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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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Improve/add default download options for ontology and bioentity #414

Open ValWood opened 7 years ago

ValWood commented 7 years ago

I'm pretty sure that nobody will know what most of these mean.

i have no idea

Evidence For example there are 7 evidence options (but we only have a single evidence field so how do they differ?, presumably you either want the evidence field, or not?)

Acc(ID) Which Acc?

Annotation extension has 4 options, what do these mean?

ValWood commented 7 years ago

Maybe these are different formats.

Is this mixing two different things together.

  1. Format type (tab delimited jsn etc)
  2. data type (ID, evidence, extension)
kltm commented 7 years ago

@ValWood This one we could use some help on but let me give you the reasoning for what is there now.

For the "annotation" searches, we have a default that makes sense: basically a GAF. With that, you can also create your own download, but given the interface (which essentially exposes the underlying datastore structure). For the other two, "ontology classes" and "bioentities", there was no obvious default format, we we just gave the custom download a few default settings and called it a day.

If you can think of a sensible/useful default for these, we can add those buttons, just like we have for "annotations".

ValWood commented 7 years ago

The default isn't a GAF though......

I still think a 2-step approach might work better.

What file format do you want (json, tab delimited, other), then which fields do you want....

Then maybe the options can be simpler (if I understood what some of the options might be for, not totally sure about that).

kltm commented 7 years ago

For annotation searches, the Download (not the custom download button) is pretty much a GAF, with a couple of hiccups

UniProtKB   Q6CI49  YALI0_A01738g       GO:0051087  PAINT_REF:21100 IBA PANTHER:PTN000473575    F   Prefoldin subunit 4 UniProtKB:Q6CI49|PTN001079374|Q6CI49_YARLI  protein NCBITaxon:284591    20151014    GO_Central

The exception being the extensions, which is the other ticket. We've considered (another ticket somewhere) just storing the GAF lines directly so we can reproduce them easier, but that's another item. However, they are mostly GAF, which is a good starting point.

As far as what the options are, ideally, most users should be steered away from the custom download widget and have a single sensible button, like for annotations (even if it is not quite a GAF).