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Quantifying Specificity of GO Terms

Phillip Lord phillip.lord at newcastle.ac.uk
Fri Apr 20 06:31:59 PDT 2007



Probably because Lin and Jiang are both normalised measures, while
Resnik is not. My over-riding suspicion has been that this distinction
is more important than anything else. 

>>>>> "RA" == Rubio, Angel <arubio at ceit.es> writes:

  RA> Some years ago, my group compared the correlation between gene
  RA> expression and different versions of semantic similarity. We
  RA> found it that the Resnik similarity measure (already used by
  RA> Dr. Lord comparing sequence and functions) outperformed other
  RA> measures also based on a corpus for the three categories (BP, MF
  RA> and CC).  Indeed, in our case these other measures (Lin and
  RA> Jiang) did not perform well at all.  Resnik similarity measure
  RA> is easy to evaluate:

  RA> Resnik(GeneProduct1, GeneProduct2) = -log(ni/nt)

  RA> Where ni: number of gene products in the corpus annotated for
  RA> the common ancestor of the annotations of a pair of gene
  RA> products (it seems a sort of tongue twister!).  nt: total number
  RA> of gene products.

  RA> I expect that it helps.

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