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.

May 15, 2008

BBC: Building a Better ChEBI

Filed under: semweb — Duncan Hull @ 4:09 pm
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molecule by vabellon, on FlickrChemical Entitites of Biological Interest, ChEBI, is a freely available dictionary [1] of molecular entities, especially small chemical compounds. Like all big dictionaries and ontologies, it has its own unique challenges. Fortunately, those nice people at the EBI are holding a workshop to discuss future developments in ChEBI. In preparation for the workshop, here are some brief notes on how ChEBI could be made better. [Disclaimer: I’m fairly new to ChEBI and “thinking out loud” here, add comments below if I’ve said anything stupid or wrong]


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