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03_10_targetTreePharma.ttl
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@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 cheminf: <http://semanticscience.org/resource/> .
@prefix qudt: <http://qudt.org/1.1/schema/qudt#> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix cito: <http://purl.org/spar/cito/> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix chembl: <http://rdf.ebi.ac.uk/terms/chembl#> .
@prefix obo_goa: <http://www.semantic-systems-biology.org/ontology/rdf/OBO#> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix goa: <http://www.semantic-systems-biology.org/ontology/rdf/GOA#> .
@prefix sio: <http://semanticscience.org/resource/> .
<#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 _:targetOrganism ;
api:variable chembl:standardType;
api:variable chembl:standardValue ;
api:variable chembl:hasQUDT ;
api:variable chembl:standardRelation ;
api:variable chembl:organismName ;
api:variable chembl:pChembl ;
api:variable chembl:dataValidityIssue ;
api:variable chembl:dataValidityComment ;
api:variable chembl:potentialDuplicate ;
api:variable chembl:targetConfScore ;
api:variable chembl:targetRelType ;
api:variable _:type ;
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 [
api:variable <http://www.openphacts.org/units/MicrogramPerMilliliter> ;
api:variable <http://www.openphacts.org/units/Millimolar> ;
api:variable <http://www.openphacts.org/units/Nanomolar> ;
api:variable <http://qudt.org/vocab/unit#Percent> ;
api:variable <http://www.openphacts.org/units/MilligramPerMilliliter> ;
api:variable <http://qudt.org/vocab/unit#MinuteTime> ;
api:variable <http://qudt.org/vocab/unit#Gram> ;
api:variable <http://www.openphacts.org/units/NanogramPerMilliliter> ;
api:variable <http://qudt.org/vocab/unit#Hour> ;
api:variable <http://www.openphacts.org/units/PicogramPerMilliliter> ;
api:variable <http://www.openphacts.org/units/Micromolar> ;
api:variable <http://www.openphacts.org/units/Molar> ;
api:variable <http://www.openphacts.org/units/MilligramPerDeciliter> ;
api:variable <http://qudt.org/vocab/unit#Day> ;
api:variable <http://qudt.org/vocab/unit#SecondTime> ;
api:variable <http://www.openphacts.org/units/Picomolar> ;
api:variable <http://qudt.org/vocab/unit#Centimeter> ;
api:variable <http://www.openphacts.org/units/GramPerLiter> ;
api:variable <http://qudt.org/vocab/unit#InternationalUnitPerLiter> ;
api:variable <http://qudt.org/vocab/unit#Kilogram> ;
api:variable <http://qudt.org/vocab/unit#DegreeCelsius> ;
api:variable <http://qudt.org/vocab/unit#MilliSecond> ;
api:variable <http://qudt.org/vocab/unit#Millimeter> ;
api:variable <http://qudt.org/vocab/unit#Micrometer> ;
api:variable <http://qudt.org/vocab/unit#Liter> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#SingleProtein> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ProteinComplexGroup> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ProteinFamily> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ProteinSelectivityGroup> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ProteinComplex> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#Organism> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#CellLine> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#Tissue> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ProteinProteinInteraction> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#UnknownTarget> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#NucleicAcid> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#SubCellular> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#UnclassifiedTarget> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ADMET> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#ChimericProtein> ;
api:variable <http://rdf.ebi.ac.uk/terms/chembl#Phenotype> ;
a api:IntermediateExpansionEndpoint ;
api:name "Target Class Pharmacology: List " ;
api:description "A page of items corresponding to acitivity values in the LDC for 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:uriTemplate "/target/tree/pharmacology/pages?uri={uri}" ;
api:exampleRequestPath "/target/tree/pharmacology/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F6.2.-.-";
api:exampleRequestPath "/target/tree/pharmacology/pages?uri=http%3A%2F%2Fpurl.uniprot.org%2Fenzyme%2F1.1.-.-&activity_type=IC50&activity_unit=nanomolar&assay_organism=Rattus%20norvegicus&target_organism=Rattus%20norvegicus&minEx-activity_value=50000&maxEx-activity_value=200000";
api:selector [
api:where "
{ SELECT DISTINCT ?chembl_target ?chembl_compound ?ocrs_compound ?node_uri ?assay_uri ?item ?target_type ?issue ?dup ?conf_score WHERE {
?chembl_target chembl:hasProteinClassification|chembl:hasTargetComponent/chembl:targetCmptXref|chembl:hasTargetComponent/skos:exactMatch/obo_goa:C|chembl:hasTargetComponent/skos:exactMatch/obo_goa:F|chembl:hasTargetComponent/skos:exactMatch/obo_goa:P ?class .
GRAPH ?g {
?class rdfs:subClassOf ?node_uri .
}
GRAPH <http://www.ebi.ac.uk/chembl> {
?item a chembl:Activity ;
chembl:hasAssay ?assay_uri ;
chembl:hasMolecule ?chembl_compound .
?assay_uri chembl:hasTarget ?chembl_target .
?chembl_target a ?target_type .
OPTIONAL {
GRAPH <http://chemistry.openphacts.org> {
?ocrs_compound skos:exactMatch ?chembl_compound .
}
}
OPTIONAL { ?item chembl:dataValidityIssue ?issue_tmp }
BIND (IF (BOUND(?issue_tmp) , true, false) AS ?issue)
OPTIONAL { ?item chembl:potentialDuplicate ?dup_tmp }
BIND (IF (BOUND(?dup_tmp) , true, false) AS ?dup)
OPTIONAL { ?assay_uri chembl:targetConfScore ?conf_score_tmp }
BIND (IF (BOUND(?conf_score_tmp) , ?conf_score_tmp, 0) AS ?conf_score)
}
} }
" ;
api:expansionVariable "chembl_compound" ;
] ;
api:viewer <#targetTreePharmaViewer> ;
api:defaultViewer <#targetTreePharmaViewer> ] .
<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" .
chembl:targetRelType api:name "target_rel_type" ;
api:label "target_rel_type" ;
api:value "ChEMBL Assay relationship type annotation. A single capital letter as follows. U: Default value - Target has yet to be curated; D: Direct protein target assigned; H: Homologous protein target assigned; M: Molecular target other than protein assigned; N: Non-molecular target assigned; S: Subcellular target assigned" ;
api:filterVariable "?assay_uri";
a rdf:Property .
chembl:organismName api:name "assay_organism" ;
api:label "assay_organism" ;
api:value "A literal organism in ChEMBL." ;
api:filterVariable "?assay_uri";
a rdf:Property .
_:targetOrganism api:name "target_organism" ;
api:label "target_organism" ;
api:value "A literal target organism in ChEMBL." ;
api:filterVariable "?chembl_target";
rdfs:subPropertyOf chembl:organismName ;
a rdf:Property .
chembl:standardType api:name "activity_type" ;
api:label "activity_type" ;
api:filterVariable "?item";
api:value "One of the activity types listed at /pharmacology/filters/activities" ;
a rdf:Property .
chembl:hasQUDT api:name "activity_unit" ;
api:label "activity_unit" ;
api:value "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed valued. For e.g. IC50: /pharmacology/filters/units/IC50" ;
api:filterVariable "?item";
a rdf:Property .
chembl:standardValue api:name "activity_value" ;
api:label "activity_value" ;
api:value "Return activity values equal to this number." ;
api:filterVariable "?item";
a rdf:Property .
chembl:standardRelation api:name "activity_relation" ;
api:label "activity_relation" ;
api:value ">, >=,= , < , <=" ;
api:filterVariable "?item";
a rdf:Property .
chembl:pChembl api:name "pChembl" ;
api:label "pChembl" ;
api:filterVariable "?item";
api:value "Return activities with a pChembl value equal to this number." ;
a rdf:Property .
_:type api:name "target_type" ;
api:label "target_type" ;
api:filterVariable "?chembl_target";
api:value "One of the types listed at /target/types. e.g. single_protein" ;
rdfs:subPropertyOf rdf:type ;
a rdf:Property .
chembl:dataValidityIssue api:name "data_validity_issue" ;
api:label "data_validity_issue" ;
api:filterVariable "?issue" ;
api:value "ChEMBL data validity issue annotation. One of: true, false." ;
rdfs:subPropertyOf api:graphFilter ;
a rdf:Property .
chembl:dataValidityComment api:name "data_validity_comment" ;
api:label "data_validity_comment" ;
api:filterVariable "?item" ;
api:value "ChEMBL data validity issue annotation. One of: 'Manually validated', 'Non standard unit for type','Outside typical range' ,'Potential missing data', 'Potential transcription error', 'Potential author error', 'Author confirmed error'." ;
a rdf:Property .
chembl:potentialDuplicate api:name "potential_duplicate" ;
api:label "potential_duplicate" ;
api:filterVariable "?dup" ;
api:value "ChEMBL potential duplicate annotation. One of: true, false." ;
rdfs:subPropertyOf api:graphFilter ;
a rdf:Property .
chembl:targetConfScore api:name "target_conf_score";
api:label "target_conf_score" ;
api:value "ChEMBL Target confidence score. An integer denoting the confidence of the target assigned. 0: Default value - Target unknown or has yet to be assigned; 1: Target assigned is non-molecular; 2: Target assigned is subcellular fraction; 3: Target assigned is molecular non-protein target; 4: Multiple homologous protein targets may be assigned; 5: Multiple direct protein targets may be assigned; 6: Homologous protein complex subunits assigned; 7: Direct protein complex subunits assigned; 8: Homologous single protein target assigned; 9: Direct single protein target assigned" ;
api:filterVariable "?conf_score" ;
rdfs:subPropertyOf api:graphFilter ;
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 .
<http://www.conceptwiki.org> api:label "ConceptWiki" .
<http://www.ebi.ac.uk/chembl> api:label "ChEMBL - RDF" .
<http://www.openphacts.org/bio2rdf/drugbank> api:label "DrugBank" .
<http://www.openphacts.org/units/MicrogramPerMilliliter> api:name "microgram_per_milliliter" .
<http://www.openphacts.org/units/Millimolar> api:name "millimolar" .
<http://www.openphacts.org/units/Nanomolar> api:name "nanomolar" .
<http://qudt.org/vocab/unit#Percent> api:name "percent" .
<http://www.openphacts.org/units/MilligramPerMilliliter> api:name "milligram_per_milliliter" .
<http://qudt.org/vocab/unit#MinuteTime> api:name "minute_time" .
<http://qudt.org/vocab/unit#Gram> api:name "gram" .
<http://www.openphacts.org/units/NanogramPerMilliliter> api:name "nanogram_per_milliliter" .
<http://qudt.org/vocab/unit#Hour> api:name "hour" .
<http://www.openphacts.org/units/PicogramPerMilliliter> api:name "picogram_per_milliliter" .
<http://www.openphacts.org/units/Micromolar> api:name "micromolar" .
<http://www.openphacts.org/units/Molar> api:name "molar" .
<http://www.openphacts.org/units/MilligramPerDeciliter> api:name "milligram_per_deciliter" .
<http://qudt.org/vocab/unit#Day> api:name "day" .
<http://qudt.org/vocab/unit#SecondTime> api:name "second_time" .
<http://www.openphacts.org/units/Picomolar> api:name "picomolar" .
<http://qudt.org/vocab/unit#Centimeter> api:name "centimeter" .
<http://www.openphacts.org/units/GramPerLiter> api:name "gram_per_liter" .
<http://qudt.org/vocab/unit#InternationalUnitPerLiter> api:name "international_unit_per_liter" .
<http://qudt.org/vocab/unit#Kilogram> api:name "kilogram" .
<http://qudt.org/vocab/unit#DegreeCelsius> api:name "degree_celsius" .
<http://qudt.org/vocab/unit#MilliSecond> api:name "milli_second" .
<http://qudt.org/vocab/unit#Millimeter> api:name "millimeter" .
<http://qudt.org/vocab/unit#Micrometer> api:name "micrometer" .
<http://qudt.org/vocab/unit#Liter> api:name "liter" .
<http://rdf.ebi.ac.uk/terms/chembl#SingleProtein> api:name "single_protein" .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinComplexGroup> api:name "protein_complex_group" .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinFamily> api:name "protein_family" .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinSelectivityGroup> api:name "protein_selectivity_group" .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinComplex> api:name "protein_complex" .
<http://rdf.ebi.ac.uk/terms/chembl#Organism> api:name "organism" .
<http://rdf.ebi.ac.uk/terms/chembl#CellLine> api:name "cell_line" .
<http://rdf.ebi.ac.uk/terms/chembl#Tissue> api:name "tissue" .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinProteinInteraction> api:name "ppi" .
<http://rdf.ebi.ac.uk/terms/chembl#UnknownTarget> api:name "unknown" .
<http://rdf.ebi.ac.uk/terms/chembl#NucleicAcid> api:name "nucleic_acid" .
<http://rdf.ebi.ac.uk/terms/chembl#SubCellular> api:name "sub_cellular" .
<http://rdf.ebi.ac.uk/terms/chembl#UnclassifiedTarget> api:name "unclassified" .
<http://rdf.ebi.ac.uk/terms/chembl#ADMET> api:name "admet" .
<http://rdf.ebi.ac.uk/terms/chembl#ChimericProtein> api:name "chimeric_protein" .
<http://rdf.ebi.ac.uk/terms/chembl#Phenotype> api:name "phenotype" .
<#targetTreePharmaViewer> a api:Viewer ;
api:name "targetTreePharmaViewer";
api:template
"?item chembl:hasMolecule ?chembl_compound;
chembl:publishedType ?published_type ;
chembl:publishedRelation ?published_relation ;
chembl:publishedValue ?published_value ;
chembl:publishedUnits ?published_unit ;
chembl:standardType ?activity_type;
chembl:standardRelation ?activity_relation;
chembl:standardValue ?activity_value;
chembl:hasQUDT ?qudt_uri;
chembl:hasAssay ?assay_uri ;
chembl:pChembl ?pChembl ;
chembl:activityComment ?act_comment ;
ops:dataValidityIssue ?issue ;
ops:dataValidityComment ?comment ;
ops:potentialDuplicate ?dup ;
chembl:hasDocument ?doi ;
bibo:pmid ?pmid ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?qudt_uri skos:prefLabel ?activity_unit .
?assay_uri chembl:hasTarget ?chembl_target ;
chembl:assayTestType ?assay_type ;
dcterms:description ?assay_description ;
chembl:targetConfDesc ?conf_desc ;
ops:targetConfScore ?conf_score ;
ops:targetRelType ?rel_type ;
chembl:targetRelDesc ?rel_desc ;
chembl:assayOrganismName ?assay_organism ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_target dcterms:title ?target_name;
chembl:targetOrganismName ?target_organism ;
ops:classifiedUnder ?class ;
chembl:hasTargetComponent ?protein ;
a ?target_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_compound skos:exactMatch ?ocrs_compound ;
skos:exactMatch ?cw_compound ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?ims_ocrs_compound_uri ops:smiles ?smiles ;
ops:inchi ?inchi ;
ops:inchikey ?inchi_key;
ops:molweight ?molweight ;
ops:ro5_violations ?num_ro5_violations ;
void:inDataset <http://chemistry.openphacts.org> .
?protein skos:exactMatch ?cw_target .
?cw_target skos:prefLabel ?protein_name ;
void:inDataset <http://www.conceptwiki.org> .
?ims_cw_compound_uri skos:prefLabel ?compound_name ;
void:inDataset <http://www.conceptwiki.org> .
";
api:where "
{
GRAPH <http://www.ebi.ac.uk/chembl> {
?item a chembl:Activity ;
chembl:hasAssay ?assay_uri ;
chembl:hasMolecule ?chembl_compound .
?assay_uri chembl:hasTarget ?chembl_target .
?chembl_target a ?target_type .
OPTIONAL { ?item chembl:dataValidityIssue ?issue_tmp }
BIND (IF (BOUND(?issue_tmp) , ?issue_tmp, false) AS ?issue)
OPTIONAL { ?item chembl:potentialDuplicate ?dup_tmp }
BIND (IF (BOUND(?dup_tmp) , ?dup_tmp, false) AS ?dup)
OPTIONAL { ?assay_uri chembl:targetConfScore ?conf_score_tmp }
BIND (IF (BOUND(?conf_score_tmp) , ?conf_score_tmp, 0) AS ?conf_score)
OPTIONAL { ?assay_uri chembl:organismName ?assay_organism }
OPTIONAL { ?assay_uri dcterms:description ?assay_description }
OPTIONAL { ?assay_uri chembl:assayTestType ?assay_type }
OPTIONAL { ?assay_uri chembl:targetConfDesc ?conf_desc }
OPTIONAL { ?assay_uri chembl:targetRelType ?rel_type ;
chembl:targetRelDesc ?rel_desc }
OPTIONAL { ?chembl_target dcterms:title ?target_name }
OPTIONAL { ?chembl_target chembl:organismName ?target_organism }
OPTIONAL { ?chembl_target chembl:hasTargetComponent ?protein .
OPTIONAL { GRAPH <http://www.conceptwiki.org> {
?cw_target skos:exactMatch ?protein ;
skos:prefLabel ?protein_name
} }
}
OPTIONAL { ?item chembl:publishedType ?published_type }
OPTIONAL { ?item chembl:publishedRelation ?published_relation }
OPTIONAL { ?item chembl:publishedValue ?published_value }
OPTIONAL { ?item chembl:publishedUnits ?published_unit }
OPTIONAL { ?item chembl:standardType ?activity_type }
OPTIONAL { ?item chembl:standardRelation ?activity_relation }
OPTIONAL { ?item chembl:standardValue ?std_value .
BIND (xsd:decimal(?std_value) as ?activity_value) }
OPTIONAL { ?item chembl:standardUnits ?activity_unit }
OPTIONAL { ?item chembl:hasQUDT ?qudt_uri }
OPTIONAL { ?item chembl:pChembl ?pChembl }
OPTIONAL { ?item chembl:activityComment ?act_comment }
OPTIONAL { ?item chembl:hasDocument ?document .
OPTIONAL { ?document owl:sameAs ?doi }
OPTIONAL { ?document bibo:pmid ?pmid }
}
OPTIONAL { ?item chembl:dataValidityComment ?comment}
}
} UNION
{
GRAPH <http://chemistry.openphacts.org> {
?ims_ocrs_compound_uri cheminf:CHEMINF_000396 ?inchi;
cheminf:CHEMINF_000399 ?inchi_key;
cheminf:CHEMINF_000018 ?smiles .
OPTIONAL { [] obo:IAO_0000136 ?ims_ocrs_compound_uri ;
a cheminf:CHEMINF_000367;
qudt:numericValue ?num_ro5_violations . }
OPTIONAL { [] obo:IAO_0000136 ?ims_ocrs_compound_uri ;
a cheminf:CHEMINF_000484 ;
qudt:numericValue ?molweight . }
}
} UNION
{
GRAPH <http://www.conceptwiki.org> {
?ims_cw_compound_uri skos:prefLabel ?compound_name .
}
} " .