PrOnto is a tool to query Gene Ontology term pair functional dissimilarity based on real biological data. GO terms that co-occur less than expected by chance in a species' annotations (annotation probabilities) or in its protein-protein interaction network (interaction probabilities) are considered functionally dissimilar:

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The current version of PrOnto has been built using the Gene Ontology annotations of UniprotGOA downloaded on Nov 24 2013 and provides association data for human, mouse, fly, worm and yeast. The tables below show the number of GO term pair association probabilities in the database for each species in each possible sub-ontology combination (CC: Cellular Component, MF: Molecular Function and BP: Biological Process)

Annotation Probabilities
 CC/CCCC/MFCC/BPMF/MFMF/BPBP/BP
human93229553765761650811077440804756656073017570
fly4063512133230515673427954301352070516339186
mouse87318149812961546343470970284407429668404056
yeast35322018586103633961244094595494109333360
worm26028113378662713276171587869635747059403

Interaction Probabilities
 CC/CCCC/MFCC/BPMF/MFMF/BPBP/BP
human86922144996521512273258294053917223665832075
fly3650851713978439724620150281033404313258675
mouse4036511441290683557612888151221726028975078
yeast35070317786253574827225887590758759122856
worm171405687960167836569207633739444117015