July 15, 2008

ChEBI, Oh ChEBI, Oh Baby!

Filed under: informatics — Duncan Hull @ 2:30 pm
Tags: , , , , , ,

cherry oh baby With sincere apologies to Jamaican reggae singer-songwriter Eric Donaldson, “ChEBI, Oh ChEBI, Oh Baby, don’t you know I’m in need of thee”?

Chemical Entities of Biological Interest (ChEBI) is a dictionary, controlled vocabulary, database, ontology of small (low molecular-weight) chemical entities that are considered to be biologically interesting, (like amphetamine (CHEBI:2679) for example). After a couple of recent meetings, ChEBI is going through some serious revision, to make it more efficient to maintain and use. Here are some brief notes on the changes, for my own benefit mostly and to collate links, but perhaps others are interested too.

Janna Hastings has created a wiki for the New ChEBI Ontology project which includes links to the ChEBI ontology remediation notes and meeting notes from 9th July 2008.

The announcement containing the details of the initial remediation release describes upcoming changes. Amongst others, they include:

  1. Making the ‘Is a’ relation transitive, so that reasoners can infer that if A is a B and B is a C then A is (also) a C.
  2. Correcting parthood relationship. ChEBI at present uses the ‘is part of’ relationship to mean possible parthood, (can’t find a good example of this right now) while parthood is defined in the OBO Relations Ontology to mean necessary parthood.
  3. The ontology contains two classes which are named using the word ‘class’ (organic functional classes (CHEBI:33244) and natural product classes (CHEBI:33243)) which need removing to bring into line with good ontological practice.
  4. The root term ChEBI ontology (ChEBI:23091) does not represent a “real” class and should be removed.

In short, ChEBI is Changing, for the better and is now indexed by ChemSpider (see comments below). Any comments or sugestions should be sent to the ChEBI team via the sourceforge tracker page or the ChEBI ontology mailing list.

[Gratuitous musical link to Cherry, Oh Cherry, Oh Baby originally by Eric Donaldson]

1 Comment »

  1. Just an fyi Duncan…we’ve just completed the deposition of the ChEBI entities of the month onto ChemSpider: http://www.chemspider.com/blog/chebi-entities-of-the-month-posted-to-chemspider.html

    I’m watching the development of the ontology and considering whether it would be a good fit onto ChemSpider. Certainly if we imported the ChEBI dataset and maintained their ontology it would be a good start…

    Comment by ChemSpiderMan — July 20, 2008 @ 1:10 am | Reply

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