UniProt: Fix keywords, and plazi example rendering

Author: JervenBolleman

examples/UniProt/109_uniprot_transporter_in_liver.ttl

@@ -39,7 +39,7 @@ WHERE
     ?organism obo:RO_0002162 taxon:9606 .
   }
 }""" ;
-    schema:keywords "federated query" , "Bgee" , "UBERON" , "tissue specificity" , "transport reaction" , "Rhea" ; 
+    schema:keywords "federated query" , "Bgee" , "UBERON" , "tissue specificity" , "transport" , "transport reaction" , "Rhea" ;
     schema:target <https://sparql.uniprot.org/sparql/> ;
     spex:federatesWith <https://www.bgee.org/sparql/> .
 

examples/UniProt/10_human_variant_leading_to_transposition_of_tyrosine_to_phenylalanine.ttl

@@ -29,6 +29,6 @@ WHERE
         BIND (substr(?value, ?begin, 1) as ?original) .
         FILTER(?original = 'Y' && ?substitution = 'F') .
 }""" ;
-    schema:keywords "variant annotation" , "search within sequence" ;
+    schema:keywords "variant" , "search within sequence" ;
     schema:target <https://sparql.uniprot.org/sparql/> .
 

examples/UniProt/11_entries_with_transmem_on_cannonical_sequence.ttl

@@ -20,6 +20,6 @@ WHERE
 	?range faldo:begin/faldo:position ?begin .
 	?range faldo:end/faldo:position ?end
 }""" ;
-    schema:keywords "transmembrane annotation" , "search within sequence" ;
+    schema:keywords "transmembrane" , "search within sequence" ;
     schema:target <https://sparql.uniprot.org/sparql/> .
 

examples/UniProt/135_plazi_proteome.ttl

@@ -6,7 +6,7 @@
 @prefix spex: <https://purl.expasy.org/sparql-examples/ontology#> .
 
 ex:135_plazi_proteome a sh:SPARQLExecutable, sh:SPARQLSelectExecutable;
-  rdfs:comment "Connect a taxonomic treatment collected by [Plazi](https://plazi.org/) in their [synospecies](https://synospecies.plazi.org/) system. We connect by what is called the dwc:id-ENA property which is encoded as a xsd:string which is the naked identifier of an NCBI taxon concept. Which in UniProt is encoded as an IRI starting with `http://purl.uniprot.org/taxonomy/'. After converting the taxon identifier we can query for Proteomes in UniProt for that taxon."^^rdf:HTML;
+  rdfs:comment """Connect a taxonomic treatment collected by <a href="https://plazi.org/">Plazi</a> in their <a href="https://synospecies.plazi.org/">synospecies</a> system. We connect by what is called the dwc:id-ENA property which is encoded as a xsd:string which is the naked identifier of an NCBI taxon concept. Which in UniProt is encoded as an IRI starting with `http://purl.uniprot.org/taxonomy/'. After converting the taxon identifier we can query for Proteomes in UniProt for that taxon."""^^rdf:HTML;
   sh:prefixes _:sparql_examples_prefixes;
   sh:select """PREFIX up: <http://purl.uniprot.org/core/>
 PREFIX trt:   <http://plazi.org/vocab/treatment#>

examples/UniProt/19_natural_variants_associated_with_pubmed_id.ttl

@@ -27,6 +27,6 @@ WHERE
   BIND(IF(CONTAINS(STR(?annotation), "#SIP"), SUBSTR(STR(?annotation),33), SUBSTR(STR(?annotation),36))AS?annotation_acc)
   BIND(SUBSTR(STR(?source),35) AS ?pubmed)
 }""" ;
-    schema:keywords "variant annotation" , "evidence tag" , "PubMed" ;
+    schema:keywords "variant" , "evidence tag" , "PubMed" ;
     schema:target <https://sparql.uniprot.org/sparql/> .
 

examples/UniProt/33_longest_variant_comment.ttl

@@ -17,6 +17,6 @@ WHERE {
         rdfs:comment ?comment . 
 } 
 ORDER BY DESC(STRLEN(?comment))""" ;
-    schema:keywords "variant annotation" , "count" ;
+    schema:keywords "variant" , "count" ;
     schema:target <https://sparql.uniprot.org/sparql/> .
 

examples/UniProt/38_find_gene_region_in_wikidata_for_known_entry.ttl

@@ -39,7 +39,7 @@ WHERE {
         FILTER(lang(?assembly) = "en")
   }
 }""" ;
-    schema:keywords "chromosome location" , "gene" , "Wikidata" , "federated query" ;
+    schema:keywords "chromosome location" , "chromosome",  "gene" , "Wikidata" , "federated query" ;
     schema:target <https://sparql.uniprot.org/sparql/> ;
     spex:federatesWith <https://query.wikidata.org/sparql> .
 

examples/UniProt/54_binding_sites_for_ligands_similar_to_heme_sachem.ttl

@@ -38,7 +38,7 @@ WHERE {
       up:ligand/rdfs:subClassOf ?ligand .
 }
 ORDER BY DESC(?ligandSimilarityScore)""" ;
-    schema:keywords "binding site" , "chemical similarity" , "idms" , "sachem" , "federated query" ;
+    schema:keywords "binding site" , "chemical similarity" , "idsm" , "sachem" , "federated query" ;
     schema:target <https://sparql.uniprot.org/sparql/> ;
     spex:federatesWith <https://idsm.elixir-czech.cz/sparql/endpoint/chebi> .
 

examples/UniProt/75_enzymes_with_at_least_two_transmembrane_domains_PDB_xray.ttl

@@ -25,7 +25,7 @@ WHERE {
     up:method up:X-Ray_Crystallography .
   ?transmembrane_annotation a up:Transmembrane_Annotation .
 } GROUP BY ?protein HAVING(COUNT(DISTINCT ?transmembrane_annotation ) >= 2)""" ;
-    schema:keywords "3D",
+    schema:keywords "3D structure",
         "PDB",
         "enzyme",
         "membrane" ;

examples/UniProt/9_human_variant_loss_of_function.ttl

@@ -21,7 +21,7 @@ WHERE
         ?annotation rdfs:comment ?text .
         FILTER (CONTAINS(?text, 'loss of function'))
 }""" ;
-    schema:keywords "variant" , "variant annotation" ;
+    schema:keywords "variant" , "taxonomy" ;
     schema:potentialAction [ schema:description "UniProtKB rest search with sparql" ;
             schema:target <https://www.uniprot.org/sparql/> ] ;
     schema:target <https://sparql.uniprot.org/sparql/> .