GAF Inference

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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)

See scratch/gaf-inference