GAF inference are incomplete because of incorrect mapping for part_of

[cmungall]

Given this test GAF

!gaf-version: 2.1
PomBase	SPCC1902.01	gaf1		GO:0001078	PMID:22900017	IDA		F	transcription factor Gaf1	SPCC417.01c	protein	taxon:4896	20170728	PomBase	directly_negatively_regulates(PomBase:SPBC32C12.02),part_of(GO:0010515)	

this command

owltools target/go-gaf.owl --gaf test.gaf  --gaf-fold-inferences > results.txt

yields

Prediction=GO:0010515 'negative regulation of induction of conjugation with cellular fusion' // PomBase SPCC1902.01     gaf1            GO:0010515      PMID:22900017   IC      GO:0001078      F       transcription factor Gaf1       SPCC417.01c     protein taxon:4896      20170728        GOC-OWL directly_negatively_regulates(PomBase:SPBC32C12.02),part_of(GO:0010515)         

which is what we expect

However, this is not recapitulated when we run a different command, which should be using the same underlying machinery

owltools target/go-gaf.owl --gaf test.gaf --createReport  --gaf-prediction-file z  --gaf-report-file zz --gaf-run-checks

however, this is only the case for newer editions of the ontology. i.e. --gaf-fold-inferences works on old and new. However, --createReport works on only on old. Very odd...

[cmungall]

Additional docs on the procedure being used here: https://github.com/owlcollab/owltools/wiki/Annotation-Extension-Folding

[cmungall]

#238

the two contexts:

owltools/OWLTools-Annotation/src/main/java/owltools/gaf/rules/go/GoAnnotationPredictionRule.java

Line 105 in 41e1f58

predictor = new FoldBasedPredictor(gafDoc, source, false);

owltools/OWLTools-Runner/src/main/java/owltools/cli/GafCommandRunner.java

Line 285 in 22c5a33

FoldBasedPredictor fbp = new FoldBasedPredictor(gafdoc, g, false);

[cmungall]

I think I've found it - the part_of in the c16 expression is somehow being mapped onto http://purl.obolibrary.org/obo/so#part_of

							String extRelString = ext.getRelation();
							OWLClass extCls = f.getOWLClass(g.getIRIByIdentifier(extClsString));
							OWLObjectProperty extRel = g.getOWLObjectPropertyByIdentifier(extRelString);

[cmungall]

I think I've found it - the part_of in the c16 expression is somehow being mapped onto http://purl.obolibrary.org/obo/so#part_of

							String extRelString = ext.getRelation();
							OWLClass extCls = f.getOWLClass(g.getIRIByIdentifier(extClsString));
							OWLObjectProperty extRel = g.getOWLObjectPropertyByIdentifier(extRelString);

[cmungall]

Also here BasicAnnotationPropagator.getDirectLinkedClasses