Replace URS ID for human ncRNAs with symbol

[hattrill]

When using RNAcentral IDs for human ncRNAs, the URS is displayed in Noctua/Alliance pathway view. Could this be replaced with the symbol?

e.g. http://noctua.geneontology.org/workbench/noctua-visual-pathway-editor/?model_id=gomodel%3A654d809000000802

for the above example URS000012F9EC_9606 (https://rnacentral.org/rna/URS000012F9EC/9606) is displayed, but would like to see hsa-miR-4691-3p

[pgaudet]

@balhoff Is this a NEO issue?

[balhoff]

@pgaudet yes I think so; the actual label value in NEO is 'URS000012F9EC_9606 Hsap'.

[pgaudet]

what does the raw data look like? Is is possible to use the gene name? 'hsa-miR-4691-3p' ?

[balhoff]

The cells in that row (and all the rows) of the GPI look like this:

1. RNAcentral
2. URS000012F9EC_9606	
3.	
4. Homo sapiens (human) hsa-miR-4691-3p	
5.	
6. miRNA
7. taxon:9606		
8. 	
9.
10.

So maybe they should be putting something in column 3 (DB_Object_Symbol)?

[vanaukenk]

@balhoff @pgaudet @hattrill

Yes, RNACentral would need to populate column 3 with the symbol in order for that to be shown in the GO-CAM models.

Also tagging @blakesweeney here to see if RNACentral could update the gpi file GO retrieves. See:
https://github.com/geneontology/go-site/blob/master/metadata/datasets/rnacentral.yaml

[blakesweeney]

Hi, that sounds like a reasonable change for us to make. If there is no rush for it I will schedule it for our next release in 3 months. If there we can do something more quickly once people are back from holidays. Let me know what is preferred.

[vanaukenk]

Thank you @blakesweeney

@hattrill
Do you have a specific time frame in mind for this, i.e. do you need this for a figure in the ncRNA paper?

[hattrill]

@vanaukenk No rush for me. Thanks