Correct the collection identifiers for three sequence_feature collect…

…ions and fix non-UTF8 characters in gene_functions collections

Glycine/max/sequence_feature/Wm82.gnm2.trnsc.Wang_Duan_2024/README.Wm82.gnm2.trnsc.Wang_Duan_2024.yml

@@ -1,5 +1,5 @@
 ---
-identifier: Wm82.gnm4.trnsc.Wang_Duan_2024
+identifier: Wm82.gnm2.trnsc.Wang_Duan_2024
 
 provenance: "The files in this directory originated from the lab of Dr. Jianxin Ma, Purdue Univeristy. Files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the SoyBase and LegumeInfo projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase and LegumeInfo projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."
 

Glycine/max/sequence_feature/Wm82.gnm4.atlas_ctACRs.Zhang_Schmitz_2024/README.Wm82.gnm4.atlas_ctACRs.Zhang_Schmitz_2024.yml

@@ -1,5 +1,5 @@
 ---
-identifier: Wm82.gnm4.atlas_ACRs.Zhang_Schmitz_2024
+identifier: Wm82.gnm4.atlas_ctACRs.Zhang_Schmitz_2024
 
 provenance: "The files in this directory originated from the lab of Dr. Bob Schmitz, Univeristy of Georgia. Files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the SoyBase and LegumeInfo projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase and LegumeInfo projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."
 

Glycine/max/sequence_feature/Wm82.gnm4.atlas_ctACRs_motifs.Zhang_Schmitz_2024/README.Wm82.gnm4.atlas_ctACRs_motifs.Zhang_Schmitz_2024.yml

@@ -1,5 +1,5 @@
 ---
-identifier: Wm82.gnm4.atlas_ACRs.Zhang_Schmitz_2024
+identifier: Wm82.gnm4.atlas_ctACRs_motifs.Zhang_Schmitz_2024
 
 provenance: "The files in this directory originated from the lab of Dr. Bob Schmitz, Univeristy of Georgia. Files in this present directory are derived, and may have changes, as noted below. The files here are held as part of the SoyBase and LegumeInfo projects, and are made available here for the purpose of reproducibility of analyses at these sites (e.g. gene family alignments and phylogenies, genome browsers, etc.) and for further use by researchers, as that research extends other analyses at the SoyBase and LegumeInfo projects. If you are conducting research on large-scale data sets for this species, please consider retrieving the data from the primary repositories. If you use the data in the present directory, please 1) please cite the data appropriately - generally referring to the original publications for this data; and if you make use of any significant modifications in the files (noted below under Transformations where applicable), then please also cite the respective database project(s) related to this directory."
 

Medicago/truncatula/gene_functions/medtr.traits.yml

@@ -165,36 +165,6 @@ references:
 
 ## DOCUMENT 6 ##
 ---
-scientific_name: Medicago truncatula
-gene_symbols:
-  - MtDMI2
-gene_symbol_long: Doesnt Make Infections
-gene_model_pub_name: Medtr5g030920
-gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920
-confidence: 5
-curators:
-  - Marlene Dorneich-Hayes
-comments:
-  - SYMRK is activated in root hairs by phosphorylation in response to the perception of NOD factors
-  - SYMRK-EGFP (enhanced green fluorescence protein) is endocytosed from the plasma membrane to intracellular puncta and affects the SYMRK signaling pathway
-  - SYMRK-suppressed mutants can't form infection threads and therefore can't form functional nodules, though they do form pseudo-nodules lacking symbiotic bacteria and fungi
-  - SYMRK overexpressing mutants form non-functional nodules without rhizobia
-phenotype_synopsis: SYMRK is necessary for nodule organogenesis.
-traits:
-  - entity_name: bioloical process involved in symbiotic interaction
-    entity: GO:0044403
-  - entity_name: kinase activity
-    entity: GO:0016301
-  - entity_name: positive regulation of receptor-mediated endocytosis
-    entity: GO:0048260
-references:
-  - citation: Dávila-Delgado, Flores-Canúl, et al., 2023
-    doi: 10.1007/s00425-023-04116-0
-    pmid: 36928335
-
-
-## DOCUMENT 7 ##
----
 gene_symbols:
   - MtCCD1
 gene_symbol_long: carotenoid cleavage dioxygenase 1
@@ -218,7 +188,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 8 ##
+## DOCUMENT 7 ##
 ---
 gene_symbols:
   - CPK3
@@ -245,7 +215,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 9 ##
+## DOCUMENT 8 ##
 ---
 gene_symbols:
   - bHLH1
@@ -276,7 +246,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 10 ##
+## DOCUMENT 9 ##
 ---
 gene_symbols:
   - LYK3
@@ -303,7 +273,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 11 ##
+## DOCUMENT 10 ##
 ---
 gene_symbols:
   - LYK4
@@ -330,7 +300,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 12 ##
+## DOCUMENT 11 ##
 ---
 gene_symbols:
   - MtAOC
@@ -355,7 +325,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 13 ##
+## DOCUMENT 12 ##
 ---
 gene_symbols:
   - CDPK1
@@ -388,7 +358,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 14 ##
+## DOCUMENT 13 ##
 ---
 gene_symbols:
   - PALM1
@@ -419,7 +389,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 15 ##
+## DOCUMENT 14 ##
 ---
 gene_symbols:
   - ANS
@@ -446,7 +416,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 16 ##
+## DOCUMENT 15 ##
 ---
 gene_symbols:
   - nork
@@ -473,7 +443,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 17 ##
+## DOCUMENT 16 ##
 ---
 gene_symbols:
   - CDC16
@@ -506,7 +476,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 18 ##
+## DOCUMENT 17 ##
 ---
 gene_symbols:
   - LIN
@@ -529,7 +499,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 19 ##
+## DOCUMENT 18 ##
 ---
 gene_symbols:
   - SUNN
@@ -560,7 +530,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 20 ##
+## DOCUMENT 19 ##
 ---
 gene_symbols:
   - FTa1
@@ -583,7 +553,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 21 ##
+## DOCUMENT 20 ##
 ---
 gene_symbols:
   - FTc
@@ -606,7 +576,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 22 ##
+## DOCUMENT 21 ##
 ---
 gene_symbols:
   - CYCLOPS
@@ -630,7 +600,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 23 ##
+## DOCUMENT 22 ##
 ---
 gene_symbols:
   - DMI1
@@ -657,7 +627,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 24 ##
+## DOCUMENT 23 ##
 ---
 gene_symbols:
   - DMI3
@@ -684,7 +654,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 25 ##
+## DOCUMENT 24 ##
 ---
 gene_symbols:
   - MtNAP1
@@ -717,7 +687,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 26 ##
+## DOCUMENT 25 ##
 ---
 gene_symbols:
   - CBF4
@@ -746,7 +716,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 27 ##
+## DOCUMENT 26 ##
 ---
 gene_symbols:
   - FCL1
@@ -777,7 +747,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 28 ##
+## DOCUMENT 27 ##
 ---
 gene_symbols:
   - VPY
@@ -804,7 +774,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 29 ##
+## DOCUMENT 28 ##
 ---
 gene_symbols:
   - FLOT2
@@ -839,7 +809,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 30 ##
+## DOCUMENT 29 ##
 ---
 gene_symbols:
   - FLOT3
@@ -866,7 +836,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 31 ##
+## DOCUMENT 30 ##
 ---
 gene_symbols:
   - FLOT4
@@ -895,7 +865,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 32 ##
+## DOCUMENT 31 ##
 ---
 gene_symbols:
   - NFP
@@ -918,7 +888,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 33 ##
+## DOCUMENT 32 ##
 ---
 gene_symbols:
   - GT3
@@ -952,7 +922,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 34 ##
+## DOCUMENT 33 ##
 ---
 gene_symbols:
   - chitIII-3
@@ -975,7 +945,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 35 ##
+## DOCUMENT 34 ##
 ---
 gene_symbols:
   - MtCre1
@@ -1008,7 +978,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 36 ##
+## DOCUMENT 35 ##
 ---
 gene_symbols:
   - ERN1
@@ -1031,7 +1001,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 37 ##
+## DOCUMENT 36 ##
 ---
 gene_symbols:
   - ERN2
@@ -1054,7 +1024,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 38 ##
+## DOCUMENT 37 ##
 ---
 gene_symbols:
   - EXPA
@@ -1077,7 +1047,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 39 ##
+## DOCUMENT 38 ##
 ---
 gene_symbols:
   - NIN
@@ -1100,7 +1070,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 40 ##
+## DOCUMENT 39 ##
 ---
 gene_symbols:
   - NRT1.3
@@ -1123,7 +1093,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 41 ##
+## DOCUMENT 40 ##
 ---
 gene_symbols:
   - NSP1
@@ -1146,7 +1116,7 @@ references:
     pmid: 25774204
 
 
-## DOCUMENT 42 ##
+## DOCUMENT 41 ##
 ---
 gene_symbols:
   - RR4
@@ -1166,7 +1136,7 @@ references:
     pmid: 26672071
 
 
-## DOCUMENT 43 ##
+## DOCUMENT 42 ##
 ---
 scientific_name: Medicago truncatula
 gene_symbols:
@@ -1190,7 +1160,7 @@ references:
     pmid: 33606812
 
 
-## DOCUMENT 44 ##
+## DOCUMENT 43 ##
 ---
 gene_symbols:
   - EIN2