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geneontology / noctua-models

This is the data repository for the models created and edited with the Noctua tool stack for GO.
http://noctua.geneontology.org/
Creative Commons Attribution 4.0 International
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YeastCyc pathways generated by pathways2GO converter #159

Closed goodb closed 3 years ago

goodb commented 3 years ago

command line to run conversion:

-b ./biopax/yeastcyc/ -o ./yeastcyc/ -bg ./yeastcyc-bg.jnl -tag YeastCyc -dc https://orcid.org/0000-0002-7334-7852 -dp https://yeastgenome.org -lego http://purl.obolibrary.org/obo/go/extensions/go-lego.owl -e YeastCyc -sssom ./target/classes/YeastCyc/obomatch-go-yeastpathway.sssom.tsv.txt

there are two new options: -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 conversion used the sssom file generated by @cmungall on Oct 7 2020, referenced: https://github.com/geneontology/go-ontology/issues/20091

It also relies on a GPI file retrieved from http://sgd-archive.yeastgenome.org/curation/literature/

The original pathway files came from https://stanford.box.com/s/mhywvmcgmd9s7hfqnhllzt0mpe3ypc1s

goodb commented 3 years ago

Ran owl/shex validator on the yeast models. All of the models are OWL consistent, but only 68 of the 187 models are shex compliant. It seems that there are large number of cardinality violations. Notable, 616 out of 1149 activity units in these models are 'complete' with respect to the basic criteria of having an enabler, an MF, and a location.

Pipeline json for shex report: gorules_report.json.txt

general stats for models and activities respectively main_report.txt activity_report.txt

goodb commented 3 years ago

@kltm @cmungall I'm going to go ahead and merge this one into dev. I want to add one more change to the reactome models (just change there titles so the search works better...) that is coming next.