Snf review roy2020 (#37)

* Removed Pant_Matsye_2014.yml and Yu_Jin_2019.yml, as neither was complete or well supported (incomplete work from Greg) * Added field scientific_name to all yml collections and added two-letter genus-species prefix (e.g., Mt, Gm, Lj) to gene symbols * Fix quoting for yaml compliance * Added gensp. prefix to each yaml file. For yaml files with multiple species, I separated these by species, prefixing each and moving it into its respective species directory. Also updated the templates. * Fix yaml errors --------- Co-authored-by: StevenCannon-USDA <[email protected]>
legumeinfo · Apr 17, 2024 · 90d5cb1 · 90d5cb1
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diff --git a/Glycine/max/studies/Pant_Matsye_2014.yml b/Glycine/max/studies/Pant_Matsye_2014.yml
diff --git a/Glycine/max/studies/Yu_Jin_2019.yml b/Glycine/max/studies/Yu_Jin_2019.yml
diff --git a/Glycine/max/studies/Zhang_Cheng_2021.yml b/Glycine/max/studies/Zhang_Cheng_2021.yml
diff --git a/Glycine/max/studies/Bai_Jing_2021.yml → Glycine/max/studies/glyma.Bai_Jing_2021.yml b/Glycine/max/studies/Bai_Jing_2021.yml → Glycine/max/studies/glyma.Bai_Jing_2021.yml
@@ -1,4 +1,5 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmPLDγ
 gene_symbol_long: Phospholipase D

diff --git a/Glycine/max/studies/Cai_Wang_2017.yml → Glycine/max/studies/glyma.Cai_Wang_2017.yml b/Glycine/max/studies/Cai_Wang_2017.yml → Glycine/max/studies/glyma.Cai_Wang_2017.yml
@@ -1,4 +1,5 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmTIR1A
 gene_symbol_long: Transport Inhibitor Response 1A
@@ -36,6 +37,7 @@ references:
     doi: 10.1111/jipb.13207
     pmid: 34962095
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmTIR1B
 gene_symbol_long: Transport Inhibitor Response 1B
@@ -73,6 +75,7 @@ references:
     doi: 10.1111/jipb.13207
     pmid: 34962095
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmTIR1C
 gene_symbol_long: Transport Inhibitor Response 1C
@@ -111,6 +114,7 @@ references:
     doi: 10.1111/jipb.13207
     pmid: 34962095
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmTIR1D
 gene_symbol_long: Transport Inhibitor Response 1D
@@ -147,6 +151,7 @@ references:
     doi: 10.1111/jipb.13207
     pmid: 34962095
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmAFB3A
 gene_symbol_long: Auxin-Signaling F-Box 3A
@@ -185,6 +190,7 @@ references:
     doi: 10.1111/jipb.13207
     pmid: 34962095
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmAFB3B
 gene_symbol_long: Auxin-Signaling F-Box 3B

diff --git a/Glycine/max/studies/Campbell_Mani_2014.yml → .../max/studies/glyma.Campbell_Mani_2014.yml b/Glycine/max/studies/Campbell_Mani_2014.yml → .../max/studies/glyma.Campbell_Mani_2014.yml
@@ -1,6 +1,7 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
-  - ChlI1a
+  - GmChlI1a
 gene_symbol_long: Mg-Chelatase Subunit Chl1a
 gene_model_pub_name: Glyma.13G232500
 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G232500
@@ -21,8 +22,9 @@ references:
     doi: 10.1534/g3.114.015255
     pmid: 25452420
 ---
+scientific_name: Glycine max
 gene_symbols:
-  - ChlI1b
+  - GmChlI1b
 gene_symbol_long: Mg-Chelatase Subunit Chl1b
 gene_model_pub_name: Glyma.15G080200
 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G080200

diff --git a/Glycine/max/studies/Chen_Cai_2020.yml → Glycine/max/studies/glyma.Chen_Cai_2020.yml b/Glycine/max/studies/Chen_Cai_2020.yml → Glycine/max/studies/glyma.Chen_Cai_2020.yml
@@ -1,7 +1,7 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmFT2b
-  - FT2b
 gene_symbol_long: Glycine max flowering locus T-like protein 2b
 gene_model_pub_name: Glyma.16G151000
 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G151000

diff --git a/Glycine/max/studies/Chen_Fang_2019.yml → Glycine/max/studies/glyma.Chen_Fang_2019.yml b/Glycine/max/studies/Chen_Fang_2019.yml → Glycine/max/studies/glyma.Chen_Fang_2019.yml
@@ -1,8 +1,9 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmSYP24
   - GmLEA2-96
-  - SYP24
+  - GmSYP24
 gene_symbol_long: Putative Syntaxin Gene
 gene_model_pub_name: Glyma.19G198600
 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G198600

diff --git a/Glycine/max/studies/Chen_Wang_2016.yml → Glycine/max/studies/glyma.Chen_Wang_2016.yml b/Glycine/max/studies/Chen_Wang_2016.yml → Glycine/max/studies/glyma.Chen_Wang_2016.yml
@@ -1,4 +1,5 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmDGAT1A
 gene_symbol_long: Diacylglycerol Acyltransferase 1A
@@ -32,6 +33,7 @@ references:
     doi: 10.1016/j.csbj.2022.06.014
     pmid: 35782726
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmDGAT2D
 gene_symbol_long: Diacylglycerol Acyltransferase 2D

diff --git a/Glycine/max/studies/Cheng_Dong_2019.yml → ...ine/max/studies/glyma.Cheng_Dong_2019.yml b/Glycine/max/studies/Cheng_Dong_2019.yml → ...ine/max/studies/glyma.Cheng_Dong_2019.yml
@@ -1,8 +1,9 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmLHY2a
-  - LCL3
-  - MYB156
+  - GmLCL3
+  - GmMYB156
 gene_symbol_long: Late Elongated Hypocotyl 2a
 gene_model_pub_name: Glyma.19G260900
 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G260900

diff --git a/...udies/Chiasson_Loughlin_2014_GmbHLHm1.yml → ...glyma.Chiasson_Loughlin_2014_GmbHLHm1.yml b/...udies/Chiasson_Loughlin_2014_GmbHLHm1.yml → ...glyma.Chiasson_Loughlin_2014_GmbHLHm1.yml
@@ -1,4 +1,5 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmbHLHm1
   - GmSAT1

diff --git a/Glycine/max/studies/Dobbels_Michno_2017.yml → ...max/studies/glyma.Dobbels_Michno_2017.yml b/Glycine/max/studies/Dobbels_Michno_2017.yml → ...max/studies/glyma.Dobbels_Michno_2017.yml
@@ -1,4 +1,5 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - KASI
 gene_symbol_long: beta-ketoacyl-ACP synthetase I

diff --git a/Glycine/max/studies/Du_Zhao_2018.yml → Glycine/max/studies/glyma.Du_Zhao_2018.yml b/Glycine/max/studies/Du_Zhao_2018.yml → Glycine/max/studies/glyma.Du_Zhao_2018.yml
@@ -1,4 +1,5 @@
 ---
+scientific_name: Glycine max
 gene_symbols:
   - GmMYB118
 gene_model_pub_name: GLYMA_17G094400