Connecting metabolic processes to organismal level processes - GAF/GPAD output and evidence

[vanaukenk]

This ticket is about this model:
http://noctua.berkeleybop.org/editor/graph/gomodel:57f1b14b00000442

This model shows the summation of information about a C. elegans gene, pmt-1, whose protein product exhibits phosphoethanolamine N-methyltransferase activity in vitro, and that when mutated exhibits defects in larval development and reproduction.

Assuming, we want BP annotations to the metabolic process as well as the organismal level processes, there are two outstanding issues with this model:

1. What is the correct representation, if any, of the link between the metabolic process and the organismal level process? The gp's role in the metabolic process was demonstrated with an in vitro assay, while the corresponding role in the organismal level process is demonstrated by a mutant phenotype. In the top of the model there are two different representations of this for the 'multicellular organism reproduction' annotation. The upper shows a 'causally upstream of or within' link between the metabolic process and the reproductive process, while the lower shows a 'causally upstream of or within' link between the enzymatic activity and the reproductive process. Both 'causally upstream of or within' links currently use IMP evidence.

2. What BP annotations should be made from this model? Currently, only the 'part_of' annotation to the metabolic process will be returned in the GAF/GPAD. The reproductive process annotation will only be returned as an annotation extension. Should the reproductive process annotation also be returned as a separate BP annotation? If so, what should the rule be for BP annotations in causal chains like this?

Annotations from the upper model:

WB WBGene00022781 enables GO:0000234 PMID:17313371 ECO:0000314 20161014 GO_Noctua contributor=http://orcid.org/0000-0002-1706-4196
WB WBGene00022781 involved_in GO:0070832 PMID:17313371 ECO:0000314 20161014 GO_Noctua causally_upstream_of_or_within(GO:0032504) contributor=http://orcid.org/0000-0002-1706-4196
WB WBGene00022781 part_of GO:0005829 PMID:17313371 ECO:0000250 UniProtKB:Q9FR44 20161014 GO_Noctua contributor=http://orcid.org/0000-0002-1706-4196

Annotations from the lower model:

WB WBGene00022781 enables GO:0000234 PMID:17313371 ECO:0000314 20161024 GO_Noctua causally_upstream_of_or_within(GO:0032504) contributor=http://orcid.org/0000-0002-1706-4196
WB WBGene00022781 involved_in GO:0070832 PMID:17313371 ECO:0000314 20161024 GO_Noctua contributor=http://orcid.org/0000-0002-1706-4196
WB WBGene00022781 part_of GO:0005829 PMID:17313371 ECO:0000250 UniProtKB:Q9FR44 20161024 GO_Noctua contributor=http://orcid.org/0000-0002-1706-4196