where the ChemSpider-InChIKey (CIK) might get enriched with ‘curated’ tag, all the others , e.g.
SQOJOAFXDQDRGF-UHFFFAOYAY-C(urrent)
SQOJOAFXDQDRGF-TWOSMEHPBO-D(eprecated)
SQOJOAFXDQDRGF-KRNPTNFHBW-D(eprecated)
and so on…
Further expert/user tags might be possible, e.g. W(rong), N(eeds help/discussion)

Especially the N(eeds help/discussion) is a great Wikipedia feature, because people can look at a special page which structures needs emergency discussion/curation.

]]> By: Chris Rusbridge http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html/comment-page-1#comment-19987 Chris Rusbridge Sun, 17 Feb 2008 16:16:55 +0000 http://www.chemspider.com/blog/how-big-is-the-challenge-of-curation-and-what-is-the-structure-of-ginkgolide-b.html#comment-19987 No comment on which is the correct structure, but some thoughts on the approach. Wikipedia has a reasonable model here, with a clear distinction between "latest" and any specific previous version in the history. So the curation process might be: a) decide which is the "correct" structure, and mark it as "curated, current" b) find all the "incorrect" structures, and mark them as "curated: deprecated (or wrong!)". with a pointer to the correct structure. Now all your links will work, and those who follow them should eventually find the correct info. Would that work? No comment on which is the correct structure, but some thoughts on the approach. Wikipedia has a reasonable model here, with a clear distinction between “latest” and any specific previous version in the history. So the curation process might be:

a) decide which is the “correct” structure, and mark it as “curated, current”

b) find all the “incorrect” structures, and mark them as “curated: deprecated (or wrong!)”. with a pointer to the correct structure.

Now all your links will work, and those who follow them should eventually find the correct info. Would that work?

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