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legumeinfo / gene-function-registry

A set of records (pages) for collecting information about gene function in a human- and machine-readable format.
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Revisions to glyma.Song_Montes-Luz_2022.yml on 26 July 2024 #48

Closed ScottKalberer closed 1 month ago

ScottKalberer commented 1 month ago

I've corrected the gene_function_registry file glyma.Song_Montes-Luz_2022.yml originally created by Marlena Dorneich-Hayes. I created the new branch glyma.Song_Montes-Luz_2022 with this revised file and pushed it up to the GitHub origin. I also changed the name of the file from glyma.Song_Montez-Luz_2022.yml to glyma.Song_Montes-Luz_2022.yml. I'm requesting review of this YML gene function file, merge of the changes into main branch, and subsequent deletion of this temporary branch on GitHub.

maxglycine commented 1 month ago

Instead of jamming the parts together to avoid spaces or dashes, can spaces be substituted with underscores? There will be times that we might want the separation in the parts but dashes in the wrong spots could be problematic. @StevenCannon-USDA @jd-campbell @adf-ncgr @ScottKalberer . The dash has somewhat a special place in SoyBase. It designated a paralog. Like BHP 1-1 would be the 1st paralog of BHP 1. If BHP 1-1 had two alleles, one would be BHP 1-1a and the other would be BHP 1-1b

StevenCannon-USDA commented 1 month ago

@maxglycine - are you referring to the symbol name, e.g. GmGA20ox?

ScottKalberer commented 1 month ago

I suggest using underscores rather than dashes. So GmGA20ox a would become GmGA20ox_a, and GmGA3ox 1a would become GmGA3ox_1a. I will also add a section for GmGA20ox_b, as I don't know why Marlena left it out originally.

maxglycine commented 1 month ago

It was a made up example easier to type than the one you gave.
GmGA20ox a => GmGA20ox_a and GmGA20ox-a => GmGA20ox_1a Just as Scott said. So the first paralog of GmGA20ox_a would be GmGA20ox_a-1. The first allele of GmGAox_a-1 would be GmGA20ox_a-1a and so on. @ScottKalberer @adf @jd-campbell @StevenCannon-USDA

StevenCannon-USDA commented 1 month ago

@maxglycine and @ScottKalberer - sounds good to me; thanks. Lets' go with GmGA20ox_a etc.

adf-ncgr commented 1 month ago

sounds good to me (to the extent I understand what you're talking about here!)

ScottKalberer commented 1 month ago

I have made the requested revisions to glyma.Song_Montes-Luz_2022.yml - in particular as regards the gene symbols. Notice that the evidence for the candidate gene GmGA20ox_b is less convincing than for either GmGA20ox_a or especially GmGA3ox_1a.