testing with a few initial oma sparql querries

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

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

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.
+}""" .
+

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.
+}""" .
+