Glyma.liu kanazawa 2008 #89
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This one mostly looks good to me, but I see that the gene_model_pub_name comes from Tsubokura, Matsumura et al., 2013 rather than the older paper. That's a good choice I think. But in that case, we should rename this document to Tsubokura_Matsumura_2013.yml. It is not crucial to rename the branch too (since it will be merged and then deleted) -- but it's probably good practice anyway, just to avoid confusion.
So, I would put the contents of this file into Tsubokura_Matsumura_2013.yml, open a new branch with that name, and close this branch.
Other changes:
The classical locus E4 (one of the classically mapped "earliness" genes) is GmphyA2.
GmphyA1 apparently has no classical locus (at least that I can see), so skip classical_locus for GmphyA1/Glyma10g28170.
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For GmphyA1:
gene_symbol_long: phytochrome A1# In the literature, I see "A1" without space
gene_model_pub_name: Glyma10g28170# Good (no change)
gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G141400# Let's use gnm4 when possible -
For GmphyA2:
gene_symbol_long: phytochrome A2# In the literature, I see "A2" without space
gene_model_pub_name: Glyma20g22160# This is the ID used in the paper
gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G090000# Let's use gnm4 when possible.
Also note: your glyma.Wm82.gnm2.ann1.Glyma.20G085500 is a different gene. Please check and confirm. My method was to enter these genes as the query at https://soybase.org/tools/translate :
glyma.Wm82.gnm1.ann1.Glyma10g28170
glyma.Wm82.gnm1.ann1.Glyma20g22160
No big comments, just switched to Tsubokura paper for public names and more info on GmphyA1.