New GWAS & QTL Trait Terms page (#91)

* Implement Trait Terms page, updating tools.yml and add trait_terms.yml and tools/trait_list

* Restructure trait terms, displaying them in phonebook-like wrapped columns.

---------

Co-authored-by: StevenCannon-USDA <[email protected]>

_data/tools.yml

@@ -67,6 +67,10 @@
   description: "Search for trait associations"
   name: "Trait Search Tool"
   url: "/tools/search/trait.html"
+- category: "Search"
+  description: "Trait terms used in soybean GWAS and QTL studies; links to the trait association search tool."
+  name: "Trait Terms"
+  url: "/tools/trait_list"
 - category: "Search"
   description: "Search for genes, proteins, metabolites or pathways"
   name: "SoyCyc"
@@ -79,28 +83,4 @@
   description: "Soybean parentage and pedigrees"
   name: "Parentage"
   url: "/tools/parentage"
-#   category: "FIXME"
-#   description: Description
-#   name: Maps
-#   url: "#"
-# -
-#   category: "FIXME"
-#   description: Description
-#   name: "QTL Search"
-#   url: "#"
-# -
-#   category: "FIXME"
-#   description: Description
-#   name: "Gene Search"
-#   url: "#"
-# -
-#   category: "FIXME"
-#   description: Description
-#   name: "Protein Domains"
-#   url: "#"
-# -
-#   category: "Search sequences and features against sequence databases"
-#   description: Description
-#   name: "Keyword Search"
-#   url: "#"
 

_data/trait_terms/abiotic.tsv

@@ -0,0 +1,5 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Canopy wilt	_	QTL	Flooding yield index	_	QTL	R/V photo-thermal sensitivity	_	QTL
+Drought index	_	QTL	Leaf Damage	_	QTL	Salt tolerance	_	QTL
+Drought tolerance	_	QTL	mqCanopy wilt	_	QTL			
+Flood tolerance	_	QTL	Plant damage	_	QTL			

_data/trait_terms/agronomic.tsv

@@ -0,0 +1,6 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Row spacing response	_	QTL	Stem diameter	GWAS	QTL	Stem weight	_	QTL
+Shoot fresh to dry weight ratio	_	QTL	Stem length	_	QTL	Total growth duration	_	QTL
+Shoot length	_	QTL	Stem shape	GWAS	_	Trailing growth	_	QTL
+Shoot weight	_	QTL	Stem strength	_	QTL	Vegetative period	_	QTL
+Sprout yield	_	QTL	Stem termination type	GWAS	_	WUE	_	QTL

_data/trait_terms/agronomic_other.tsv

@@ -0,0 +1,7 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Hilum color	GWAS	_	P aquisition efficiency	_	QTL	Pod color	_	QTL
+Iron deficiency chlorosis	GWAS	_	P concentration	_	QTL	Pubescence color	GWAS	_
+Leaflet chlorophyll	GWAS	QTL	P use efficiency	_	QTL	Pubescence density	_	QTL
+Leaflet N	_	QTL	Petiole color	_	QTL	Pubescence length	_	QTL
+Leaflet P	_	QTL	pH sensitivity	_	QTL	Root P	_	QTL
+Net photosyn rate	_	QTL	Plant P	_	QTL	Shoot P	_	QTL

_data/trait_terms/agronomic_reproductive.tsv

@@ -0,0 +1,7 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+cqR8 Full maturity	_	QTL	Photoperiod insensitivity	_	QTL	Pods per node	_	QTL
+Days to flower	GWAS	_	Pod dehiscence	_	QTL	R8 full maturity	GWAS	_
+First flower	GWAS	QTL	Pod maturity	_	QTL	Reproductive period	GWAS	QTL
+Flower color	GWAS	QTL	Pod number	GWAS	QTL	Reproductive period photo-thermal sensitivity	_	QTL
+Flower form	_	QTL	Pod shattering	GWAS	_	Reproductive stage length	GWAS	QTL
+Flower number	_	QTL	Pod weight	_	QTL	Reproductive to vegetative period ratio	_	QTL

_data/trait_terms/agronomic_root.tsv

@@ -0,0 +1,8 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Lateral root size	_	QTL	Root area development	_	QTL	Root morphology	_	QTL
+Node number	GWAS	QTL	Root density	_	QTL	Root nodule number	_	QTL
+Nodule number	_	QTL	Root diameter	_	QTL	Root nodule weight	_	QTL
+Nodule size	_	QTL	Root diameter change	_	QTL	Root to Shoot weight ratio	_	QTL
+Nodule weight	_	QTL	Root length	_	QTL	Root volume	_	QTL
+Nodule weight per plant	_	QTL	Root length development	_	QTL	Root weight	_	QTL
+Root area	_	QTL	Root length plus Rhizobia	_	QTL	Root width	_	QTL

_data/trait_terms/agronomic_structure.tsv

@@ -0,0 +1,8 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Branch number	GWAS	_	Internode length	GWAS	QTL	Lodging	GWAS	QTL
+Branching	_	QTL	Leaflet area	GWAS	QTL	mqPlant height	_	QTL
+Canopy height	_	QTL	Leaflet ash	_	QTL	Plant height	GWAS	QTL
+Canopy width	GWAS	QTL	Leaflet length	GWAS	QTL	Plant height to Lodging ratio	_	QTL
+Hypocotyl length	_	QTL	Leaflet shape	GWAS	QTL	Plant weight	_	QTL
+Hypocotyl weight	_	QTL	Leaflet weight	_	QTL			
+Interbranch length	GWAS	_	Leaflet width	GWAS	QTL			

_data/trait_terms/biotic.tsv

@@ -0,0 +1,12 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Asian Soybean Rust	_	QTL	Japanese beetle resistance	_	QTL	SCN	GWAS	QTL
+Bean pyralid	_	QTL	Jav root-knot nematode	_	QTL	SDS	_	QTL
+BSR	_	QTL	Necrosis	_	QTL	SDS disease incidence	_	QTL
+Common cutworm	_	QTL	Peanut root-knot nematode	_	QTL	SDS disease index	_	QTL
+Corn earworm	_	QTL	Phomopsis seed decay	_	QTL	SDS dry matter retention	GWAS	_
+cqSCN	_	QTL	Phytoph	_	QTL	SDS root retention	GWAS	_
+cqSDS	_	QTL	Pod borer	_	QTL	Southern root-knot nematode	_	QTL
+Foxglove aphid	_	QTL	Rag	_	QTL	Soybean mosaic virus	GWAS	QTL
+Fusarium lesion length	_	QTL	Rhizoc root and hypocot rota	_	QTL	Tobacco ring spot virus	_	QTL
+Fusarium root rot	_	QTL	Rhizoc root and hypocot rotb	_	QTL	Tobacco ringspot virus	GWAS	_
+Indo soy dwarf virus	_	QTL	Sclero	GWAS	QTL			

_data/trait_terms/other.tsv

@@ -0,0 +1,8 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Acid detergent fiber	_	QTL	Chlorophyll flourescence ETo/TRo	_	QTL	Leaflet trigonelline	_	QTL
+Acid phosphatase activity	_	QTL	Chlorophyll flourescence PIabs	_	QTL	Neutral detergent fiber	_	QTL
+Al tolerance	_	QTL	Chlorophyll flourescence REo/Eto	_	QTL	Somatic emb per explant	_	QTL
+Carbon isotope discrimination	_	QTL	Chlorophyll flourescence TRo/ABS	_	QTL	Somatic embryogen effic	_	QTL
+Cellwall polysacch composition	_	QTL	Chlorosis	_	QTL	Somatic embryogenesis	_	QTL
+Chlorimuron sensitivity	_	QTL	Fe effic	_	QTL			
+Chlorophyll flourescence ABS/RC	_	QTL	Leaf carotenoid content	GWAS				

_data/trait_terms/seed_agronomy.tsv

@@ -0,0 +1,4 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Seed abortion	_	QTL	Seed N at R7	_	QTL	Seed winter hardiness	_	QTL
+Seed N at R5	_	QTL	Seed set	GWAS	QTL			
+Seed N at R6	_	QTL	Seed viability	_	QTL			

_data/trait_terms/seed_composition.tsv

@@ -0,0 +1,23 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+cqSeed agglutinin	_	QTL	Seed daidzein	_	QTL	Seed oil	GWAS	QTL
+cqSeed oil	_	QTL	Seed fucose	_	QTL	Seed oil to protein ratio	GWAS	QTL
+cqSeed phytate	_	QTL	Seed galactose	_	QTL	Seed oleic	_	QTL
+cqSeed protein	_	QTL	Seed genistein	_	QTL	Seed oligosaccharide	_	QTL
+Crude fat	_	QTL	Seed Glu	_	QTL	Seed palmitic	_	QTL
+Crude protein	_	QTL	Seed glucose	_	QTL	Seed palmitic plus stearic	_	QTL
+mqSeed oil	_	QTL	Seed Gly	_	QTL	Seed pectin	_	QTL
+Seed acidic fraction	_	QTL	Seed glycinin	_	QTL	Seed Phe	_	QTL
+Seed agglutinin	_	QTL	Seed glycinin plus beta-conglycinin	_	QTL	Seed phytate	_	QTL
+Seed Ala	_	QTL	Seed glycinin to beta-conglycinin ratio	_	QTL	Seed Pro	_	QTL
+Seed alpha-linolenic acid	GWAS	_	Seed glycitein	_	QTL	Seed protein	GWAS	QTL
+Seed amino acids	GWAS	_	Seed His	_	QTL	Seed Ser	_	QTL
+Seed anthocyanin content	_	QTL	Seed Ile	_	QTL	Seed starch	_	QTL
+Seed antioxidant content	_	QTL	Seed isoflavone	GWAS	QTL	Seed stearic	GWAS	QTL
+Seed arabinose plus galactose	_	QTL	Seed Leu	_	QTL	Seed sucrose	_	QTL
+Seed Arg	_	QTL	Seed linoleic	_	QTL	Seed Thr	_	QTL
+Seed Asp	_	QTL	Seed linolenic	_	QTL	Seed tocopherol	_	QTL
+Seed basic fraction	_	QTL	Seed long-chain fatty acid	GWAS	_	Seed total isoflavone	_	QTL
+Seed cadmium	_	QTL	Seed Lys	_	QTL	Seed Trp	_	QTL
+Seed calcium	_	QTL	Seed Met	_	QTL	Seed Tyr	_	QTL
+Seed conglycinin	_	QTL	Seed Met plus Cys	_	QTL	Seed Val	_	QTL
+Seed Cys	_	QTL	Seed nickel	_	QTL			

_data/trait_terms/seed_structure.tsv

@@ -0,0 +1,8 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+Seed coat color	GWAS	QTL	Seed height	GWAS	QTL	Seed volume	GWAS	QTL
+Seed coat cracking	_	QTL	Seed height to width ratio	_	QTL	Seed weight	GWAS	QTL
+Seed coat hardness	_	QTL	Seed length	_	QTL	Seed width	_	QTL
+Seed coat luster	GWAS	_	Seed length to height ratio	_	QTL	Seed width to height ratio	GWAS	_
+Seed fill	_	QTL	Seed length to thickness ratio	GWAS	QTL	Seed width to thickness ratio	_	QTL
+Seed fragrance	_	QTL	Seed length to width ratio	_	QTL			
+Seed hardness	_	QTL	Seed thickness	GWAS	QTL			

_data/trait_terms/seed_yield.tsv

@@ -0,0 +1,5 @@
+Term.1	GWAS.1	QTL.1	Term.2	GWAS.2	QTL.2	Term.3	GWAS.3	QTL.3
+cqSeed weight	_	QTL	Seed yield	GWAS	QTL	Total seed number	GWAS	_
+cqSeed yield	_	QTL	Seed yield to Plant height ratio	_	QTL			
+Seed number	_	QTL	Seed yield to weight ratio	_	QTL			
+Seed weight per plant	_	QTL	Seeds per plant	GWAS	QTL			

_data/trait_terms/trait_categories.yml

@@ -0,0 +1,13 @@
+---
+- abiotic
+- agronomic
+- agronomic_other
+- agronomic_reproductive
+- agronomic_root
+- agronomic_structure
+- biotic
+- other
+- seed_agronomy
+- seed_composition
+- seed_structure
+- seed_yield

tools/trait_list/index.html

@@ -0,0 +1,48 @@
+---
+title: Trait List
+sitemap: trait_list 
+layout: default
+---
+{% assign qtl_base = '/tools/search/trait.html?page=1&genus=Glycine&type=QTL&traits=' %}
+{% assign gwas_base = '/tools/search/trait.html?page=1&genus=Glycine&type=GWAS&traits=' %}
+{% assign separator = "     " %}
+
+<h2>Genetic trait terms and categories for soybean</h2>
+
+<p> 
+The traits below have been used in soybean GWAS and/or QTL studies.<br> 
+Click on a "GWAS" or "QTL" link to populate a query in the <a href="/tools/search/trait.html">Trait Association Search</a> page.
+</p>
+
+{% for trait_category in site.data.trait_terms.trait_categories %}
+
+  {% assign words = trait_category | split: '_' %}
+  {% capture display_trait %}
+  {% for word in words %} {{ word | capitalize }} {% endfor %}{% endcapture %}
+  <b>{{ display_trait }}</b>
+
+  <table>
+    {% for row in site.data.trait_terms[trait_category] %}
+      {% tablerow pair in row %}
+        {% if pair[0] contains "Term" %}
+          {{ separator }} {{ pair[1] }}
+          {% assign search_term = pair[1] | url_encode %}
+        {% elsif pair[0] contains "G" %}
+          {% if pair[1] == "GWAS" %}
+            <a href="{{- gwas_base | append: search_term -}}"> &nbsp; GWAS &nbsp; </a>
+          {% else %}
+            {{ separator }} -
+          {% endif %}
+        {% elsif pair[0] contains "Q" %}
+          {% if pair[1] == "QTL" %}
+            <a href="{{- qtl_base | append: search_term -}}"> QTL &nbsp; </a>
+          {% else %}
+            {{ separator }} -
+          {% endif %}
+        {% endif %}
+      {% endtablerow %}
+    {% endfor %}
+  </table>
+  <br>
+
+{% endfor %}