Skip to main content

Table 4 A sample query for getting the orthologs of a given gene

From: The Orthology Ontology: development and applications

SELECT ?gene ?species ?database WHERE {

?common_ancestor a orth:OrthologsCluster.

?common_ancestor ort:hasHomologous ?tree_node1.

?common_ancestor orth:hasHomologous ?tree_node2.

?common_ancestor void:inDataset ?dataset.

?dataset orth:hasSource ?database.

?tree_node1 orth:hasHomologous* ?gene1.

?tree_node2 orth:hasHomologous* ?gene2.

?gene1 a orth:Gene.

?gene2 a orth:Gene.

?gene1 obo:RO_0002162 ?species1.

?gene2 obo:RO_0002162 ?species2.

?gene1 dcterms:identifier ?id.

?gene2 dcterms:identifier ?gene.

?species2 rdfs:label ?species.

bind(str(?id) as ?str_id)

FILTER (?tree_node1 != ?tree_node2 && ?species1 != ?species2)

VALUES (?str_id ?species1 ?species2) {(“SAA1” ncbit:9606 ncbit:10090)}

}

  1. In this example, the mouse (ncbit:10090) orthologs of the human (ncbit:9606) gene SAA1 are retrieved. obo:RO_0002162 stands for the property in_taxon