183_protein_count_by_clade_single_hop

taxonomy
clade
aggregation

Compare the number of reviewed proteins in two named taxonomic clades (Primates, Rodentia), using a single-hop ?organism rdfs:subClassOf ?clade rather than the transitive rdfs:subClassOf+ or rdfs:subClassOf* form. UniProt's taxonomy is pre-flattened: every taxon carries a direct rdfs:subClassOf edge to every one of its ancestors, not only its immediate parent (verified live: taxon 9606, Homo sapiens, has 30 direct rdfs:subClassOf triples, one per ancestor up to cellular organisms), so a single hop already reaches every member of a clade at any depth and is far cheaper than the transitive path

Use at

https://sparql.uniprot.org/sparql/

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT
  ?clade
  ?cladeName
  (COUNT(DISTINCT ?protein) AS ?proteinCount)
WHERE {
  VALUES ?clade { <http://purl.uniprot.org/taxonomy/9443> <http://purl.uniprot.org/taxonomy/9989> }
  ?clade up:scientificName ?cladeName .
  ?protein up:reviewed true ;
    up:organism ?organism .
  ?organism rdfs:subClassOf ?clade .
}
GROUP BY ?clade ?cladeName

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v1("?clade"):::projected 
  v2("?cladeName"):::projected 
  v4("?organism")
  v3("?protein"):::projected 
  v5("?proteinCount")
  c3(["true^^xsd:boolean"]):::literal 
  bind0[/VALUES ?clade/]
  bind0-->v1
  bind00([http://purl.uniprot.org/taxonomy/9443])
  bind00 --> bind0
  bind01([http://purl.uniprot.org/taxonomy/9989])
  bind01 --> bind0
  v1 --"up:scientificName"-->  v2
  v3 --"up:reviewed"-->  c3
  v3 --"up:organism"-->  v4
  v4 --"rdfs:subClassOf"-->  v1
  bind2[/"count(?protein)"/]
  v3 --o bind2
  bind2 --as--o v5