NAME

go-gaf-inference.pl

SYNOPSIS

go-gaf-inference.pl --infer go/ontology/obo_format_1_2/gene_ontology_ext.obo go/gene-associations/gene_association.sgd.gz

DESCRIPTION

Performs inference upon a GAF (Gene Association File), generating ICs based on configurable criteria

INFERENCE

Pass in --infer on the command line

Inter-ontology part_of inference

Example:

go-gaf-inference.pl --infer --per-file go/ontology/obo_format_1_2/gene_ontology_ext.obo go/gene-associations/gene_association*.gz

generates IC BP annotations for MF annotations where a part_of link is asserted or can be inferred

TO BE DOCUMENTED

Other types of inference

NOT YET IMPLEMENTED

VALIDATION

Pass in --validate on the command line

Taxon validation

http://wiki.geneontology.org/index.php/Category:Taxon

go-gaf-inference.pl --validate -i scratch/go-taxon/TaxonGOLinksFile.obo -i scratch/go-taxon/ncbitax-slim.obo -i scratch/go-taxon/UnionTerms.obo -i ontology/editors/gene_ontology_write.obo gene-associations/gene_association.goa_chicken.gz

Writes out taxonomically invalid annotations. Uses the correct semantics for union terms.

Other types of validation

NOT YET IMPLEMENTED