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geneontology / gocamgen

Base repo for constructing GO-CAM model RDF
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Generalize the 'has input' conversion for 'binding' and all children #50

Open vanaukenk opened 5 years ago

vanaukenk commented 5 years ago

Doing some QC on the imports, I realized that WB (and others) have annotations to other children of 'binding' (GO:0005488) that use the IPI (ECO:0000353) evidence code and contain an entry in the With/From field.

To be consistent in how we model 'binding' annotations in GO-CAM, we'll need to broaden our conversion rule so that any annotation to GO:0005488 that has an entry in the With/From field, will convert the With/From value to a 'has input' annotation extension, just like we're doing for 'protein binding' (GO:0005515) and its children.

For an example, see the 'miRNA binding' (GO:0035198) annotation in this alg-1 model.

@dustine32 - let me know if you need any more info or examples. Thx.

dustine32 commented 5 years ago

@vanaukenk Good call! I've occasionally been seeing some DNA binding examples and was wondering if they should get the same treatment.

Should be a one-line change. Maybe even make this "top-level binding term" MOD-specific configurable like the filter rules?

vanaukenk commented 5 years ago

@dustine32 - I think we can go ahead and make this a general rule across all the MODs.

If a curator annotated to 'binding' or a child and entered something in the With/From field, we will want to translate all of those values to 'has input'.

@ukemi - sound okay to you?

dustine32 commented 5 years ago

Changed root term (used for determining whether to translate with/from to has_input edges) to "binding" GO:0005488 whereas it was previously "protein binding" GO:0005515. You can see this now works for other terms like "DNA binding": image In the model for MGI:MGI:97747 from line:

MGI MGI:97747   enables GO:0003677  MGI:MGI:3529655|PMID:15681609   ECO:0000353 UniProtKB:P28700        20050715    MGI
vanaukenk commented 5 years ago

This looks okay to me on the USC server. I'd like to double-check other models, but they should be fine. Thanks!

ukemi commented 5 years ago

The translation looks good. The annotation looks strange. I may alter this one.

vanaukenk commented 5 years ago

Note that we still need to work with @balhoff to make sure the GPAD output works as we want.

dustine32 commented 4 years ago

Finally found an example of a DNA binding IPI in noctua-dev: MGI:MGI:1096381 image From line:

MGI MGI:1096381 enables GO:0003677 MGI:MGI:1276614|PMID:9704006 ECO:0000353 UniProtKB:Q61221 20110329 MGI

@vanaukenk @ukemi If this looks good we can finally close this ticket!

ukemi commented 4 years ago

I think that there is an issue with this that I pointed out in the example in #37. We should only use this conversion for binding annotations that use the IPI evidence code. If they use another evidence code, like ISO, they should be retained in the 'with' field.