refactor (networks/sp): reordered

datasci4health · May 28, 2024 · 229da67 · 229da67
1 parent 426ed06
commit 229da67
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diff --git a/networks/species-pathways/sparql/species-pathways-proteins.md b/networks/species-pathways/sparql/species-pathways-proteins.md
@@ -4,88 +4,6 @@
 
 * UniProt (better): https://sparql.uniprot.org/sparql
 
-# Wnt signaling pathway (GO:0016055)
-
-* URI: https://amigo.geneontology.org/amigo/term/GO:0016055
-
-## All superclasses of the pathway 
-
-~~~sparql
-PREFIX obo:  <http://purl.obolibrary.org/obo/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-SELECT DISTINCT ?super ?labels
-WHERE {
-  obo:GO_0016055 rdfs:subClassOf ?super .
-  ?super rdfs:label ?labels .
-}
-~~~
-
-## All subclasses of the pathway
-
-~~~sparql
-PREFIX obo:  <http://purl.obolibrary.org/obo/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-SELECT DISTINCT ?sub ?label
-WHERE {
-  ?sub rdfs:subClassOf obo:GO_0016055 .
-  ?sub rdfs:label ?label .
-}
-~~~
-
-## All properties and objects related to the pathway
-
-~~~sparql
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-
-SELECT DISTINCT ?property ?object
-WHERE {
-  obo:GO_0016055 ?property ?object .
-}
-~~~
-
-## All subjects and properties related to the pathway
-
-~~~sparql
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-
-SELECT DISTINCT ?subject ?property
-WHERE {
-   ?subject ?property obo:GO_0016055 .
-}
-~~~
-
-## All subjects (URI and label) classified with the pathway
-
-~~~sparql
-PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX obo:     <http://purl.obolibrary.org/obo/>
-PREFIX up_core: <http://purl.uniprot.org/core/>
-
-SELECT DISTINCT ?uri ?label
-WHERE {
-  ?uri up_core:classifiedWith obo:GO_0016055 .
-  ?uri rdfs:label ?label .
-}
-~~~
-
-## All proteins (URI and label) classified with the pathway
-
-~~~sparql
-PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX obo:     <http://purl.obolibrary.org/obo/>
-PREFIX up_core: <http://purl.uniprot.org/core/>
-
-SELECT DISTINCT ?protein ?label
-WHERE {
-  ?protein up_core:classifiedWith obo:GO_0016055 .
-  ?protein rdf:type up_core:Protein .
-  ?protein rdfs:label ?label .
-}
-~~~
-
 # PRICKLE2 - Prickle-like protein 2 (UniProtKB:Q7Z3G6)
 
 * URI: http://purl.uniprot.org/uniprot/Q7Z3G6
@@ -151,7 +69,7 @@ http://purl.obolibrary.org/obo/GO_0060071,"Wnt signaling pathway, planar cell po
 PREFIX up:      <http://purl.uniprot.org/uniprot/>
 PREFIX up_core: <http://purl.uniprot.org/core/>
 
-SELECT DISTINCT ?protein ?taxon ?scientific_name
+SELECT DISTINCT ?taxon ?scientific_name
 WHERE {
   up:Q7Z3G6 up_core:organism ?taxon .
   ?taxon up_core:scientificName ?scientific_name .
@@ -224,6 +142,86 @@ WHERE {
 
 # Wnt signaling pathway (GO:0016055)
 
+* URI: https://amigo.geneontology.org/amigo/term/GO:0016055
+
+## All superclasses of the pathway 
+
+~~~sparql
+PREFIX obo:  <http://purl.obolibrary.org/obo/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?super ?labels
+WHERE {
+  obo:GO_0016055 rdfs:subClassOf ?super .
+  ?super rdfs:label ?labels .
+}
+~~~
+
+## All subclasses of the pathway
+
+~~~sparql
+PREFIX obo:  <http://purl.obolibrary.org/obo/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?sub ?label
+WHERE {
+  ?sub rdfs:subClassOf obo:GO_0016055 .
+  ?sub rdfs:label ?label .
+}
+~~~
+
+## All properties and objects related to the pathway
+
+~~~sparql
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT DISTINCT ?property ?object
+WHERE {
+  obo:GO_0016055 ?property ?object .
+}
+~~~
+
+## All subjects and properties related to the pathway
+
+~~~sparql
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT DISTINCT ?subject ?property
+WHERE {
+   ?subject ?property obo:GO_0016055 .
+}
+~~~
+
+## All subjects (URI and label) classified with the pathway
+
+~~~sparql
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo:     <http://purl.obolibrary.org/obo/>
+PREFIX up_core: <http://purl.uniprot.org/core/>
+
+SELECT DISTINCT ?uri ?label
+WHERE {
+  ?uri up_core:classifiedWith obo:GO_0016055 .
+  ?uri rdfs:label ?label .
+}
+~~~
+
+## All proteins (URI and label) classified with the pathway
+
+~~~sparql
+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo:     <http://purl.obolibrary.org/obo/>
+PREFIX up_core: <http://purl.uniprot.org/core/>
+
+SELECT DISTINCT ?protein ?label
+WHERE {
+  ?protein up_core:classifiedWith obo:GO_0016055 .
+  ?protein rdf:type up_core:Protein .
+  ?protein rdfs:label ?label .
+}
+~~~
+
 ## All proteins classified with the pathway and their organism with the scientific name
 
 ~~~sparql

diff --git a/networks/species-pathways/sparql/species-pathways-proteins.sparql b/networks/species-pathways/sparql/species-pathways-proteins.sparql
@@ -4,77 +4,6 @@
 
 * UniProt (better): https://sparql.uniprot.org/sparql
 
-# Wnt signaling pathway (GO:0016055)
-# ----------------------------------
-
-* URI: https://amigo.geneontology.org/amigo/term/GO:0016055
-
-# All superclasses of the pathway 
-
-PREFIX obo:  <http://purl.obolibrary.org/obo/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-SELECT DISTINCT ?super ?labels
-WHERE {
-  obo:GO_0016055 rdfs:subClassOf ?super .
-  ?super rdfs:label ?labels .
-}
-
-# All subclasses of the pathway
-
-PREFIX obo:  <http://purl.obolibrary.org/obo/>
-PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-
-SELECT DISTINCT ?sub ?label
-WHERE {
-  ?sub rdfs:subClassOf obo:GO_0016055 .
-  ?sub rdfs:label ?label .
-}
-
-# All properties and objects related to the pathway
-
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-
-SELECT DISTINCT ?property ?object
-WHERE {
-  obo:GO_0016055 ?property ?object .
-}
-
-# All subjects and properties related to the pathway
-
-PREFIX obo: <http://purl.obolibrary.org/obo/>
-
-SELECT DISTINCT ?subject ?property
-WHERE {
-   ?subject ?property obo:GO_0016055 .
-}
-
-# All subjects (URI and label) classified with the pathway
-
-PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX obo:     <http://purl.obolibrary.org/obo/>
-PREFIX up_core: <http://purl.uniprot.org/core/>
-
-SELECT DISTINCT ?uri ?label
-WHERE {
-  ?uri up_core:classifiedWith obo:GO_0016055 .
-  ?uri rdfs:label ?label .
-}
-
-# All proteins (URI and label) classified with the pathway
-
-PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
-PREFIX obo:     <http://purl.obolibrary.org/obo/>
-PREFIX up_core: <http://purl.uniprot.org/core/>
-
-SELECT DISTINCT ?protein ?label
-WHERE {
-  ?protein up_core:classifiedWith obo:GO_0016055 .
-  ?protein rdf:type up_core:Protein .
-  ?protein rdfs:label ?label .
-}
-
 # PRICKLE2 - Prickle-like protein 2 (UniProtKB:Q7Z3G6)
 # ----------------------------------------------------
 
@@ -150,8 +79,6 @@ WHERE {
   ?gene rdfs:label ?label .
 }
 
-
-
 # Wnt signaling pathway, planar cell polarity pathway (GO:0060071)
 # ----------------------------------------------------------------
 
@@ -200,6 +127,74 @@ WHERE {
 # Wnt signaling pathway (GO:0016055)
 # ----------------------------------
 
+* URI: https://amigo.geneontology.org/amigo/term/GO:0016055
+
+# All superclasses of the pathway 
+
+PREFIX obo:  <http://purl.obolibrary.org/obo/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?super ?labels
+WHERE {
+  obo:GO_0016055 rdfs:subClassOf ?super .
+  ?super rdfs:label ?labels .
+}
+
+# All subclasses of the pathway
+
+PREFIX obo:  <http://purl.obolibrary.org/obo/>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?sub ?label
+WHERE {
+  ?sub rdfs:subClassOf obo:GO_0016055 .
+  ?sub rdfs:label ?label .
+}
+
+# All properties and objects related to the pathway
+
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT DISTINCT ?property ?object
+WHERE {
+  obo:GO_0016055 ?property ?object .
+}
+
+# All subjects and properties related to the pathway
+
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT DISTINCT ?subject ?property
+WHERE {
+   ?subject ?property obo:GO_0016055 .
+}
+
+# All subjects (URI and label) classified with the pathway
+
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo:     <http://purl.obolibrary.org/obo/>
+PREFIX up_core: <http://purl.uniprot.org/core/>
+
+SELECT DISTINCT ?uri ?label
+WHERE {
+  ?uri up_core:classifiedWith obo:GO_0016055 .
+  ?uri rdfs:label ?label .
+}
+
+# All proteins (URI and label) classified with the pathway
+
+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo:     <http://purl.obolibrary.org/obo/>
+PREFIX up_core: <http://purl.uniprot.org/core/>
+
+SELECT DISTINCT ?protein ?label
+WHERE {
+  ?protein up_core:classifiedWith obo:GO_0016055 .
+  ?protein rdf:type up_core:Protein .
+  ?protein rdfs:label ?label .
+}
+
 # All proteins classified with the pathway and their organism with the scientific name
 
 PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>