03_04_targetMembers.ttl

@base <http://www.openphacts.org/api#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix uniprot: <http://purl.uniprot.org/core/> .
@prefix api: <http://purl.org/linked-data/api/vocab#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix ops: <http://www.openphacts.org/api#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix chembl: <http://rdf.ebi.ac.uk/terms/chembl#> .
@prefix obo: <http://www.semantic-systems-biology.org/ontology/rdf/OBO#> .
@prefix goa: <http://www.semantic-systems-biology.org/ontology/rdf/GOA#> .

<#target> a api:API ;
	rdfs:label "Target"@en ;
	api:sparqlEndpoint <http://alpha.openphacts.org:8890/sparql/> ;
	api:contentNegotiation api:parameterBased ;
	api:variable <#input> ;
        api:variable chembl:organismName ;
	api:variable uniprot:organism ;
	api:dataset <http://www.ebi.ac.uk/chembl> ;
	api:dataset <http://purl.uniprot.org/enzyme/> ;
        api:dataset <http://www.geneontology.org> ;
	api:vocabulary rdfs: ;
	api:vocabulary skos: ;
	api:vocabulary uniprot: ;
	api:vocabulary dcterms: ;
	api:description "An API configuration to return information about targets." ;
	api:endpoint [
		a api:IntermediateExpansionEndpoint ;
		api:name "Target Class Members: List" ;
		api:description "A list of targets classified with the given class in the supported hierarchies. Currently supported hierarchies are the Enzyme Classification, the ChEMBL Target Tree and the Gene Ontology." ;
		api:itemTemplate "{uri}" ;
		api:variable <http://purl.uniprot.org/enzyme> ;
		api:variable <http://www.ebi.ac.uk/chembl/target> ;
		api:variable <http://www.geneontology.org> ;
		api:uriTemplate "/target/members/pages?uri={uri}" ;
		api:exampleRequestPath "/target/members/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F6.2.-.-";
		api:exampleRequestPath "/target/members/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F6.2.-.-&target_organism=Homo%20sapiens";
		api:selector [
			api:where
"VALUES ?g { <http://purl.uniprot.org/enzyme/inference> <http://www.ebi.ac.uk/chembl/target/inference> <http://www.geneontology.org/inference> }
GRAPH ?g {
        ?child_node rdfs:subClassOf ?node_uri.
        FILTER ( isURI(?child_node) )
}
{ ?item obo:C ?child_node .
?item uniprot:reviewed true }
UNION { ?item obo:F ?child_node .
?item uniprot:reviewed true }
UNION { ?item obo:P ?child_node .
?item uniprot:reviewed true }
UNION { ?item uniprot:enzyme|uniprot:domain/uniprot:enzyme|chembl:hasProteinClassification ?child_node }
VALUES ?g2 {<http://purl.uniprot.org> <http://www.ebi.ac.uk/chembl> <http://www.openphacts.org/goa> }
GRAPH ?g2 {
	?item [] []
}
{ ?item dcterms:title ?chembl_name
FILTER (?chembl_name != '') }
UNION { ?item goa:description ?uniprot_name
FILTER (?uniprot_name != '') }
OPTIONAL {
	{?mapping skos:relatedMatch/skos:exactMatch ?item }
	UNION { ?item skos:relatedMatch/skos:exactMatch ?mapping }
	MINUS { ?mapping a chembl:ProteinComplexGroup }
	{ ?mapping goa:description ?mapping_name }
	UNION { ?mapping dcterms:title ?mapping_name }
	FILTER ( ?mapping_name != '' )
	{ ?mapping uniprot:organism ?mapping_org_uri }
	UNION { ?mapping chembl:organismName ?mapping_org
		GRAPH <http://www.ebi.ac.uk/chembl> {
			?mapping a ?mapping_type
			FILTER ( ?mapping_type != chembl:UniprotRef )
		}
	}
	BIND(IF(BOUND(?mapping_org), <http://www.ebi.ac.uk/chembl>, <http://purl.uniprot.org>) AS ?mapping_dataset)
}
OPTIONAL { ?item uniprot:organism ?uniprot_organism
	BIND (?item AS ?uniprot_target) }
OPTIONAL {
	GRAPH <http://www.ebi.ac.uk/chembl> {
		?item a ?target_type
	}
}
OPTIONAL { ?item chembl:organismName ?chembl_organism
	BIND (?item AS ?chembl_target) }
"] ;
		api:expansionVariable "item" ;
		api:viewer <#targetMemberViewer> ;
		api:defaultViewer <#targetMemberViewer> ] .

<http://www.ebi.ac.uk/chembl> api:label "ChEMBL - RDF" .
<http://purl.uniprot.org/enzyme/> api:label "Enzyme Classification" .
<http://www.geneontology.org> api:name "Gene Ontology" .

<http://www.ebi.ac.uk/chembl/target> api:name "chembl" .
<http://purl.uniprot.org/enzyme> api:name "enzyme" .
<http://www.geneontology.org> api:name "go" .

chembl:organismName api:name "target_organism" ;
	api:label "target_organism" ;
	api:value "A literal organism in ChEMBL." ;
	api:filterVariable "?item";
	a rdf:Property .

uniprot:organism api:name "target_organism_uri" ;
        api:label "target_organism_uri" ;
        api:value "An organism URI from Uniprot. e.g. http://purl.uniprot.org/taxonomy/386043" ;
        api:filterVariable "?item";
        a rdf:Property .

<#input> api:name "uri" ;
        api:label "uri";
        api:value "A class URI from one of the supported hierarchies. e.g.: http://purl.uniprot.org/enzyme/6.2.-.-" ;
        rdfs:range rdfs:Resource .

<#targetMemberViewer> a api:Viewer ;
	api:name "targetMemberViewer";
	api:template
"?ims_uniprot_target_uri skos:prefLabel ?uniprot_name ;
	uniprot:organism ?uniprot_organism ;
	void:inDataset <http://purl.uniprot.org> .
?ims_chembl_target_uri skos:prefLabel ?chembl_name ;
	chembl:organismName ?chembl_organism ;
        rdf:type ?target_type ;
        void:inDataset <http://www.ebi.ac.uk/chembl> .
?item skos:exactMatch ?mapping .
?mapping skos:prefLabel ?mapping_name ;
	uniprot:organism ?mapping_org_uri ;
	chembl:organismName ?mapping_org ;
	a ?mapping_type ;
	void:inDataset ?mapping_dataset .
ops:no_mappings_found rdfs:label 'No mappings found' .
";
	api:where
"
{ GRAPH <http://www.openphacts.org/goa> {
	?ims_uniprot_target_uri goa:description ?uniprot_name
	GRAPH <http://purl.uniprot.org> {
		?ims_uniprot_target_uri uniprot:organism ?uniprot_organism
	}
}
} UNION {
  GRAPH <http://www.ebi.ac.uk/chembl> {
	?ims_chembl_target_uri dcterms:title ?chembl_name
	OPTIONAL { ?ims_chembl_target_uri a ?target_type }
	OPTIONAL { ?ims_chembl_target_uri chembl:organismName ?chembl_organism }
  }
}
FILTER (?uniprot_name != '')
" .