This branch adds the ability to run the conversion without pre-generating an entity ontology as was done for the Reactome import project. Right now, this option is tuned specifically for making conversion of the YeastCyc pathway collection. It could be generalized further, but it is certain that nearly any pathway collection will require customizations like you see here for YeastCyc.
Two new command line options have been added:
-e YeastCyc
-sssom ./target/classes/YeastCyc/obomatch-go-yeastpathway.sssom.tsv.txt
-e YeastCyc tells the converter to use neo classes directly rather than relying on building a seperate entity ontology (use -e REACTO for the entity ontology approach)
-sssom provides an automatically generated mapping file that is used to add GO types to instances without manually curated classifications.
This branch adds the ability to run the conversion without pre-generating an entity ontology as was done for the Reactome import project. Right now, this option is tuned specifically for making conversion of the YeastCyc pathway collection. It could be generalized further, but it is certain that nearly any pathway collection will require customizations like you see here for YeastCyc.
The code here was used to build https://github.com/geneontology/noctua-models/pull/159
Two new command line options have been added: -e YeastCyc -sssom ./target/classes/YeastCyc/obomatch-go-yeastpathway.sssom.tsv.txt
-e YeastCyc tells the converter to use neo classes directly rather than relying on building a seperate entity ontology (use -e REACTO for the entity ontology approach) -sssom provides an automatically generated mapping file that is used to add GO types to instances without manually curated classifications.