Relation composition
Simple composition rules
rules for is_a and part_of
TODO: fill in examples
Basic transitivity compositions:
The following rules arise from the definitions give in the OBO Relation Ontology
rules for regulates
With the addition of the regulates relations in GO, the composition rules expand.
First the standard interaction with is_a:
In the above R stands for any of: regulates, negatively_regulates, positively_regulates
Note that regulates is not itself transitive, but we may wish to include a weaker transitive relation (see below)
Note that positively and negatively regulates are sub-relations of regulates; i.e.
- IF: X negatively_regulates Y
- THEN: X regulates Y
The regulates relations are transitive over part_of; i.e.
- regulates . part_of → regulates transitivity over part_of
- negatively_regulates . part_of → negatively_regulates transitivity over part_of
- positively_regulates . part_of → positively_regulates transitivity over part_of
rules involving gene products
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.