Open ValWood opened 7 years ago
Maybe these are different formats.
Is this mixing two different things together.
@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".
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).
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).
I'm pretty sure that nobody will know what most of these mean.
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?