Synch

.vscode/extensions.json

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+{
+	"recommendations": ["redhat.vscode-yaml"]
+}

.vscode/settings.json

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+{
+  "yaml.format.enable": true,
+  "yaml.format.proseWrap": "never",
+  "yaml.validate": true,
+  "yaml.hover": true,
+  "yaml.completion": true,
+  "yaml.schemas": {
+      "schema.json": "[A-Z]*/**/*.yml"
+  }
+}

Glycine/max/wip_marlene/Cai_Wang_2017.yml

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+---
+gene_symbols:
+  - GmTIR1a
+gene_symbol_long: Transport Inhibitor Response 1a
+gene_model_pub_name: Glyma02G152800
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G152800
+confidence: 5
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - RNAi knockdowns of TIR1a have reduced nodulation. Transgenic overexpression of TIR1a increases nodulation.
+phenotype_synopsis: TIR1a is an auxin receptor which positively regulates root growth and nodulation. TIR1a is strongly expressed in developing nodules, main and lateral roots, and especially in main root tips and lateral root primordia. Expression in roots decreases as nodulation progresses. TIR1a is upregulated by auxin.
+traits:
+  - entity_name: auxin receptor activity
+    entity: GO:0038198
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: root development
+    entity: GO:0048364
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: positive regulation of lateral root development
+    entity: GO:1901333
+references:
+  - citation: Cai, Wang et. al., 2017
+    doi: 10.1111/nph.14632
+    pmid: 28598036
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095
+---
+gene_symbols:
+  - GmTIR1b
+gene_symbol_long: Transport Inhibitor Response 1b
+gene_model_pub_name: Glyma10G021500
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G021500
+confidence: 4
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - RNAi knockdowns of TIR1b have reduced nodulation.
+phenotype_synopsis: TIR1b is an auxin receptor which positively regulates root growth and nodulation. TIR1b is most strongly expressed in developing nodules and main and lateral roots. Expression in roots decreases as nodulation progresses.
+traits:
+  - entity_name: auxin receptor activity
+    entity: GO:0038198
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: root development
+    entity: GO:0048364
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: positive regulation of lateral root development
+    entity: GO:1901333
+references:
+  - citation: Cai, Wang et. al., 2017
+    doi: 10.1111/nph.14632
+    pmid: 28598036
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095
+---
+gene_symbols:
+  - GmTIR1c
+gene_symbol_long: Transport Inhibitor Response 1c
+gene_model_pub_name: Glyma19G206800
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G206800
+confidence: 5
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - RNAi knockdowns of TIR1c have reduced nodulation. Transgenic overexpression of TIR1c increases nodulation.
+phenotype_synopsis: TIR1c is an auxin receptor which positively regulates root growth and nodulation. It is most strongly expressed in developing nodules and root meristems. Expression in roots is upregulated by Bradyrhizobium japonicum and auxin but downregulated by miR393d.
+traits:
+  - entity_name: auxin receptor activity
+    entity: GO:0038198
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: root development
+    entity: GO:0048364
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: regulation of root meristem growth
+    entity: GO:0010082
+  - relation_name: positively regulates
+    relation: RO:0002213
+references:
+  - citation: Cai, Wang et. al., 2017
+    doi: 10.1111/nph.14632
+    pmid: 28598036
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095
+---
+gene_symbols:
+  - GmTIR1d
+gene_symbol_long: Transport Inhibitor Response 1d
+gene_model_pub_name: Glyma03G209400
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G209400
+confidence: 4
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - RNAi knockdowns of TIR1d have reduced nodulation.
+phenotype_synopsis: TIR1d is an auxin receptor which positively regulates root growth and nodulation. It is most strongly expressed in developing nodules, main and lateral root tips, and lateral root primordia.
+traits:
+  - entity_name: auxin receptor activity
+    entity: GO:0038198
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: root development
+    entity: GO:0048364
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: positive regulation of lateral root development
+    entity: GO:1901333
+references:
+  - citation: Cai, Wang et. al., 2017
+    doi: 10.1111/nph.14632
+    pmid: 28598036
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095
+---
+gene_symbols:
+  - GmAFB3a
+gene_symbol_long: Auxin-signalling F-Box 3a
+gene_model_pub_name: Glyma19G100200
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G100200
+confidence: 5
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - RNAi knockdowns of AFB3a have reduced nodulation. Transgenic overexpression of AFB3a did not increase nodulation.
+phenotype_synopsis: AFB3a is an auxin receptor which has a minor role in the positive regulation of root growth and nodulation. It is most strongly expressed in developing nodules, main and lateral roots, and especially in main root tips and lateral root primordia. AFB3a is upregulated by presence of auxin but downregulated by miR393d.
+traits:
+  - entity_name: auxin receptor activity
+    entity: GO:0038198
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: root development
+    entity: GO:0048364
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: positive regulation of lateral root development
+    entity: GO:1901333
+references:
+  - citation: Cai, Wang et. al., 2017
+    doi: 10.1111/nph.14632
+    pmid: 28598036
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095
+---
+gene_symbols:
+  - GmAFB3b
+gene_symbol_long: Auxin-signalling F-Box 3b
+gene_model_pub_name: Glyma16G050500
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G050500
+confidence: 4
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - RNAi knockdowns of AFB3b have reduced nodulation.
+phenotype_synopsis: AFB3a is an auxin receptor. Expression of AFB3b is barely detectable in roots and developing nodules. It is likely involved in shoot development rather than in root growth and nodulation.
+traits:
+  - entity_name: auxin receptor activity
+    entity: GO:0038198
+  - relation_name: positively regulates
+    relation: RO:0002213
+  - entity_name: shoot system development
+    entity: GO:0048367
+references:
+  - citation: Cai, Wang et. al., 2017
+    doi: 10.1111/nph.14632
+    pmid: 28598036
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095

Glycine/max/wip_marlene/Chen_Wang_2016.yml

@@ -14,7 +14,7 @@ traits:
   - entity_name: regulation of triglyceride biosynthetic process
     entity: GO:0010866
   - entity_name: seed development
-    entity: GO:0048316 
+    entity: GO:0048316
 references:
   - citation: Chen, Wang et. al., 2016
     doi: 10.1038/srep28541
@@ -28,23 +28,23 @@ references:
     doi: 10.1016/j.csbj.2022.06.014
     pmid: 35782726
 ---
- gene_symbols:
-   - GmDGAT2D
- gene_symbol_long: DiacylGlycerol AcylTransferase 2D
- gene_model_pub_name: Glyma.01G156000
- gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G156000 
- confidence: 3
- curators:
+gene_symbols:
+  - GmDGAT2D
+gene_symbol_long: DiacylGlycerol AcylTransferase 2D
+gene_model_pub_name: Glyma.01G156000
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G156000
+confidence: 3
+curators:
   - Marlene Dorneich-Hayes
- comments:
+comments:
   - Overexpression enhances triacylglycerol biosynthesis in flower tissues. Upregulated by temperature stress, downregulated by insect bites and jasmonate. It produces similar results when transformed into other species.
- phenotype_synopsis: DGAT2D controls synthesis of many triacylglycerols, using 18:1 and 18:2 acyl CoA as acyl donors. Oil accumulates most in flowers.
- traits:
-   - entity_name: regulation of triglyceride biosynthetic process
-     entity: GO:0010866
-   - entity_name: seed development
-     entity: GO:0048316  
- references:
-   - citation: Chen, Wang et. al., 2016
-     doi: PMC4921965
-     pmid: 27345221
+phenotype_synopsis: DGAT2D controls synthesis of many triacylglycerols, using 18:1 and 18:2 acyl CoA as acyl donors. Oil accumulates most in flowers.
+traits:
+  - entity_name: regulation of triglyceride biosynthetic process
+    entity: GO:0010866
+  - entity_name: seed development
+    entity: GO:0048316
+references:
+  - citation: Chen, Wang et. al., 2016
+    doi: PMC4921965
+    pmid: 27345221

Glycine/max/wip_marlene/Ge_Yu_2016.yml

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+---
+gene_symbols:
+  - GmBS1
+gene_symbol_long: Big Seeds 1
+gene_model_pub_name: Glyma10g38970
+gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma10g38970
+confidence: 4
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - GmBS1 was silenced in transgenic soy plants.
+phenotype_synopsis: GmBS1 affects the size of seeds, seed pods, and leaves. Downregulation of BS1 increases seed size, weight, and amino acid content.
+traits:
+  - entity_name: regulation of seed growth
+    entity: GO:0080113
+  - entity_name: seed development
+    entity: GO:0048316
+  - entity_name: seed size
+    entity: TO:0000391
+  - entity_name: fat and essential oil content
+    entity: TO:0000604
+references:
+  - citation: Ge, Yu et. al., 2016
+    doi: 10.1073/pnas.1611763113
+    pmid: 27791139
+  - citation: Zuo, Ikram et. al., 2022
+    doi: 10.1016/j.csbj.2022.06.014
+    pmid: 35782726

Glycine/max/wip_marlene/Indrasumunar_Searle_2012.yml

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+---
+gene_symbols:
+  - GmNFR1α
+gene_symbol_long: Nod Factor Receptor 1α
+gene_model_pub_name: Glyma02G270800
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G270800
+confidence: 5
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - Mutants lacking NFR1α don't form nodules. Transgenic overexpression increased the number of nodules per plant and allowed plants to form nodules in unfavorable conditions.
+phenotype_synopsis: NFR1α codes for a receptor kinase which controls nodule number.
+traits:
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+  - relation_name: positively regulates
+    relation: RO:0002213
+references:
+  - citation: Indrasumunar, Searle et. al., 2012
+    doi: 10.1111/j.1365-313X.2010.04398.x
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095
+---
+gene_symbols:
+  - GmNFR1β
+gene_symbol_long: Nod Factor Receptor 1β
+gene_model_pub_name: Glyma14G046200
+gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G046200
+confidence: 5
+curators:
+  - Marlene Dorneich-Hayes
+comments:
+  - Mutants with functional NFR1β but nonfunctional NFR1α have very minimal nodulation. Overexpression of NFR1β did not increase nodule number.
+phenotype_synopsis: NFR1β codes for a redundant receptor kinase. Its mRNA transcripts are unstable and its expression is not sufficient to induce a healthy level of nodulation.
+traits:
+  - entity_name: regulation of biological process involved in symbiotic interaction
+    entity: GO:0043903
+  - entity_name: nodulation
+    entity: GO:0009877
+references:
+  - citation: Indrasumunar, Searle et. al., 2012
+    doi: 10.1111/j.1365-313X.2010.04398.x
+  - citation: Yang, Lan et. al., 2022
+    doi: 10.1111/jipb.13207
+    pmid: 34962095