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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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Update ontology objects and ontology object generation/loading scripts #119

Closed janakagithub closed 5 years ago

janakagithub commented 5 years ago

Ontology objects added and updated: KBaseOntology.OntologyDictionary.EBI_EC_ontologyDictionary.json KBaseOntology.OntologyDictionary.KEGG_KO_ontologyDictionary.json KBaseOntology.OntologyDictionary.KEGG_RXN_ontologyDictionary.json KBaseOntology.OntologyDictionary.MetaCyc_RXN_ontologyDictionary.json KBaseOntology.OntologyDictionary.ModelSEED_RXN_ontologyDictionary.json Ontology Translational objects KEGG Rxn -> ModelSEED EC -> ModelSEED MetaCyc ->ModelSEED

samseaver commented 5 years ago

I don't have a problem with this merger, but I'm concerned about where the MetaCyc ontology came from, did you download a recent release of the database? I've got version 22.5 in my MetaCyc mirror. What is the MetaCyc XML file?

janakagithub commented 5 years ago

Scripts that I have setup parse MetaCyc ->ModelSEED ontology translations from ModelSEEDDatabase/Biochemistry/Aliases/Provenance/Reactions_Aliases.tsv Upon updating Reactions_Aliases.tsv ontology translations would update as well. As for the MetaCyc dictionary, it was generated using the MetaCycReactionsFull.xml produced from Jeff at LLNL, which I believe is upto date.

samseaver commented 5 years ago

@janakagithub OK if the xml file was generated directly from MetaCyc, I'd rather not keep it in the repository to avoid any potential licensing issues, can you remove only the xml file? We can keep any derived and re-organized data.

janakagithub commented 5 years ago

Metacyc Reaction file removed from the PR.

samseaver commented 5 years ago

OK, thanks, looks good.