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go-pombase's logic flow for GO-CAM model generation

Takes genes from BP gene set: genes annotated (directly or indirectly) to a BP term, e.g. GO:0010971.

For each gene, finds a gene-to-MF annotation w/ extension “part_of(BP term)”, e.g. “part_of(GO:0010971)”.

• If no MF found, find MF annotation w/ extension “has_direct_input” to a gene also in gene set.
• If still no MF annotation, take any MF annotation for gene.
• Grab CC annotations for a gene if it has a MF annotation containing an "occurs in(CC term)" in its extension field OR there is only one direct CC annotation for the gene.
• The MF and CC annotations tied to a gene (enabled_by) make up an annoton.

For each annoton:

• NamedIndividuals gene & MF term
• MF enabled_by gene (evidence annotated to this axiom)
• MF part_of BP

For each annoton’s CC annotations:

• NamedIndividual for CC term
• MF occurs_in CC (evidence annotated to this axiom)

Connect annotons:

• Has_direct_input connections for each annoton:
• Find existing individual(s) for connection obj
• If triple of (obj,relation,*) exists and obj == annoton’s MF, create new obj individual because obj should already be declared for annoton.
• If obj == annoton’s MF, attach connection to * to annoton’s MF.