Relation composition

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Simple composition rules

TODO: fill in examples

Basic transitivity compositions:

The following rules arise from the definitions give in the OBO Relation Ontology

With the addition of the regulates relations in GO, the composition rules expand.

First the standard interaction with is_a:

  • is_a . R → R transitivity over is_a
  • R . is_a → R transitivity under is_a

In the above R stands for any of: regulates, negatively_regulates, positively_regulates

Example of relation composition

This example assumes that amongst our annotations we have:

  • MGI Bcl2 - (direct/asserted) annotation to positive regulation of anti-apoptosis
  • RGD Apoe - (direct/asserted) annotation to anti-apoptosis

For the sake of the example, we assume that these are the only annotations that were created for these genes. We ignore evidence codes here (assuming they are trusted annotations)

This page uses oboedit to illustrate the relationships between the gene produts and different kinds of process. It may seem odd to view annotations in OE, but according to our formalism the links between proteins and the processes they participate in are not a different kind of beast from the other kinds of links in GO. Still, we'll hopefully have this in AmiGO too shortly.

You can get the subset of GO used to make these screenshots here:

It should also be possible to do queries using the OE2 link search box too - e.g. ask for genes that bear some relation to apoptosis and get back "Bcl2 negative_regulator_of GO:apoptosis". However, the link search doesn't appear to be working properly in conjunction with the reasoner - Amina is working on this.