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IMPORTANT: If you leave a comment here, please sign it by adding four tildes (~~~~) after your post. Thanks! Harry Brumer 05:21, 29 July 2009 (CEST)


Nomenclature of sugar ring faces

  • Confusion about sugar ring faces; GH people seem to prefer calling the faces based on the sides relative to the anomeric carbon (C1), but lectin (or sugar-binding protein) people usually call them according to a definition of faces of ring compounds (PMID: 16592816). They are unfortunately "upside down" (D. Ross). ShinyaFushinobu 07:06, 31 August 2009 (UTC)
    • Thanks for the comment. I've passed this on to User:Steve Withers and User:Spencer Williams, who are maintaining the lexicon for their comments. Harry Brumer 07:45, 31 August 2009 (UTC)
    • Dear Shinya, the nomenclature of Wimmer et al. works well for many compound classes, but has limitations with sugars. In particular, there is potential conflict with the use of the terms alpha and beta, which for carbohydrates is used for the anomeric configuration. When using the Wimmer nomenclature, for D-sugars the alpha face is the same as that which the alpha anomeric substituent is oriented. However, for L-sugars, the nomenclature for faces and the anomeric orientations are opposed. I appreciate that different communities have different 'lexicons'; in the case of GHs teh anomeric configuration is frequently discussed in close concert with the face of the molecule and so the use of the anomeric configuration to define faces would appear more convenient. As a point of interest - do you happen to know whether IUPAC or IUBMB has adopted a formal definition of the face of a molecule? The closest I have seen for sugars is the top and bottom faces defined in the "CONFORMATIONAL NOMENCLATURE FOR FIVE- AND SIX-MEMBERED RING FORMS OF MONOSACCHARIDES AND THEIR DERIVATIVES (Pure & Appi. Chem., 1981, Vol.53, pp.1901—1905).Spencer Williams 12:07, 31 August 2009 (UTC)
  • I must confess I was not aware of this other nomenclature.. Personally I do not see that we can use other than the IUPAC carbohydrate nomenclature or all hell would break loose. However, perhaps when the CBM section is included we should make a note there about the lectin nomenclature (or even now in the Lexicon).Steve Withers 14:28, 31 August 2009 (UTC)
  • Thanks for responding. In the case of D-glucose, the hydrophobic "down (alpha-anomer side)" face is beta-face in the Wimmer/lectin nomenclature. It's very unfortunate for the sugar ring case as described in that paper (p2440 right column). I like the GH nomenclature because it is intuitive, and Rose et al. suggested a possibility of developing a local system for each unfortunate case. However, I cannot find any official definition (like by IUPAC/IUBMB) yet.ShinyaFushinobu 09:30, 1 September 2009 (UTC)

GH category page, order of families

  • It would be nice if the glycoside hydrolase pages under the category link were ordered numerically; perhaps a tabulated series of links could be created in numercial order? Spencer Williams
    • This is an issue with the way the Category tags are listed in alphabetical order. One work-around could be to modify the tag in each page with a sort key. See http://meta.wikimedia.org/wiki/Help:Category#Sort_key Harry Brumer 05:21, 29 July 2009 (CEST)
    • Fixed: added sort keys in the format "GH001" to all existing pages during the first week of August 2009 (at Cellulase GRC). Harry Brumer 20:42, 6 August 2009 (UTC)

Automated lisiting of references in bibliography

The use of the pmid and isbn tags for inserting references is great. Is it possible to include doi's? This would be good for papers that are not in pubmed. Or could you use CrossRef?Spencer Williams 02:20, 1 September 2009 (UTC)

  • Good idea. However, this is at the moment difficult.
    • The extension that sources the bibliographic info by PMID or ISBN is called Biblio (http://www.mediawiki.org/wiki/Extension:Biblio). It basically works by pulling data from either PubMed or the ISBNdb server and does some magic to format the data in the form you see presented. I've recently communicated with the developer of Biblio, and he has informed me that he has stopped developing the code as of sometime in 2006. Therefore, it would take some serious coding on our side to expand the extension to use other DB's.
    • As far as I know, there are no other comparable extensions out there, which may have more bredth (Compare Biblio with Cite, which is the system used by Wikipedia and is also running on CAZypedia, if one care to test it out.) One problem with DOI's, of course, is that the DOI server doesn't return information, but is simply a redirect system, which links to pages where each publisher presents data in a different page format.
    • For the moment, I think the 90/10 solution (10% of the work to cover 90% of the cases) is Biblio. For non-PubMed refs., you'll have to get the full reference data and format it yourself, but adding in the DOI is a nice touch (see the Sinnott ref. in the header for the Lexicon for an example). If you see something else come up, we can try it.

Harry Brumer 07:07, 1 September 2009 (UTC)

Link to the next/previous GH family pages

Could a link to the next and previous GH family be placed at the top (or bottom) of each GH page. This would make it easier to systematically browse through the GH pages without needing to go back to the GH category page.Spencer Williams 09:51, 29 September 2009 (UTC)

  • Good idea. Funny - I asked the same thing of the CAZy DB a couple of years ago, even before their dropdown menu was put in place. This may be possible with some fancy template tricks to install the right code on each page which determines the family number and calculates one forward & back. that's a bit beyond my coding skills at the moment, but keep an eye out for solutions on other wikis.

Harry Brumer 09:59, 29 September 2009 (UTC)

Link to organisms

How about using the Taxonomy browser in NCBI for making external links to organism names? e.g. Hypocrea jecorina ShinyaFushinobu 08:23, 27 October 2009 (UTC)

  • Sure! You can start with this on the pages you are curating as a test. Just watch to make sure the links don't change a lot over time - we don't want to have lots of broken links which need constant attention. If these are stable like a DOI, then no problem. Harry Brumer 08:35, 27 October 2009 (UTC)
    • Thanks. I believe that NCBI will maintain the Taxonomy browser for a long time. You can also search obsolete names. Try "Trichoderma reesei" and "Bacillus stearothermophilus". But, I hate dead links, too. Too many external links may be dangerous. ShinyaFushinobu 08:52, 27 October 2009 (UTC)
      • I agree about being careful with how we use external links - I think the number should be minimized, but it's hard to imagine setting a general policy about this. I would rather leave it to the Responsible Curators to decide when it's useful for their own pages for now. Harry Brumer 09:06, 27 October 2009 (UTC)
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