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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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SynGO2LEGO models regenerated through @dosumis' code; issue #55 #75

Closed dustine32 closed 6 years ago

dustine32 commented 6 years ago

Just ran file SynGO_export_test.json for examples.

kltm commented 6 years ago

Clarifying that only nine models changed?

dustine32 commented 6 years ago

@kltm Yep, only nine. I only ran it on a few annotations for examples.

If you'd like, I can run the full JSON source file containing 2179 models and submit a new PR? Thanks!

thomaspd commented 6 years ago

Yes, I think we should try on all the SynGO models, now that they are using ORCIDs. @kltm is there anything else we need to resolve first?

kltm commented 6 years ago

@dustine32 @thomaspd I'm happy to take any number onto dev, but all of them would naturally make looking for additional issues easier.

dustine32 commented 6 years ago

@kltm @thomaspd Cool, I'll get all of the models converted then. So the first issue that popped up when running the whole list was an out-of-date ontology file "go-simple.ofn". This file's from late Aug 2017 and the new annotations use terms added after that. Ex. GO:0099170

@dosumis Do you know where I can get an updated ofn file?

In the meantime I'll try to fish out other issues in the model list.

dosumis commented 6 years ago

@kltm @thomaspd Cool, I'll get all of the models converted then. So the first issue that popped up when running the whole list was an out-of-date ontology file "go-simple.ofn". This file's from late Aug 2017 and the new annotations use terms added after that. Ex. GO:0099170

@dosumis Do you know where I can get an updated ofn file?

Just grab the latest GO file. http://purl.obolibrary.org/obo/go.owl should be fine.

dustine32 commented 6 years ago

Awesome @dosumis thanks! Now it looks like it made it through most models before one to an obsolete term erred it out again.

I can probably skip SynGO annotations to obsolete terms, right @thomaspd ? Specifically, UniProtKB:P70569 annotated GO:0099090 (model SYNGO:1805).