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Table 1 Summary of comparison between STOP and GO annotations

From: STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation

Species Annotation source/gold standard Recall Precision F-measure
human Entrez Gene/Entrez Gene 0.993 0.678 0.806
Entrez Gene/GOA 0.979 0.674 0.798
  UniProt/GOA 0.998 0.608 0.756
mouse Entrez Gene/Entrez Gene 0.990 0.791 0.879
Entrez Gene/MGI 0.990 0.791 0.879
  UniProt/GOA 0.999 0.746 0.854
rat Entrez Gene/Entrez Gene 0.987 0.724 0.835
Entrez Gene/RGD 0.959 0.713 0.818
  UniProt/GOA 0.999 0.736 0.847
fly Entrez Gene/Entrez Gene 0.987 0.767 0.863
Entrez Gene/FlyBase 0.978 0.762 0.857
  UniProt/GOA 0.992 0.751 0.855
worm Entrez Gene/Entrez Gene 0.998 0.783 0.878
Entrez Gene/WormBase 0.998 0.783 0.878
  UniProt/GOA 0.999 0.788 0.881
yeast Entrez Gene/Entrez Gene 0.994 0.798 0.885
Entrez Gene/SGD 0.994 0.798 0.885
  UniProt/GOA 0.998 0.630 0.773
E. coli Entrez Gene/Entrez Gene 1.000 0.611 0.758
Entrez Gene/EcoCyc 0.340 0.354 0.347
  UniProt/GOA 0.964 0.826 0.890
  1. Annotations based on Entrez Gene descriptions are compared against the gene2go annotations from Entrez Gene and species-specific databases where the annotations have been downloaded from http://www.geneontology.org, and STOP annotations based on UniProt descriptions are compared against GOA annotations. Recall and Precision are calculated for each gene and subsequently averaged. The F-measure is the harmonic mean of these average Recall and Precision values.