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01_09_compoundTreePharmaCount.ttl
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@base <http://www.openphacts.org/api> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dcterms: <http://purl.org/dc/terms/>.
@prefix api: <http://purl.org/linked-data/api/vocab#> .
@prefix gc: <http://puelia-php.googlecode.com/svn/trunk/documents/config.ttl#> .
@prefix rel: <http://vocab.org/relationship/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix drugbank: <http://bio2rdf.org/drugbank_vocabulary:> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix ops: <http://www.openphacts.org/api#> .
@prefix chembl: <http://rdf.ebi.ac.uk/terms/chembl#> .
@prefix chembl-ops: <http://www.openphacts.org/terms/chembl#> .
@prefix bibo: <http://purl.org/ontology/bibo/> .
@prefix cheminf: <http://semanticscience.org/resource/> .
<#compound> a api:API ;
rdfs:label "Compound"@en ;
api:sparqlEndpoint <http://alpha.openphacts.org:8890/sparql/> ;
api:contentNegotiation api:parameterBased ;
api:variable <#input> ;
api:variable _:targetOrganism ;
api:variable chembl:organismName ;
api:variable chembl:standardType;
api:variable chembl:standardValue ;
api:variable chembl:hasQUDT ;
api:variable chembl:standardRelation ;
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.conceptwiki.org> ;
api:dataset <http://www.ebi.ac.uk/chembl>;
api:dataset <http://www.openphacts.org/bio2rdf/drugbank> ;
api:vocabulary <http://semanticscience.org/resource/> ;
api:vocabulary <http://bio2rdf.org/drugbank_vocabulary:> ;
api:vocabulary <http://www.w3.org/2004/02/skos/core#> ;
api:vocabulary <http://www.openphacts.org/api#> ;
api:vocabulary <http://rdf.ebi.ac.uk/terms/chembl#> ;
api:description "An API configuration to return information about compounds" ;
api:endpoint [
a api:ItemEndpoint ;
api:name "Compound Class Pharmacology: Count" ;
api:description "The total number of activity values in the LDC for a given Compound class. Currently only the ChEBI Ontology is supported. " ;
api:uriTemplate "/compound/tree/pharmacology/count?uri={uri}" ;
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> ;
api:itemTemplate "{uri}" ;
api:exampleRequestPath "/compound/tree/pharmacology/count?uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_100";
api:exampleRequestPath "/compound/tree/pharmacology/count?uri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_100&assay_organism=Mus%20musculus&minEx-activity_value=10000&activity_unit=nanomolar";
api:viewer <#compoundClassPharmaCountViewer> ;
api:defaultViewer <#compoundClassPharmaCountViewer> . ] .
<http://www.openphacts.org/api#> api:label "ops" .
<http://rdf.ebi.ac.uk/terms/chembl#> api:label "chembl" .
<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" .
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 "?target_uri";
rdfs:subPropertyOf chembl:organismName ;
a rdf:Property .
chembl:standardType api:name "activity_type" ;
api:label "activity_type" ;
api:filterVariable "?activity_uri";
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 "?activity_uri";
a rdf:Property .
chembl:standardValue api:name "activity_value" ;
api:label "activity_value" ;
api:value "Return activity values equal to this number." ;
api:filterVariable "?activity_uri";
a rdf:Property .
chembl:standardRelation api:name "activity_relation" ;
api:label "activity_relation" ;
api:value ">, >=,= , < , <=" ;
api:filterVariable "?activity_uri";
a rdf:Property .
chembl:pChembl api:name "pChembl" ;
api:label "pChembl" ;
api:filterVariable "?activity_uri";
api:value "Return activities with a pChembl value equal to this number." ;
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 "?activity_uri" ;
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 .
_:type api:name "target_type" ;
api:label "target_type" ;
api:filterVariable "?target_uri";
api:value "One of the types listed at /target/types. e.g. single_protein" ;
rdfs:subPropertyOf rdf:type ;
a rdf:Property .
<#input> api:name "uri" ;
api:label "uri";
api:value "A ChEBI Class URI. e.g.: http://purl.obolibrary.org/obo/CHEBI_100" ;
rdfs:range rdfs:Resource .
<#compoundClassPharmaCountViewer> a api:Viewer ;
api:name "compoundClassPharmaCountViewer" ;
api:template
"?ops_item ops:compoundPharmacologyTotalResults ?count . " ;
api:where
"{ SELECT (COUNT(?activity_uri) AS ?count) WHERE {
GRAPH <http://www.ebi.ac.uk/chebi/inference> {
?subclass rdfs:subClassOf ?node_uri .
}
GRAPH <http://www.ebi.ac.uk/chebi> {
?chebi_compound rdfs:subClassOf|rdfs:subClassOf/owl:someValuesFrom ?subclass .
}
GRAPH <http://www.ebi.ac.uk/chembl> {
?chembl_compound skos:exactMatch ?chebi_compound .
?activity_uri a chembl:Activity ;
chembl:hasMolecule ?chembl_compound ;
chembl:hasAssay ?assay_uri .
?assay_uri chembl:hasTarget ?target_uri .
OPTIONAL { ?activity_uri chembl:dataValidityIssue ?issue_tmp }
BIND (IF (BOUND(?issue_tmp) , ?issue_tmp, false) AS ?issue)
OPTIONAL { ?activity_uri 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)
}
} }" .