Define what qualifies a GPAD line as a distinct assertion individual in GO-CAM about gocamgen HOT 19 OPEN

The with/from field qualifies (or was originally intended to qualify) the evidence, so the individuals should be collapsed, but each ref/evidence_code/with is a separate piece of evidence.

The one caveat to that is that I thought we had decided to express binding annotations in a formally correct way with the bound entity being an input. then we would spit them back out as they currently are in the with field. @vanaukenk is that still the plan?

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@ukemi
Yes, that is still the plan for protein binding annotations. If we hadn't done this for protein binding, then not only would we have been inconsistent with GO-CAM, but we would not have been able to collapse the evidence for this particular term.

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OK, I think we can still work with that protein binding caveat. I now see the protein binding section on the wiki.

So basically, DO split out distinct with/from values into multiple assertions (translated with different has_input entities) IF the primary term is protein binding (and descendants or just GO:0005515?), ELSE collapse these different with/from values onto the same assertion individual.

@ukemi @vanaukenk Sound correct?

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Yes. That sounds correct.

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Cool, thanks! I updated the header/line thingy in my first comment to clarify how with/from is being handled.

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@dustine32

We will want to split out distinct With/From values into multiple assertions for GO:0005515 and also its children, as we may have annotations to terms like 'protein kinase binding' GO:0019901 that still refer to different entities in the With/From field.

I'll update the protein binding section of the wiki to make it clearer which of the options we chose.

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@dustine32

I've updated the import rules section for protein binding. Please let me know if anything is unclear or doesn't look right to you:

http://wiki.geneontology.org/index.php/Noctua_MOD_Imports#Protein_Binding_Annotations

Thx.

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Thanks @vanaukenk ! That definitely is more straight-forward. I just wanted to make sure I understand the last point:

Evidence will not be combined for annotations to protein binding or its children

So multiple GPAD lines with same GP-term-with/from-etc (the header fields above) values won't be collapsed into the same assertion if their evidence code-references (line fields) vary? More simply, each protein binding GPAD line will have its own assertion individual in GO-CAM?

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Is this true even for annotation lines that have the same value in the 'with' field?
Ex:

MGI MGI:1340046 enables GO:0005515 MGI:MGI:4845793|PMID:21068328 ECO:0000353 UniProtKB:Q8K1S1 20130311 MGI
MGI MGI:1340046 enables GO:0005515 MGI:MGI:4441002|PMID:20220021 ECO:0000353 UniProtKB:Q8K1S1 20130311 MGI

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@dustine32
Yes, we can combine protein binding GPAD lines if they are the same GP-term-with/from but different references. @ukemi - is that what you are meaning to illustrate above?

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Another potential illustration.
These three annotations could be combined as evidence for a single Noctua instance since they refer to the same binding (EGL-1 binds CED-9) but just cite different references (and have different annotation dates).

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Whereas in this example (just looking at the WB annotations, ignore the SWIE one), we would have two separate protein binding annotations:

One that combined three pieces of evidence and the WB:WBGene00000418 in the With/From field and one with a single piece of evidence and WB:WBGene00001170.

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Here's an example where it looks like we could combine evidence for a cellular component annotation, but haven't yet:

ced-9 (WB:WBGene00000423)

lat-1 (WB:WBGene00002251) is another example of two CC annotations whose evidence could be merged into a single individual.

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@vanaukenk Oh ok, that's what I was thinking too. Differing references alone shouldn't require multiple assertion individuals. I also forgot that all protein binding and descendant term annotations should be using the same IPI evidence code, so that removes one variable.

Thanks so much for clarifying!

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@vanaukenk I think those two examples are now collapsing correctly. Here they are on my dev server:

• WB:WBGene00000423 to [GO:0005739] mitochondrion; also protein binding:
  http://68.181.46.18:8910/editor/graph/gomodel:7a272ea7-f66c-42eb-ba20-804f1c4cb815
• WB:WBGene00002251 to [GO:0005887] integral component of plasma membrane:
  http://68.181.46.18:8910/editor/graph/gomodel:d9e069b1-ea00-4403-9ee4-9acd0a866f64

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@dustine32 - the two CC examples above are indeed now collapsing correctly. Thanks!

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@vanaukenk have you set up a formal testing document? If not, I will have a shot at it.

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Yes, I started with this spreadsheet here:

https://docs.google.com/spreadsheets/d/1XFuD6LOyFKXNk94jIK8zv1TrESfwCJo-RnrXQ3tzmJg/edit

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@vanaukenk @ukemi The latest iteration of WB, MGI models are now up on noctua-dev so this can be tested there now. This won't have the fix for the comma-separated with/from snafu that @ukemi pointed out here but I've since fixed it on my USC server.

Here are some stats from the import attached to the PR.

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