Wholesale rearrangement. Removed all wip_name directories and moved y…

…aml files into new studies/ directories.
legumeinfo · Jan 4, 2024 · f957f0a · f957f0a
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Showing 84 changed files with 57 additions and 3,454 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1 @@
+.DS_Store
diff --git a/Glycine/max/wip_greg/done/Bai_Jing_2021.yml → Glycine/max/studies/Bai_Jing_2021.yml b/Glycine/max/wip_greg/done/Bai_Jing_2021.yml → Glycine/max/studies/Bai_Jing_2021.yml
diff --git a/Glycine/max/wip_marlene/Cai_Wang_2017.yml → Glycine/max/studies/Cai_Wang_2017.yml b/Glycine/max/wip_marlene/Cai_Wang_2017.yml → Glycine/max/studies/Cai_Wang_2017.yml
diff --git a/...x/wip_marlene/done/Campbell_Mani_2014.yml → Glycine/max/studies/Campbell_Mani_2014.yml b/...x/wip_marlene/done/Campbell_Mani_2014.yml → Glycine/max/studies/Campbell_Mani_2014.yml
diff --git a/..._greg/done/supplemental/Chen_Cai_2020.yml → Glycine/max/studies/Chen_Cai_2020.yml b/..._greg/done/supplemental/Chen_Cai_2020.yml → Glycine/max/studies/Chen_Cai_2020.yml
diff --git a/Glycine/max/wip_greg/done/Chen_Fang_2019.yml → Glycine/max/studies/Chen_Fang_2019.yml b/Glycine/max/wip_greg/done/Chen_Fang_2019.yml → Glycine/max/studies/Chen_Fang_2019.yml
diff --git a/Glycine/max/wip_marlene/Chen_Wang_2016.yml → Glycine/max/studies/Chen_Wang_2016.yml b/Glycine/max/wip_marlene/Chen_Wang_2016.yml → Glycine/max/studies/Chen_Wang_2016.yml
diff --git a/...reg/done/supplemental/Cheng_Dong_2019.yml → Glycine/max/studies/Cheng_Dong_2019.yml b/...reg/done/supplemental/Cheng_Dong_2019.yml → Glycine/max/studies/Cheng_Dong_2019.yml
diff --git a/...teven/Chiasson_Loughlin_2014_GmbHLHm1.yml → ...udies/Chiasson_Loughlin_2014_GmbHLHm1.yml b/...teven/Chiasson_Loughlin_2014_GmbHLHm1.yml → ...udies/Chiasson_Loughlin_2014_GmbHLHm1.yml
diff --git a/...max/wip_greg/done/Dobbels_Michno_2017.yml → Glycine/max/studies/Dobbels_Michno_2017.yml b/...max/wip_greg/done/Dobbels_Michno_2017.yml → Glycine/max/studies/Dobbels_Michno_2017.yml
diff --git a/Glycine/max/wip_will/done/Du_Zhao_2018.yml → Glycine/max/studies/Du_Zhao_2018.yml b/Glycine/max/wip_will/done/Du_Zhao_2018.yml → Glycine/max/studies/Du_Zhao_2018.yml
diff --git a/Glycine/max/wip_will/done/Fang_Li_2014.yml → Glycine/max/studies/Fang_Li_2014.yml b/Glycine/max/wip_will/done/Fang_Li_2014.yml → Glycine/max/studies/Fang_Li_2014.yml
diff --git a/Glycine/max/wip_marlene/Ge_Yu_2016.yml → Glycine/max/studies/Ge_Yu_2016.yml b/Glycine/max/wip_marlene/Ge_Yu_2016.yml → Glycine/max/studies/Ge_Yu_2016.yml
diff --git a/...x/wip_wei/done/Head_Galos_2012_traits.yml → ...ne/max/studies/Head_Galos_2012_traits.yml b/...x/wip_wei/done/Head_Galos_2012_traits.yml → ...ne/max/studies/Head_Galos_2012_traits.yml
diff --git a/Glycine/max/wip_will/done/Hu_Jin_2014.yml → Glycine/max/studies/Hu_Jin_2014.yml b/Glycine/max/wip_will/done/Hu_Jin_2014.yml → Glycine/max/studies/Hu_Jin_2014.yml
diff --git a/.../wip_marlene/Indrasumunar_Searle_2011.yml → .../max/studies/Indrasumunar_Searle_2011.yml b/.../wip_marlene/Indrasumunar_Searle_2011.yml → .../max/studies/Indrasumunar_Searle_2011.yml
diff --git a/...max/wip_marlene/done/Khatri_Pant_2022.yml → Glycine/max/studies/Khatri_Pant_2022.yml b/...max/wip_marlene/done/Khatri_Pant_2022.yml → Glycine/max/studies/Khatri_Pant_2022.yml
diff --git a/Glycine/max/wip_will/done/Li_Liu_2019.yml → Glycine/max/studies/Li_Liu_2019.yml b/Glycine/max/wip_will/done/Li_Liu_2019.yml → Glycine/max/studies/Li_Liu_2019.yml
diff --git a/...x/wip_brandon/done/traits_determinacy.yml → Glycine/max/studies/Liang_Chen_2022.yml b/...x/wip_brandon/done/traits_determinacy.yml → Glycine/max/studies/Liang_Chen_2022.yml
@@ -25,24 +25,3 @@ references:
     pmid: 25005919
 
 
----
-classical_locus:
-gene_symbols:
-  - GmDT1
-gene_symbol_long: Determinacy 1
-gene_model_pub_name: Glyma.19g194300
-gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G194300
-confidence: 5
-curators:
-  - Brandon Jordan
-phenotype_synopsis: determinate stem growth habit
-traits:
-  - entity_name: meristem identity
-    entity: TO:0006017
-    relation_name: terminal
-    relation: PATO:0002476
-references:
-  - citation: Liu, Watanabe et al., 2010
-    doi: doi.org/10.1104/pp.109.150607
-    pmid: 20219831
-
diff --git a/Glycine/max/wip_will/done/Liu_Liao_2020.yml → Glycine/max/studies/Liu_Liao_2020.yml b/Glycine/max/wip_will/done/Liu_Liao_2020.yml → Glycine/max/studies/Liu_Liao_2020.yml
diff --git a/Glycine/max/studies/Liu_Watanabe_2010.yml b/Glycine/max/studies/Liu_Watanabe_2010.yml
@@ -0,0 +1,21 @@
+---
+classical_locus:
+gene_symbols:
+  - GmDT1
+gene_symbol_long: Determinacy 1
+gene_model_pub_name: Glyma.19g194300
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G194300
+confidence: 5
+curators:
+  - Brandon Jordan
+phenotype_synopsis: determinate stem growth habit
+traits:
+  - entity_name: meristem identity
+    entity: TO:0006017
+    relation_name: terminal
+    relation: PATO:0002476
+references:
+  - citation: Liu, Watanabe et al., 2010
+    doi: doi.org/10.1104/pp.109.150607
+    pmid: 20219831
+
diff --git a/Glycine/max/wip_marlene/Lu_Cheng_2020.yml → Glycine/max/studies/Lu_Cheng_2020.yml b/Glycine/max/wip_marlene/Lu_Cheng_2020.yml → Glycine/max/studies/Lu_Cheng_2020.yml
diff --git a/Glycine/max/wip_marlene/done/Lu_Wei_2021.yml → Glycine/max/studies/Lu_Wei_2021.yml b/Glycine/max/wip_marlene/done/Lu_Wei_2021.yml → Glycine/max/studies/Lu_Wei_2021.yml
diff --git a/...ne/max/wip_greg/done/Manan_Ahmad_2017.yml → Glycine/max/studies/Manan_Ahmad_2017.yml b/...ne/max/wip_greg/done/Manan_Ahmad_2017.yml → Glycine/max/studies/Manan_Ahmad_2017.yml
diff --git a/...ax/wip_marlene/done/Noman_Jameel_2019.yml → Glycine/max/studies/Noman_Jameel_2019.yml b/...ax/wip_marlene/done/Noman_Jameel_2019.yml → Glycine/max/studies/Noman_Jameel_2019.yml
diff --git a/Glycine/max/wip_marlene/done/Pan_Yu_2021.yml → Glycine/max/studies/Pan_Yu_2021.yml b/Glycine/max/wip_marlene/done/Pan_Yu_2021.yml → Glycine/max/studies/Pan_Yu_2021.yml
diff --git a/Glycine/max/wip_greg/Pant_Matsye_2014.yml → Glycine/max/studies/Pant_Matsye_2014.yml b/Glycine/max/wip_greg/Pant_Matsye_2014.yml → Glycine/max/studies/Pant_Matsye_2014.yml
diff --git a/Glycine/max/wip_marlene/Pham_Lee_2010.yml → Glycine/max/studies/Pham_Lee_2010.yml b/Glycine/max/wip_marlene/Pham_Lee_2010.yml → Glycine/max/studies/Pham_Lee_2010.yml
diff --git a/Glycine/max/wip_greg/done/Qi_Li_2014.yml → Glycine/max/studies/Qi_Li_2014.yml b/Glycine/max/wip_greg/done/Qi_Li_2014.yml → Glycine/max/studies/Qi_Li_2014.yml
diff --git a/.../wip_marlene/done/Redekar_Glover_2020.yml → Glycine/max/studies/Redekar_Glover_2020.yml b/.../wip_marlene/done/Redekar_Glover_2020.yml → Glycine/max/studies/Redekar_Glover_2020.yml
diff --git a/...x/wip_marlene/done/Reid_Ferguson_2011.yml → Glycine/max/studies/Reid_Ferguson_2011.yml b/...x/wip_marlene/done/Reid_Ferguson_2011.yml → Glycine/max/studies/Reid_Ferguson_2011.yml
diff --git a/...p_greg/done/RojasRodas_Rodriguez_2013.yml → ...max/studies/RojasRodas_Rodriguez_2013.yml b/...p_greg/done/RojasRodas_Rodriguez_2013.yml → ...max/studies/RojasRodas_Rodriguez_2013.yml
diff --git a/Glycine/max/wip_marlene/Searle_Men_2003.yml → Glycine/max/studies/Searle_Men_2003.yml b/Glycine/max/wip_marlene/Searle_Men_2003.yml → Glycine/max/studies/Searle_Men_2003.yml
diff --git a/...e/max/wip_marlene/done/Shi_Zhang_2020.yml → Glycine/max/studies/Shi_Zhang_2020.yml b/...e/max/wip_marlene/done/Shi_Zhang_2020.yml → Glycine/max/studies/Shi_Zhang_2020.yml
diff --git a/Glycine/max/wip_marlene/Song_Li_2013.yml → Glycine/max/studies/Song_Li_2013.yml b/Glycine/max/wip_marlene/Song_Li_2013.yml → Glycine/max/studies/Song_Li_2013.yml
diff --git a/.../max/wip_marlene/Song_Montez-Luz_2022.yml → Glycine/max/studies/Song_Montez-Luz_2022.yml b/.../max/wip_marlene/Song_Montez-Luz_2022.yml → Glycine/max/studies/Song_Montez-Luz_2022.yml
diff --git a/...ip_marlene/Soyano_Hirakawa_2014_lotja.yml → ...ax/studies/Soyano_Hirakawa_2014_lotja.yml b/...ip_marlene/Soyano_Hirakawa_2014_lotja.yml → ...ax/studies/Soyano_Hirakawa_2014_lotja.yml
diff --git a/...x/wip_greg/done/Sugawara_Umehara_2019.yml → ...ine/max/studies/Sugawara_Umehara_2019.yml b/...x/wip_greg/done/Sugawara_Umehara_2019.yml → ...ine/max/studies/Sugawara_Umehara_2019.yml
diff --git a/Glycine/max/wip_marlene/Tang_Su_2017.yml → Glycine/max/studies/Tang_Su_2017.yml b/Glycine/max/wip_marlene/Tang_Su_2017.yml → Glycine/max/studies/Tang_Su_2017.yml
diff --git a/...ne/max/wip_marlene/done/Tian_Liu_2019.yml → Glycine/max/studies/Tian_Liu_2019.yml b/...ne/max/wip_marlene/done/Tian_Liu_2019.yml → Glycine/max/studies/Tian_Liu_2019.yml
diff --git a/...wei/done/Vadivel_McDowell_2021_traits.yml → ...ine/max/studies/Vadivel_McDowell_2021.yml b/...wei/done/Vadivel_McDowell_2021_traits.yml → ...ine/max/studies/Vadivel_McDowell_2021.yml
diff --git a/Glycine/max/wip_marlene/Wang_Guo_2021.yml → Glycine/max/studies/Wang_Guo_2021.yml b/Glycine/max/wip_marlene/Wang_Guo_2021.yml → Glycine/max/studies/Wang_Guo_2021.yml
diff --git a/Glycine/max/wip_will/done/Wang_Li_2021.yml → Glycine/max/studies/Wang_Li_2021.yml b/Glycine/max/wip_will/done/Wang_Li_2021.yml → Glycine/max/studies/Wang_Li_2021.yml
diff --git a/.../max/wip_marlene/done/Wang_Shine_2014.yml → Glycine/max/studies/Wang_Shine_2014.yml b/.../max/wip_marlene/done/Wang_Shine_2014.yml → Glycine/max/studies/Wang_Shine_2014.yml
diff --git a/Glycine/max/wip_marlene/Wang_Wang_2014.yml → Glycine/max/studies/Wang_Wang_2014.yml b/Glycine/max/wip_marlene/Wang_Wang_2014.yml → Glycine/max/studies/Wang_Wang_2014.yml
diff --git a/Glycine/max/wip_will/done/Wang_Wang_2015.yml → Glycine/max/studies/Wang_Wang_2015.yml b/Glycine/max/wip_will/done/Wang_Wang_2015.yml → Glycine/max/studies/Wang_Wang_2015.yml
diff --git a/Glycine/max/wip_marlene/Wang_Yang_2020.yml → Glycine/max/studies/Wang_Yang_2020.yml b/Glycine/max/wip_marlene/Wang_Yang_2020.yml → Glycine/max/studies/Wang_Yang_2020.yml
diff --git a/Glycine/max/wip_marlene/Wang_Yuan_2019.yml → Glycine/max/studies/Wang_Yuan_2019.yml b/Glycine/max/wip_marlene/Wang_Yuan_2019.yml → Glycine/max/studies/Wang_Yuan_2019.yml
diff --git a/Glycine/max/wip_will/done/Wu_Price_2014.yml → Glycine/max/studies/Wu_Price_2014.yml b/Glycine/max/wip_will/done/Wu_Price_2014.yml → Glycine/max/studies/Wu_Price_2014.yml
diff --git a/Glycine/max/wip_marlene/Yan_Wang_2018.yml → Glycine/max/studies/Yan_Wang_2018.yml b/Glycine/max/wip_marlene/Yan_Wang_2018.yml → Glycine/max/studies/Yan_Wang_2018.yml
diff --git a/.../max/wip_marlene/done/Yang_Zhang_2021.yml → Glycine/max/studies/Yang_Zhang_2021.yml b/.../max/wip_marlene/done/Yang_Zhang_2021.yml → Glycine/max/studies/Yang_Zhang_2021.yml
diff --git a/Glycine/max/wip_will/done/Yu_Chang_2019.yml → Glycine/max/studies/Yu_Chang_2019.yml b/Glycine/max/wip_will/done/Yu_Chang_2019.yml → Glycine/max/studies/Yu_Chang_2019.yml
diff --git a/Glycine/max/wip_marlene/Yu_Jin_2019.yml → Glycine/max/studies/Yu_Jin_2019.yml b/Glycine/max/wip_marlene/Yu_Jin_2019.yml → Glycine/max/studies/Yu_Jin_2019.yml
diff --git a/...ip_greg/done/supplemental/Yue_Li_2021.yml → Glycine/max/studies/Yue_Li_2021.yml b/...ip_greg/done/supplemental/Yue_Li_2021.yml → Glycine/max/studies/Yue_Li_2021.yml
diff --git a/...ine/max/wip_marlene/Zhang_Burton_2008.yml → Glycine/max/studies/Zhang_Burton_2008.yml b/...ine/max/wip_marlene/Zhang_Burton_2008.yml → Glycine/max/studies/Zhang_Burton_2008.yml
diff --git a/Glycine/max/wip_marlene/Zhang_Cheng_2021.yml → Glycine/max/studies/Zhang_Cheng_2021.yml b/Glycine/max/wip_marlene/Zhang_Cheng_2021.yml → Glycine/max/studies/Zhang_Cheng_2021.yml
diff --git a/...x/wip_marlene/done/Zhang_Goettel_2020.yml → Glycine/max/studies/Zhang_Goettel_2020.yml b/...x/wip_marlene/done/Zhang_Goettel_2020.yml → Glycine/max/studies/Zhang_Goettel_2020.yml
diff --git a/Glycine/max/wip_greg/done/Zhang_Luo_2013.yml → Glycine/max/studies/Zhang_Luo_2013.yml b/Glycine/max/wip_greg/done/Zhang_Luo_2013.yml → Glycine/max/studies/Zhang_Luo_2013.yml
diff --git a/Glycine/max/wip_marlene/Zhang_Sun_2017.yml → Glycine/max/studies/Zhang_Sun_2017.yml b/Glycine/max/wip_marlene/Zhang_Sun_2017.yml → Glycine/max/studies/Zhang_Sun_2017.yml
diff --git a/Glycine/max/wip_marlene/Zhang_Wang_2021.yml → Glycine/max/studies/Zhang_Wang_2021.yml b/Glycine/max/wip_marlene/Zhang_Wang_2021.yml → Glycine/max/studies/Zhang_Wang_2021.yml
diff --git a/Glycine/max/wip_will/Zhao_Bi_2019.yml → Glycine/max/studies/Zhao_Bi_2019.yml b/Glycine/max/wip_will/Zhao_Bi_2019.yml → Glycine/max/studies/Zhao_Bi_2019.yml
diff --git a/Glycine/max/wip_will/done/Zhao_Li_2018.yml → Glycine/max/studies/Zhao_Li_2018.yml b/Glycine/max/wip_will/done/Zhao_Li_2018.yml → Glycine/max/studies/Zhao_Li_2018.yml
diff --git a/...ine/max/wip_marlene/done/Zhou_He_2014.yml → Glycine/max/studies/Zhou_He_2014.yml b/...ine/max/wip_marlene/done/Zhou_He_2014.yml → Glycine/max/studies/Zhou_He_2014.yml
diff --git a/.../max/wip_marlene/Zhou_Lakhssassi_2021.yml → Glycine/max/studies/Zhou_Lakhssassi_2021.yml b/.../max/wip_marlene/Zhou_Lakhssassi_2021.yml → Glycine/max/studies/Zhou_Lakhssassi_2021.yml
diff --git a/Glycine/max/wip_marlene/Zhuang_Xue_2021.yml → Glycine/max/studies/Zhuang_Xue_2021.yml b/Glycine/max/wip_marlene/Zhuang_Xue_2021.yml → Glycine/max/studies/Zhuang_Xue_2021.yml
diff --git a/Glycine/max/wip_brandon/done/glyma_work.citations.txt b/Glycine/max/wip_brandon/done/glyma_work.citations.txt
diff --git a/Glycine/max/wip_jackie/To_delete_Campbell_Mani_2014.yml b/Glycine/max/wip_jackie/To_delete_Campbell_Mani_2014.yml
diff --git a/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.citations.txt b/Glycine/max/wip_steven/Oellrich_Walls_2015_glyma.citations.txt