editable organisms and dynamic links to homology repo

_layouts/organism-page.html

@@ -2,8 +2,22 @@
 layout: default
 ---
 <a class="btn btn-sm btn-pill btn-organism" style="float: right;" href="/browse/organisms.html">Organisms</a>
-<h1 id="title"> {{ page.title }}</h1>
-    <p>This is an organism page.</p>
+<h1 id="title"> {{ page.title }}
+  <a href="https://github.com/wikipathways/wikipathways.github.io/edit/main/_organisms/{{ page.slug }}.md"
+  target="_blank"> 
+    <span title="Edit organism profile" style="color: #666; font-size: 0.6em;">
+      <i class="fa fa-pencil"></i>
+    </span>
+  </a>
+</h1>
+<p>This is an organism page.</p>
+{% if page.homology %}
+  <p><em>Access hundreds of additional pathways in GPML format for this species 
+    inferred from {{ page.homology }} by homology mapping: 
+    <a href="https://github.com/wikipathways/wikipathways-homology/tree/main/pathways/{{ page.bridgedb-code }}" target="_blank">browse</a>
+     or <a href="https://github.com/wikipathways/wikipathways-homology/archive/refs/heads/main.zip" target="_blank">download</a> 
+     repository.</em></p>
+{% endif %}
     <ul class="nav nav-tabs">
       <li class="nav-item">
         <a class="nav-link active" data-toggle="tab" href="#gallery">Gallery</a>
@@ -13,7 +27,7 @@ <h1 id="title"> {{ page.title }}</h1>
       </li>
     </ul>
     {% assign sorted_pathways = site.pathways | where: "organisms", page.latin | sort: "title" %}
-    <b>This organism has {{sorted_pathways.size}} pathways:</b>
+    <b>This organism has {{sorted_pathways.size}} curated pathways:</b>
     <div class="tab-content" >
       <div class="tab-pane fade show active" id="gallery" role="tabpanel">
         <br/>

_organisms/arabidopsis.md

@@ -1,7 +1,10 @@
 ---
 common: "Arabidopsis"
 latin: "Arabidopsis thaliana"
+bridgedb-code: At
 ncbi: " 3702"
 title: "Arabidopsis pathways"
+description:
+homology: 
 group: "Plants"
 ---

_organisms/bsubtilis.md

@@ -1,7 +1,10 @@
 ---
 common: "B. subtilis"
 latin: "Bacillus subtilis"
+bridgedb-code: Bs
 ncbi: " 1423"
 title: "Bsubtilis pathways"
+description:
+homology: 
 group: "Bacteria"
 ---

_organisms/caulobacter_vibrioides.md

@@ -1,7 +1,10 @@
 ---
 common: "C. vibrioides"
 latin: "Caulobacter vibrioides"
+bridgedb-code: Cv
 ncbi: " 155892"
 title: "Caulobacter vibrioides pathways"
+description:
+homology: 
 group: "Bacteria"
 ---

_organisms/celegans.md

@@ -1,7 +1,10 @@
 ---
 common: "C. elegans"
 latin: "Caenorhabditis elegans"
+bridgedb-code: Ce
 ncbi: " 6239"
 title: "Celegans pathways"
+description:
+homology: 
 group: "Invertebrates"
 ---

_organisms/chicken.md

@@ -1,7 +1,10 @@
 ---
 common: "Chicken"
 latin: "Gallus gallus"
+bridgedb-code: Gg
 ncbi: " 9031"
 title: "Chicken pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/cow.md

@@ -1,7 +1,10 @@
 ---
 common: "Cow"
 latin: "Bos taurus"
+bridgedb-code: Bt
 ncbi: " 9913"
 title: "Cow pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/dog.md

@@ -1,7 +1,10 @@
 ---
 common: "Dog"
 latin: "Canis familiaris"
+bridgedb-code: Cf
 ncbi: " 9615"
 title: "Dog pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/ecoli.md

@@ -1,7 +1,10 @@
 ---
 common: "E. coli"
 latin: "Escherichia coli"
+bridgedb-code: Ec
 ncbi: "  562"
 title: "Ecoli pathways"
+description:
+homology: 
 group: "Bacteria"
 ---

_organisms/fruitfly.md

@@ -1,7 +1,10 @@
 ---
 common: "Fruitfly"
 latin: "Drosophila melanogaster"
+bridgedb-code: Dm
 ncbi: " 7227"
 title: "Fruitfly pathways"
+description:
+homology: 
 group: "Invertebrates"
 ---

_organisms/fusarium_graminearum.md

@@ -1,7 +1,10 @@
 ---
 common: "F. graminearum"
 latin: "Gibberella zeae"
+bridgedb-code: Gz
 ncbi: " 5518"
 title: "Fusarium graminearum pathways"
+description:
+homology: 
 group: "Fungi"
 ---

_organisms/horse.md

@@ -1,7 +1,10 @@
 ---
 common: "Horse"
 latin: "Equus caballus"
+bridgedb-code: Qc
 ncbi: " 9796"
 title: "Horse pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/human.md

@@ -1,7 +1,10 @@
 ---
 common: "Human"
 latin: "Homo sapiens"
+bridgedb-code: Hs
 ncbi: " 9606"
 title: "Human pathways"
+description:
+homology: 
 group: "Vertebrates"
 ---

_organisms/japanese_rice.md

@@ -1,7 +1,10 @@
 ---
 common: "Japanese rice"
 latin: "Oryza sativa"
+bridgedb-code: Os
 ncbi: " 4530"
 title: "Japanese rice pathways"
+description:
+homology: 
 group: "Plants"
 ---

_organisms/maize.md

@@ -1,7 +1,10 @@
 ---
 common: "Maize"
 latin: "Zea mays"
+bridgedb-code: Zm
 ncbi: " 4577"
 title: "Maize pathways"
+description:
+homology: 
 group: "Plants"
 ---

_organisms/malaria_parasite.md

@@ -1,7 +1,10 @@
 ---
 common: "Malaria parasite"
 latin: "Plasmodium falciparum"
+bridgedb-code: Pf
 ncbi: " 5833"
 title: "Malaria parasite pathways"
+description:
+homology: 
 group: "Parasites"
 ---

_organisms/mosquito.md

@@ -1,7 +1,10 @@
 ---
 common: "Mosquito"
 latin: "Anopheles gambiae"
+bridgedb-code: Ag
 ncbi: " 7165"
 title: "Mosquito pathways"
+description:
+homology: 
 group: "Invertebrates"
 ---

_organisms/mouse.md

@@ -1,7 +1,10 @@
 ---
 common: "Mouse"
 latin: "Mus musculus"
+bridgedb-code: Mm
 ncbi: "10090"
 title: "Mouse pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/mtuberculosis.md

@@ -1,7 +1,10 @@
 ---
 common: "Tuberculosis"
 latin: "Mycobacterium tuberculosis"
+bridgedb-code: Mx
 ncbi: " 1773"
 title: "Mtuberculosis pathways"
+description:
+homology: 
 group: "Bacteria"
 ---

_organisms/pig.md

@@ -1,7 +1,10 @@
 ---
 common: "Pig"
 latin: "Sus scrofa"
+bridgedb-code: Ss
 ncbi: " 9823"
 title: "Pig pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/rat.md

@@ -1,7 +1,10 @@
 ---
 common: "Rat"
 latin: "Rattus norvegicus"
+bridgedb-code: Rn
 ncbi: "10116"
 title: "Rat pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---

_organisms/tomato.md

@@ -1,7 +1,10 @@
 ---
 common: "Tomato"
 latin: "Solanum lycopersicum"
+bridgedb-code: Sl
 ncbi: " 4081"
 title: "Tomato pathways"
+description:
+homology: 
 group: "Plants"
 ---

_organisms/wine_grape.md

@@ -1,7 +1,10 @@
 ---
 common: "Wine grape"
 latin: "Vitis vinifera"
+bridgedb-code: Vv
 ncbi: "29760"
 title: "Wine grape pathways"
+description:
+homology: 
 group: "Plants"
 ---

_organisms/yeast.md

@@ -1,7 +1,10 @@
 ---
 common: "Yeast"
 latin: "Saccharomyces cerevisiae"
+bridgedb-code: Sc
 ncbi: " 4932"
 title: "Yeast pathways"
+description:
+homology: 
 group: "Fungi"
 ---

_organisms/zebrafish.md

@@ -1,7 +1,10 @@
 ---
 common: "Zebrafish"
 latin: "Danio rerio"
+bridgedb-code: Dr
 ncbi: " 7955"
 title: "Zebrafish pathways"
+description:
+homology: Human
 group: "Vertebrates"
 ---