Fix some nextprot queries where the prefixes dc and dcterms were poin…

…ting to the same namespace. Now using dcterms only to avoid duplicates
sib-swiss · Sep 13, 2024 · 36bce2c · 36bce2c
1 parent 3c89d01
commit 36bce2c
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Showing 5 changed files with 5 additions and 10 deletions.
diff --git a/examples/neXtProt/NXQ_00253.ttl b/examples/neXtProt/NXQ_00253.ttl
@@ -8,7 +8,6 @@ ex:NXQ_00253 a sh:SPARQLExecutable,
     rdfs:comment "Human pathways in which at least one protein is mitochondrial GOLD"@en ;
     sh:prefixes _:sparql_examples_prefixes ;
     sh:select """PREFIX : <http://nextprot.org/rdf/>
-PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX nextprot_cv: <http://nextprot.org/rdf/terminology/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
@@ -29,7 +28,7 @@ select ?pathwayname (group_concat(distinct ?gen ; SEPARATOR = ',') as ?gene) WHE
  ?pathway a wp:Pathway .
  ?pathway wp:organism ?organism .
  filter(contains(str(?organism),"9606"))
- ?pathway dc:title ?pathwayname .
+ ?pathway dcterms:title ?pathwayname .
  }
 
  ?entry a :Entry .

diff --git a/examples/neXtProt/NXQ_00254.ttl b/examples/neXtProt/NXQ_00254.ttl
@@ -8,7 +8,6 @@ ex:NXQ_00254 a sh:SPARQLExecutable,
     rdfs:comment "Proteins with associated pathways in WikiPathways"@en ;
     sh:prefixes _:sparql_examples_prefixes ;
     sh:select """PREFIX : <http://nextprot.org/rdf/>
-PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
@@ -29,7 +28,7 @@ SELECT DISTINCT ?entry ?gen ?pathwayname WHERE {
  ?pathway a wp:Pathway .
  ?pathway wp:organism ?organism .
  filter(contains(str(?organism),"9606")) # Human proteins
- ?pathway dc:title ?pathwayname .
+ ?pathway dcterms:title ?pathwayname .
  }
  ?entry a :Entry .
  ?entry :gene / :recommendedName / rdfs:label ?gen .

diff --git a/examples/neXtProt/NXQ_00269.ttl b/examples/neXtProt/NXQ_00269.ttl
@@ -8,7 +8,6 @@ ex:NXQ_00269 a sh:SPARQLExecutable,
     rdfs:comment "Proteins with associated cancer pathways in WikiPathways (via Disease Ontology classification)"@en ;
     sh:prefixes _:sparql_examples_prefixes ;
     sh:select """PREFIX : <http://nextprot.org/rdf/>
-PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
@@ -26,7 +25,7 @@ SELECT DISTINCT ?entry (str(?gen) as ?gene) ?pathwayname WHERE {
  ?pathway a wp:Pathway .
  ?pathway wp:organism ?organism .
  filter(contains(str(?organism),"9606")) # Human proteins
- ?pathway dc:title ?pathwayname .
+ ?pathway dcterms:title ?pathwayname .
  ?pathway wp:ontologyTag <http://purl.obolibrary.org/obo/DOID_162> . # Parent id for all cancers
  }
  ?entry a :Entry .

diff --git a/examples/neXtProt/NXQ_00270.ttl b/examples/neXtProt/NXQ_00270.ttl
@@ -8,7 +8,6 @@ ex:NXQ_00270 a sh:SPARQLExecutable,
     rdfs:comment "Proteins belonging to Rett syndrome pathways, and their subcellular locations (GOLD)"@en ;
     sh:prefixes _:sparql_examples_prefixes ;
     sh:select """PREFIX : <http://nextprot.org/rdf/>
-PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
@@ -29,7 +28,7 @@ select ?entry (str(?gen) AS ?gene) ?pathwayname (group_concat(distinct str(?locl
  ?pathway a wp:Pathway .
  ?pathway wp:organism ?organism .
  filter(contains(str(?organism),"9606"))
- ?pathway dc:title ?pathwayname .
+ ?pathway dcterms:title ?pathwayname .
  filter(regex(?pathwayname,"rett","i")).
  }
  ?entry a :Entry .

diff --git a/examples/neXtProt/NXQ_00272.ttl b/examples/neXtProt/NXQ_00272.ttl
@@ -8,7 +8,6 @@ ex:NXQ_00272 a sh:SPARQLExecutable,
     rdfs:comment "Proteins involved in coronaviruses/SARS-CoV-2 pathways with associated medical information"@en ;
     sh:prefixes _:sparql_examples_prefixes ;
     sh:select """PREFIX : <http://nextprot.org/rdf/>
-PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX dcterms: <http://purl.org/dc/terms/>
 PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX wp: <http://vocabularies.wikipathways.org/wp#>
@@ -29,7 +28,7 @@ SELECT DISTINCT ?entry (str(?gen) AS ?gene) ?pathwayname (str(?discom) AS ?disco
  ?pathway wp:organism ?organism .
  filter(contains(str(?organism),"9606"))
 
- ?pathway dc:title ?pathwayname .
+ ?pathway dcterms:title ?pathwayname .
  filter(regex(?pathwayname,"sars-cov-2","i")|| regex(?pathwayname,"corona","i") ).
  }