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geneontology / amigo

AmiGO is the public interface for the Gene Ontology.
http://amigo.geneontology.org
BSD 3-Clause "New" or "Revised" License
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Add IEA filter to Matrix tool #569

Open ValWood opened 5 years ago

ValWood commented 5 years ago

Hi @kltm

Would it be possible to add an IEA filter to the matrix tool?

I'm sorting out the paper and checking the rules. It's very time-consuming to do the checking and rule building. It would be really helpful if I could ignore the IEA annotations as I don't need to validate those for rule building...

Cheers Val

kltm commented 5 years ago

@ValWood Hm. Well, currently the matrix tool is "bioentity" oriented, and the bioentities do not have the evidence-to-term information stored with them. We could add an annotation version of the output maybe, which would give you the ability to work with evidence, but that would change some of your interactions.

ValWood commented 5 years ago

Ah OK, I think I remember you telling me that. I can muddle along.

One question, I came across two rule violations today but when I clicked the link to Amigo and then checked the annotations I could not find the violating terms. Is the Matrix using the current version of the ontology and annotations? (i.e same as live AmiGO?)

kltm commented 5 years ago

@ValWood Argh--I hate it when people have to muddle along. I'll try and keep this in mind as we move towards rewriting the indexer. As well, we will soon have other data stores that we may be able to query for the same information.

The Matrix tool report, as it stands now, is referencing the last release of the GO, at amigo.geneontology.org. (E.g. http://current.geneontology.org/reports/shared-annotation-check.html)

The Matrix tool itself (e.g. http://amigo.geneontology.org/matrix) should always be pointing to the amigo that is hosting it; e.g. http://amigo.geneontology.org/matrix points to http://amigo.geneontology.org . If you find that this is not the case, if you can give me an example I can look into it.

ValWood commented 5 years ago

@ValWood Argh--I hate it when people have to muddle along.

This isn't so bad. It slows thing a little, but now I know which organisms are IEA only I can ignore those and it doesn't take too long to find the primary annotations. For the stuff I'm doing now for the paper it isn't too bad. But I'm only doing a fairly small proportion of the matrix and the end is in sight. Down the line evidence filters would be useful.

Re the things I could not find, I can't remember the examples and I haven't come across any recently so I might be mistaken.

ValWood commented 5 years ago

@pfey03 asked about this too!