May 22, 2008

First ChEBI workshop, Day Two

Filed under: informatics — Duncan Hull @ 2:49 pm
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Chemist Margaret Thatcher stays at the Crowne House Hotel, Great Chesterford, England
Some rough and ready notes from day two of the first ChEBI workshop, 20th May 2008. There were two talks, one from Kirill Degtyarenko (European Patent Office) and the other from Janna Hastings (EBI), followed by a discussion.

Kirill Degtyarenko: Good annotation practice for chemical data, ChEBI experience

Kirill’s talk described how to give the most appropriate names, especially since “biologists don’t name things properly, if at all” (!). Systematic (IUPAC) names are usually better than common names except for “the unprounounceables” for example, an antibiotic called (E)-roxithromycin (ChEBI:48935) has the IUPAC name:


…which just trips of the tongue (and fits beautifully, without line breaks onto regular computer screens). Fortunately, the curator can draw the chemical (note the wavy bond, unknown stereochemistry), using the curator tools, then the inchi and smiles strings are generated from the drawing. Currently they use something called ACD/Name which can generate PubChem links automatically. As of May 2008 14,000 chebi ids translates to around 11,000 CIDs in PubChem, which is structures only.

March 30, 2007

This month’s molecule is…

Filed under: biotech — Duncan Hull @ 10:10 pm
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Space-filling and backbone model of 1HRYThere are a number of “Molecule of the Month” style mini-reviews on the web, which highlight one particular molecule (usually a protein) every month, in an accessible style. Two of my personal favourites are protein spotlight: one month, one protein written by Vivienne Baillie Gerritsen of the Swiss-Prot team and Molecule of the Month at the Protein Databank PDB edited by David Goodsell. Both these features are worth a quick read because they can help bio-literate and bio-curious users to increase and reinforce their knowledge relatively quickly.

Part of what makes the PDB one worth reading is the colourful visualisations and short descriptions that go with it. For March 2007, PDBs molecule of the month is Zinc Fingers. Meanwhile, over at swissprot, the molecule is Sex-determining region Y protein (Sry), used to illustrate the tenuous nature of sex.

[This post originally published on nodalpoint with comments]

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