14

Retrieve pairwise orthologous genes of the Cyanobacterium-aponinum psb27- gene that are found in the MBGD database but are not present in OMA

Use at

• https://sparql.omabrowser.org/sparql

PREFIX oma: <http://omabrowser.org/ontology/oma#>
PREFIX orth: <http://purl.org/net/orth#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX lscr: <http://purl.org/lscr#>
PREFIX mbgd: <http://purl.jp/bio/11/mbgd#>

SELECT ?protein2 ?species WHERE {
  SERVICE <http://sparql.nibb.ac.jp/sparql> {
    SELECT ?protein2 ?species WHERE {
      ?cluster_mbgd a orth:OrthologsCluster ;
          orth:hasHomologous ?node1_mbgd ;
        orth:hasHomologous ?node2_mbgd .
      ?node1_mbgd orth:hasHomologous* ?gene1 .
      ?node2_mbgd orth:hasHomologous* ?gene2 .
      ?gene1 mbgd:uniprot <http://purl.uniprot.org/uniprot/K9Z723> .
      ?gene2 mbgd:uniprot ?protein2 ;
        mbgd:organism ?taxon .
      OPTIONAL {
        ?taxon mbgd:species ?species .
      }
      FILTER (?node1_mbgd != ?node2_mbgd)
    }
  }
  FILTER NOT EXISTS { # keep only those that do not exist in OMA
    ?cluster a orth:OrthologsCluster ;
      orth:hasHomologousMember ?node1 ;
      orth:hasHomologousMember ?node2 .
    ?node1 orth:hasHomologousMember* ?protein_OMA_1.
    ?node2 orth:hasHomologousMember* ?protein_OMA_2.
    ?protein_OMA_1 lscr:xrefUniprot <http://purl.uniprot.org/uniprot/K9Z723>.
    ?protein_OMA_2 lscr:xrefUniprot ?protein2.
    FILTER (?node1 != ?node2)
  }
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v3("?cluster")
  v9("?cluster_mbgd")
  v10("?gene1")
  v11("?gene2")
  v1("?node1")
  v7("?node1_mbgd")
  v2("?node2")
  v8("?node2_mbgd")
  v6("?protein2"):::projected 
  v4("?protein_OMA_1")
  v5("?protein_OMA_2")
  v13("?species"):::projected 
  v12("?taxon")
  c2(["orth:OrthologsCluster"]):::iri 
  c5([http://purl.uniprot.org/uniprot/K9Z723]):::iri 
  f0[["not  "]]
  subgraph f0e0["Exists Clause"]
    e0f0[["?node1 != ?node2"]]
    e0f0 --> e0v1
    e0f0 --> e0v2
    e0v3 --"a"-->  e0c2
    e0v3 --"orth:hasHomologousMember"-->  e0v1
    e0v3 --"orth:hasHomologousMember"-->  e0v2
    e0v1 --"orth:hasHomologousMember"-->  e0v4
    e0v2 --"orth:hasHomologousMember"-->  e0v5
    e0v4 --"lscr:xrefUniprot"-->  e0c5
    e0v5 --"lscr:xrefUniprot"-->  e0v6
    e0v3("?cluster"):::projected 
    e0v1("?node1"):::projected 
    e0v2("?node2"):::projected 
    e0v6("?protein2"):::projected 
    e0v4("?protein_OMA_1"):::projected 
    e0v5("?protein_OMA_2"):::projected 
    e0c2(["orth:OrthologsCluster"]):::iri 
    e0c5([http://purl.uniprot.org/uniprot/K9Z723]):::iri 
  end
  f0--EXISTS--> f0e0
  f0 --> v1
  f0 --> v2
  f0 --> v3
  f0 --> c1
  f0 --> c2
  f0 --> c3
  f0 --> v4
  f0 --> v5
  f0 --> c4
  f0 --> c5
  f0 --> v6
  f1[["?node1 != ?node2"]]
  f1 --> v1
  f1 --> v2
  v3 --"a"-->  c2
  v3 --"orth:hasHomologousMember"-->  v1
  v3 --"orth:hasHomologousMember"-->  v2
  v1 --"orth:hasHomologousMember"-->  v4
  v2 --"orth:hasHomologousMember"-->  v5
  v4 --"lscr:xrefUniprot"-->  c5
  v5 --"lscr:xrefUniprot"-->  v6
  subgraph s1["http://sparql.nibb.ac.jp/sparql"]
    style s1 stroke-width:4px;
    f2[["?node1_mbgd != ?node2_mbgd"]]
    f2 --> v7
    f2 --> v8
    v9 --"a"-->  c2
    v9 --"orth:hasHomologous"-->  v7
    v9 --"orth:hasHomologous"-->  v8
    v7 --"orth:hasHomologous"-->  v10
    v8 --"orth:hasHomologous"-->  v11
    v10 --http://purl.jp/bio/11/mbgd#uniprot-->  c5
    v11 --http://purl.jp/bio/11/mbgd#uniprot-->  v6
    v11 --http://purl.jp/bio/11/mbgd#organism-->  v12
    subgraph optional0["(optional)"]
    style optional0 fill:#bbf,stroke-dasharray: 5 5;
      v12 -.http://purl.jp/bio/11/mbgd#species.->  v13
    end
  end