From f3631e7cfb9fb7c60fa00cb68701af03b5c67dc8 Mon Sep 17 00:00:00 2001
From: Adrian Altenhoff <adrian.altenhoff@inf.ethz.ch>
Date: Tue, 21 May 2024 16:26:12 +0200
Subject: [PATCH] testing with a few initial oma sparql querries

---
 check.sh                |  3 ++-
 convertToOneTurtle.sh   |  3 ++-
 oma/01-rat-proteins.ttl | 20 ++++++++++++++++++++
 oma/02-all-species.ttl  | 16 ++++++++++++++++
 4 files changed, 40 insertions(+), 2 deletions(-)
 create mode 100644 oma/01-rat-proteins.ttl
 create mode 100644 oma/02-all-species.ttl

diff --git a/check.sh b/check.sh
index 159b5339c..74aedeac8 100755
--- a/check.sh
+++ b/check.sh
@@ -17,7 +17,7 @@ prefixes=$(sparql --results=TSV --data=prefixes.ttl "PREFIX sh:<http://www.w3.or
 echo "Prefixes found"
 
 project="*"
-while getopts nuhrsgmcpb: option; do
+while getopts nuhrsgmcbop: option; do
     case "$option" in
         p) project="$OPTARG";;
         u) project="uniprot";;
@@ -29,6 +29,7 @@ while getopts nuhrsgmcpb: option; do
         c) project="covid";;
         b) project="bgee";;
 	    n) project="nextprot";;
+        o) project="oma";;
         h) help; exit 0;;
         *) help; exit 1;;
     esac
diff --git a/convertToOneTurtle.sh b/convertToOneTurtle.sh
index 579c493d6..d0c7c7676 100755
--- a/convertToOneTurtle.sh
+++ b/convertToOneTurtle.sh
@@ -3,7 +3,7 @@
 
 
 project="uniprot"
-while getopts nuhrsgmcbp: option; do
+while getopts nuhrsgmcbop: option; do
     case "$option" in
         p) project="$OPTARG";;
         u) project="uniprot";;
@@ -15,6 +15,7 @@ while getopts nuhrsgmcbp: option; do
         c) project="covid";;
         n) project="nextprot";;
         b) project="bgee";;
+        o) project="oma";;
         h) help; exit 0;;
         *) help; exit 1;;
     esac
diff --git a/oma/01-rat-proteins.ttl b/oma/01-rat-proteins.ttl
new file mode 100644
index 000000000..168387979
--- /dev/null
+++ b/oma/01-rat-proteins.ttl
@@ -0,0 +1,20 @@
+prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/>
+prefix sh: <http://www.w3.org/ns/shacl#>
+prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
+prefix schema:<https://schema.org/>
+ex:1
+    a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
+    sh:prefixes _:sparql_examples_prefixes ;
+    schema:target <https://sparql.omabrowser.org/sparql/> ;
+    rdfs:comment """Find all Rattus norvegicus' proteins present in OMA RDF database.""" ;
+    sh:select """SELECT ?protein ?OMA_link
+WHERE
+{
+    ?protein a orth:Protein.
+    ?protein  orth:organism ?organism.
+    ?inTaxon rdfs:label 'in taxon'@en.
+    ?organism ?inTaxon ?taxon.
+    ?taxon  up:scientificName 'Rattus norvegicus'.
+    ?protein rdfs:seeAlso ?OMA_link.
+}""" .
+
diff --git a/oma/02-all-species.ttl b/oma/02-all-species.ttl
new file mode 100644
index 000000000..2e2657520
--- /dev/null
+++ b/oma/02-all-species.ttl
@@ -0,0 +1,16 @@
+prefix ex: <https://sparql.omabrowser.org/.well-known/sparql-examples/>
+prefix sh: <http://www.w3.org/ns/shacl#>
+prefix rdfs:<http://www.w3.org/2000/01/rdf-schema#>
+prefix schema:<https://schema.org/>
+ex:1
+    a sh:SPARQLSelectExecutable, sh:SPARQLExecutable ;
+    sh:prefixes _:sparql_examples_prefixes ;
+    schema:target <https://sparql.omabrowser.org/sparql/> ;
+    rdfs:comment """Which species are available on OMA database and their scientific names?""" ;
+    sh:select """SELECT ?species ?sciname WHERE
+{
+    ?species a up:Taxon.
+    ?species up:scientificName ?sciname.
+    ?species up:rank up:Species.
+}""" .
+