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This is a place to discuss issues around the Planteome annotation data and store useful scripts etc.
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Comma-separated synonym fields in GO GAF file #30

Closed serenalotreck closed 2 years ago

serenalotreck commented 2 years ago

I've been using the GAF files from Planteome to get the names and synonyms of database items, and I noticed that one of the GO files seems to have synonym fields that are separated by commas, rather than by pipe characters (|) like they're supposed to be.

The file I've noticed this in is go_gene_Orzya_Gramene.assoc. I was wondering if this was intentional/for some reason, or if this is a mistake?

Thanks!

elserj commented 2 years ago

@jaiswalp Can you please take a look at this file and let me know if these are multiple synonyms or one synonym with commas? I think they are multiple, but I can't find the source file on gramene and I want to confirm before I make any changes.

Also, should the quotes be removed?

If you confirm they are multiple, I will make the changes.

jaiswalp commented 2 years ago

go ahead and make changes

On 11/4/2021 9:40 AM, elserj wrote:

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Also, should the quotes be removed?

If you confirm they are multiple, I will make the changes.

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cooperl09 commented 2 years ago

Why are some of the gene names in square brackets? Also, looks like some of the synonyms are duplicated: https://browser.planteome.org/amigo/gene_product/GR_gene:GR:0060146

elserj commented 2 years ago

I don't know, I'm removing those as well. I believe once I get it done correctly, the duplicates will resolve automatically as part of the loading process in AmiGO. I will write a quick script to find and fix the dupes in the annotation file though.

elserj commented 2 years ago

This should be fixed now. Please let me know if you find any I missed.