May 15, 2008

BBC: Building a Better ChEBI

Filed under: semweb — Duncan Hull @ 4:09 pm
Tags: , , , , , , , , ,

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]

ChEBI: Too much, too young?

Some dictionaries try to describe too much. When it comes to writing down knowledge, it isn’t always easy to know where to stop. To define scope, the BI in ChEBI stands for “Biological Interest”. So this begs the question, why does ChEBI describe all sorts of subatomic particles that are of little (or no) biological relevance? While electrons (ChEBI:10545) and protons (ChEBI:24636) play an important role in Biology, you have to wonder what the biological interest of neutrinos (ChEBI:36352) and bosons (ChEBI:36341) is. Who decides what is “biologically interesting” and how?

Then there is the inescapable legacy of IUPAC, which ChEBI aligns itself with closely, but unfortunately IUPAC is a bit dated and cumbersome (or so I’m told).

ChEBI: I just can’t get enough?

Some people are never happy. Take any dictionary or ontology and they will pick holes in it. “It doesn’t say this, it doesn’t say that, this is wrong” etc. In no particular order:

If I missed anything off the list, of things that are “wrong” with ChEBI, please let me know. If you’re going to the workshop, see you there (alongwith Christoph Steinbeck and maybe Kirill Degtyarenko I suppose)


  1. Kirill Degtyarenko et al [2008] ChEBI: a database and ontology for chemical entities of biological interest Nucleic Acids Research January; 36(Database issue): D344-D350 doi:10.1093/nar/gkm791 pubmed.gov/17932057
  2. Michael Bada and Lawrence Hunter [2008] Identification of OBO Nonalignments and Its Implications for OBO Enrichment. Bioinformatics. 2008 May 7 [Epub ahead of print] pubmed.gov/18463117, 10.1093/bioinformatics/btn194
  3. Michael Bada, Robert Stevens, Carole Goble, Yolanda Gil, Michael Ashburner, Judith A Blake, Michael J Cherry, Midori Harris and Suzanna Lewis (2004) A short study on the success of the Gene Ontology Journal of Web Semantics, 1(2):235-240, DOI:10.1016/j.websem.2003.12.003

Gratuitous musical link: Much too much, much too young… The Specials

[Atomium, crystalline Iron ChEBI:18248, picture by victor abellón]. Thanks also to Paul Dobson and Doug Kell for help putting some of these notes together.

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1 Comment »

  1. […] Building a Better ChEBI […]

    Pingback by Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » ChEBI — May 15, 2008 @ 10:58 pm | Reply

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