NAME

GOBO::InferenceEngine::GAFInferenceEngine

SYNOPSIS

DESCRIPTION

An GOBO::InferenceEngine for making inferences over a GAF (Gene Association File).

Rules

infer_annotations(ArrayRef[GOBO::Annotation])

In the future this will be configurable.

For now there is only one kind of GAF inference:

Cross-ontology promotion

Given an annotation to an GOBO::TermNode F, this will generate an IC annotation to P, if it is possible to infer a F part_of P link AND the inferred annotation is not redundant with either existing annotations OR with another inference

This tool should produce *sound* inferences: that is, an annotation should only be propagated over is_a and part_of. The output file should be *minimally redundant* : the only additional annotations produced should be inferred annotations in an ontology not identical to the ontology of the original asserted annotation. A further constraint is that the inferred annotation would not be redundant with any asserted annotations within the inferred ontology.

Generated annotations would have code IC and be WITH the GO ID of the original asserted annotation.

SEE ALSO

bin/go-gaf-inference.pl