From bdc685c22e90d6ad7df84747cbb0ceb87144f7b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Santanch=C3=A8?= <santanche@gmail.com>
Date: Mon, 27 May 2024 18:43:37 -0300
Subject: [PATCH] feat (networks/sp): species vs pathway new examples

---
 .../cypher/mapping-copilot.cypher             |  4 ++
 networks/species-pathways/sparql/README.md    |  5 ++
 ...parql-0C6994E8CA10512E548BBEE6D1618936.csv |  5 ++
 .../sparql/species-pathways-proteins.sparql   | 53 +++++++++++++++++++
 4 files changed, 67 insertions(+)
 create mode 100644 networks/species-pathways/cypher/mapping-copilot.cypher
 create mode 100644 networks/species-pathways/sparql/README.md
 create mode 100644 networks/species-pathways/sparql/outputs/sparql-0C6994E8CA10512E548BBEE6D1618936.csv

diff --git a/networks/species-pathways/cypher/mapping-copilot.cypher b/networks/species-pathways/cypher/mapping-copilot.cypher
new file mode 100644
index 0000000..e2d3b7c
--- /dev/null
+++ b/networks/species-pathways/cypher/mapping-copilot.cypher
@@ -0,0 +1,4 @@
+// Create a node of the type Disease and name Diabetes Mellitus
+
+CREATE (:Disease {name: 'Diabetes Mellitus'})
+
diff --git a/networks/species-pathways/sparql/README.md b/networks/species-pathways/sparql/README.md
new file mode 100644
index 0000000..dc7db30
--- /dev/null
+++ b/networks/species-pathways/sparql/README.md
@@ -0,0 +1,5 @@
+# UniProt RDF
+
+https://sparql.uniprot.org/uniprot
+https://sparql.uniprot.org/pathways
+https://sparql.uniprot.org/uniref
\ No newline at end of file
diff --git a/networks/species-pathways/sparql/outputs/sparql-0C6994E8CA10512E548BBEE6D1618936.csv b/networks/species-pathways/sparql/outputs/sparql-0C6994E8CA10512E548BBEE6D1618936.csv
new file mode 100644
index 0000000..a3d0617
--- /dev/null
+++ b/networks/species-pathways/sparql/outputs/sparql-0C6994E8CA10512E548BBEE6D1618936.csv
@@ -0,0 +1,5 @@
+object, label
+http://purl.obolibrary.org/obo/GO_0005737,"cytoplasm"
+http://purl.obolibrary.org/obo/GO_0031965,"nuclear membrane"
+http://purl.obolibrary.org/obo/GO_0008270,"zinc ion binding"
+http://purl.obolibrary.org/obo/GO_0060071,"Wnt signaling pathway, planar cell polarity pathway"
diff --git a/networks/species-pathways/sparql/species-pathways-proteins.sparql b/networks/species-pathways/sparql/species-pathways-proteins.sparql
index 11d9597..35647ac 100644
--- a/networks/species-pathways/sparql/species-pathways-proteins.sparql
+++ b/networks/species-pathways/sparql/species-pathways-proteins.sparql
@@ -218,3 +218,56 @@ WHERE {
   ?protein up_core:organism taxon:10090 .
 }
 
+
+# Cluster Casein kinase I isoform delta - 100% (UniRef100_Q9DC28)
+# ---------------------------------------------------------------
+
+# All subjects and properties related to the cluster
+
+PREFIX up_ref: <http://purl.uniprot.org/uniref/>
+
+SELECT DISTINCT ?subject ?property
+WHERE {
+  ?subject ?property up_ref:UniRef100_Q9DC28 .
+}
+
+# All properties and objects related to the cluster
+
+PREFIX up_ref: <http://purl.uniprot.org/uniref/>
+
+SELECT DISTINCT ?property ?object
+WHERE {
+  up_ref:UniRef100_Q9DC28 ?property ?object .
+}
+
+# The UniParc which this cluster is member of
+
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX up_core: <http://purl.uniprot.org/core/>
+PREFIX up_ref: <http://purl.uniprot.org/uniref/>
+
+SELECT DISTINCT ?uniparc ?label
+WHERE {
+  up_ref:UniRef100_Q9DC28 up_core:member ?uniparc .
+  ?uniparc rdfs:label ?label .
+}
+
+-----
+uniparc
+UPI0000027B20
+-----
+
+# All properties and objects related to the UniParc
+
+PREFIX rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs:    <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX up_core: <http://purl.uniprot.org/core/>
+PREFIX up_arc:  <http://purl.uniprot.org/uniparc/>
+
+SELECT DISTINCT ?protein ?organism ?scientific_name
+WHERE {
+  up_arc:UPI0000027B20 up_core:sequenceFor ?protein .
+  ?protein rdf:type up_core:Protein .
+  ?protein up_core:organism ?organism .
+  ?organism up_core:scientificName ?scientific_name .
+}
\ No newline at end of file