01_05_compoundClassifications.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 void: <http://rdfs.org/ns/void#> .
@prefix go: <http://www.geneontology.org/formats/oboInOwl#> .

<#compound> a api:API ;
	rdfs:label "Compound"@en ;
	api:sparqlEndpoint <http://alpha.openphacts.org:8890/sparql/> ;
	api:contentNegotiation api:parameterBased ;
	api:variable _:hierarchy ;
	api:variable <#input> ;
	api:dataset <http://www.ebi.ac.uk/chebi> ;
        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 compounds." ;
	api:endpoint [
		a api:ItemEndpoint ;
		api:name "Compound Classifications" ;
		api:description "The classes the given compound URI has been classified with. Currently supported hierarchies are the ChEBI Ontology and the Gene Ontology. " ;
		api:itemTemplate "{uri}" ;
		api:variable <http://www.ebi.ac.uk/chebi> ;
		api:variable <http://www.geneontology.org> ;
		api:uriTemplate "/compound/classifications?uri={uri}" ;
		api:exampleRequestPath "/compound/classifications?uri=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5" ;
                api:exampleRequestPath "/compound/classifications?uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_15904&tree=go" ;
		api:viewer <#compoundClassificationsViewer> ;
		api:defaultViewer <#compoundClassificationsViewer> ] .

<http://www.ebi.ac.uk/chebi> api:label "ChEBI Ontology" .
<http://www.geneontology.org> api:label "Gene Ontology" .

<http://www.ebi.ac.uk/chebi> api:name "chebi" .
<http://www.geneontology.org> api:name "go" .

_:hierarchy api:name "tree" ;
	api:label "tree" ;
	api:value "Restrict results by hierarchy. Currently one of 'chebi', 'go'" ;
	api:filterVariable "?g" ;
	rdfs:subPropertyOf api:graphFilter ;
	a rdf:Property .

<#input> api:name "uri" ;
        api:label "uri";
        api:value "A compound URI.  e.g.: http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5" ;
        rdfs:range rdfs:Resource .

<#compoundClassificationsViewer> a api:Viewer ;
	api:name "compoundClassificationsViewer";
	api:template
"?ops_item skos:exactMatch ?chembl_compound_uri ;
	skos:exactMatch ?cw_compound_uri .
?chembl_compound_uri ops:hasChebiClassification ?chebi_class ;
	ops:hasChebiClassification ?chebi_other_class ;
	void:inDataset <http://www.ebi.ac.uk/chembl> .
?chebi_input ops:hasGoClassification ?go_class ;
	skos:prefLabel ?chebi_input_label ;
	void:inDataset <http://www.geneontology.org> .
?go_input ops:hasChebiClassification ?chebi_class ;
	skos:prefLabel ?go_input_label ;
        void:inDataset <http://www.ebi.ac.uk/chembl> .
?cw_compound_uri skos:prefLabel ?cw_label ;
	void:inDataset <http://www.conceptwiki.org> .
?chebi_class skos:prefLabel ?chebi_label ;
	ops:classificationType rdf:type ;
        void:inDataset <http://www.ebi.ac.uk/chebi> .
rdf:type skos:prefLabel 'Type' .
?chebi_other_class skos:prefLabel ?chebi_other_label ;
        ops:classificationType ?chebi_class_type ;
        void:inDataset <http://www.ebi.ac.uk/chebi> .
?chebi_class_type skos:prefLabel ?chebi_class_type_label .
?go_class skos:prefLabel ?go_label ;
	void:inDataset <http://www.geneontology.org> .
<http://www.ebi.ac.uk/chebi> skos:prefLabel 'ChEBI Ontology' .
<http://www.geneontology.org> skos:prefLabel 'GeneOntology' . ";
	api:where
"	GRAPH <http://www.ebi.ac.uk/chembl> {
		?chembl_compound_uri skos:exactMatch ?chebi_compound
        	GRAPH ?g {
			{ ?chebi_compound rdfs:subClassOf ?chebi_class .
			?chebi_class rdfs:label ?chebi_label .
			FILTER(!isBlank(?chebi_class)) }
			OPTIONAL { ?chebi_compound rdfs:subClassOf _:bNode .
				_:bNode owl:someValuesFrom ?chebi_other_class ;
					owl:onProperty ?chebi_class_type .
	                        ?chebi_other_class rdfs:label ?chebi_other_label .
	                        ?chebi_class_type rdfs:label ?chebi_class_type_label }
		}
	}
	{ GRAPH <http://www.conceptwiki.org> {
                ?cw_compound_uri skos:prefLabel ?cw_label
        } } UNION
	{ GRAPH <http://www.geneontology.org> {
		BIND(?ops_item AS ?chebi_input)
		BIND( CONCAT('CHEBI:',STRAFTER(STR(?ops_item),'_')) AS ?input_label )
        	?go_class go:hasDefinition/go:hasDbXref/rdfs:label ?input_label
		GRAPH <http://www.ebi.ac.uk/chebi> {
			?chebi_input rdfs:label ?chebi_input_label
		}
		GRAPH ?g {
                        ?go_class rdfs:label ?go_label
		}}
	} UNION
        { GRAPH <http://www.geneontology.org> {
		BIND(?ops_item AS ?go_input)
                ?ops_item go:hasDefinition/go:hasDbXref/rdfs:label ?output_label
		BIND(IRI(CONCAT('http://purl.obolibrary.org/obo/CHEBI_', STRAFTER(?output_label, ':'))) AS ?chebi_class)
		GRAPH <http://www.geneontology.org> {
			?go_input rdfs:label ?go_input_label
		}
		GRAPH ?g {
                        ?chebi_class rdfs:label ?chebi_label
                }} .
        }"