11

rq turtle/ttl

• transmembrane annotation
• search within sequence

Select all UniProtKB entries with annotated transmembrane regions and the regions' begin and end coordinates on the canonical sequence

Use at

• https://sparql.uniprot.org/sparql/

PREFIX faldo: <http://biohackathon.org/resource/faldo#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT ?protein ?begin ?end
WHERE 
{
	?protein a up:Protein .
	?protein up:annotation ?annotation .
	?annotation a up:Transmembrane_Annotation .
	?annotation up:range ?range .
	?range faldo:begin/faldo:position ?begin .
	?range faldo:end/faldo:position ?end
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v2("?annotation")
  v4("?begin"):::projected 
  v5("?end"):::projected 
  v1("?protein"):::projected 
  v3("?range")
  a1((" "))
  a2((" "))
  c2(["up:Protein"]):::iri 
  c4(["up:Transmembrane_Annotation"]):::iri 
  v1 --"a"-->  c2
  v1 --"up:annotation"-->  v2
  v2 --"a"-->  c4
  v2 --"up:range"-->  v3
  v3 --"faldo:begin"-->  a1
  a1 --"faldo:position"-->  v4
  v3 --"faldo:end"-->  a2
  a2 --"faldo:position"-->  v5