GAF Inference
This page describes the various kinds of inference that can be and is done on a GAF
Propagation over is_a
If G is annotated to X, and X is_a Y then G is annotated to Y
We never manifest these as ICs in a GAF, as this would cause the size of the GAFs to explode. We assume tools will implement this rule
Propagation over part_of
If G is annotated to X, and X part_of Y then G is annotated to Y
We never manifest these as ICs in a GAF, as this would cause the size of the GAFs to explode. We assume tools will implement this rule
F part_of P
Annotations propagate over part_of regardless of whether the part_of is intra- or inter-ontology. Normal GAF Inference techniques can be used. See propagation over part_of above.
We can manifest IC annotations for these. We use gene_ontology_ext, which has the inter-ontology links.
The algorithm is in two parts:
- find all inferred annotations in which the inferred annotation is in a different ontology - exclude annotations if they are redundant (with either new inferred ICs or existing annotations for that gene)