search

legumeinfo / glycinemine

An InterMine for Glycine species
GNU Lesser General Public License v3.0
0 stars 1 forks source link

GO-category selector in the GO enrichment widget #23

Closed StevenCannon-USDA closed 3 years ago

StevenCannon-USDA commented 5 years ago

In the Gene Ontology Enrichment widget, changing the ontology category (molecular_function, cellular_component, biological_process) seems not to affect the GO enrichment set in the widget display. My hypothesis: the widget displays any GO terms, from any of the categories, regardless of the Ontology selection; in other words, the Ontology selector is a red herring / nonfunctional. Why I think this: the listed GO terms seem to include both molecular_function and biological_process terms (using the attached list, in SoyMine): defense response [GO:0006952] is a biological_process pectinesterase activity [GO:0030599] is a molecular_function

So, perhaps "nothing to do" on this bug - unless feed it upstream to either remove the Ontology button or make it work?

Test file for use in SoyMine (upload to "Analyze") pangenome.gt5.Wm82.gnm2.lis.gz

adf-ncgr commented 5 years ago

good call; it looks like the selector for the dropdown is actually making relevant calls with appropriate filtering requested, e.g. if I change to cellular component it asks for something like: https://mines.legumeinfo.org/legumemine/service/list/enrichment?callback=jQuery20304608373604432525_1552664953778&widget=go_enrichment_for_gene&list=Gene+list+for+all+organisms+15+Mar+2019+9.49&correction=None&maxp=0.10&token=B186Q9c8x2b0d8S4U3W8&errorCorrection=None&pValue=0.10&filter=cellular_component&_=1552664953788

It looks like our GO Terms have appropriate ontology categories (aka "aspects") in GO Term Namespace field, so I guess the bug is probably in the enrichment code somewhere. Will let @sammyjava sort it out, though he may be at the NCGR-hosted "Integrative omics" conference today.

sammyjava commented 3 years ago

Moved to mine-issues