{
"basePath": "https://beta.openphacts.org/1.5",
"apiVersion": "v1.5",
"apis": [
{
"path": "/compound" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Information" ,
"description": "Returns information about a single compound including (but not limited to): molecular weight, biotransformation, protein binding and toxicity.
Response template:
?ops_item skos:exactMatch ?cw_compound_uri .
?cw_compound_uri skos:prefLabel ?compound_name ;
void:inDataset <http://www.conceptwiki.org> .
?ops_item skos:exactMatch ?ocrs_compound_uri .
?ocrs_compound_uri ops:smiles ?smiles ;
ops:inchi ?inchi ;
ops:inchikey ?inchiKey ;
ops:logp ?alogp ;
ops:hb a ?hba ;
ops:hbd ?hbd ;
ops:ro5_violations ?num_ro5_violations ;
ops:ps a ?psa ;
ops:rtb ?rtb ;
ops:molweight ?molweight ;
ops:molformul a ?molformula ;
void:inDataset <http://ops.rsc.org> .
?ops_item skos:exactMatch ?chembl_compound_uri .
?chembl_compound_uri ?bNode1 ?mw_freebase ;
a ?mol_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?ops_item skos:exactMatch ?db_compound_uri .
?db_compound_uri drugbank:metabolism ?metabolism ;
drugbank:description ?description ;
drugbank:proteinBinding ?proteinBinding ;
drugbank:toxicity ?toxicity ;
drugbank:meltingPoint ?meltingPoint ;
drugbank:genericName ?drug_name ;
drugbank:drugType ?drugType ;
ops:drugInteraction ?interaction ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
?interaction ops:interactingDrug ?interacting_drug ;
drugbank:text ?interaction_text ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
?ops_item skos:exactMatch ?aers_compound_uri .
?aers_compound_uri ops:reportedAdverseEvent ?event ;
skos:prefLabel ?aers_drug_name ;
void:inDataset <http://aers.data2semantics.org/> .
?event skos:prefLabel ?event_label ;
void:inDataset <http://aers.data2semantics.org/> .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5" ,
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/batch" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Information: Batch" ,
"description": "Information about compounds provided in a list sperated by '|'.
Response template:
?ims_cw_compound_uri skos:prefLabel ?compound_name ;
void:inDataset <http://www.conceptwiki.org> .
?ims_ocrs_compound_uri ops:smiles ?smiles ;
ops:inchi ?inchi ;
ops:inchikey ?inchiKey ;
ops:logp ?alogp ;
ops:hb a ?hba ;
ops:hbd ?hbd ;
ops:ro5_violations ?num_ro5_violations ;
ops:ps a ?psa ;
ops:rtb ?rtb ;
ops:molweight ?molweight ;
ops:molformul a ?molformula ;
void:inDataset <http://ops.rsc.org> .
?ims_chembl_compound_uri ?bNode1 ?mw_freebase ;
a ?mol_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?ims_db_compound_uri drugbank:biotransformation ?biotransformation ;
drugbank:description ?description ;
drugbank:proteinBinding ?proteinBinding ;
drugbank:toxicity ?toxicity ;
drugbank:meltingPoint ?meltingPoint ;
ops:drugInteraction ?interaction ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
?interaction ops:interactingDrug ?interacting_drug ;
drugbank:text ?interaction_text ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri_list" ,
"description": "A list of compound URIs separated by '|' characters" ,
"defaultValue": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5|http://www.conceptwiki.org/concept/dd758846-1dac-4f0d-a329-06af9a7fa413" ,
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/members/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Class Members: Count" ,
"description": "The number of compounds classified with the given class in the supported hierarchies. Currently the only supported hierarchy is the ChEBI Ontology.
Response template:
?ops_item ops:memberCount ?count .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.obolibrary.org/obo/CHEBI_24431",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/members/pages" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Class Members: List" ,
"description": "A list of compounds classified with the given class in the supported hierarchies. Currently the only supported hierarchy is the ChEBI Ontology.
Response template:
?item skos:exactMatch ?compound_ocrs ;
skos:exactMatch ?compound_cw .
?compound_cw skos:prefLabel ?compound_name
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"dataType": "string",
"defaultValue": "http://purl.obolibrary.org/obo/CHEBI_24431",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?child_node",
"DESC(?child_node)",
"?compound_name",
"DESC(?compound_name)",
"?cw_compound",
"DESC(?cw_compound)",
"?item",
"DESC(?item)",
"?node_uri",
"DESC(?node_uri)",
"?ocrs_compound",
"DESC(?ocrs_compound)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/classifications" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Classifications" ,
"description": "The classes the given compound URI has been classified with. Currently supported hierarchies are the ChEBI Ontology and the Gene Ontology.
Response 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' .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI" ,
"defaultValue": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "tree" ,
"description": "Restrict results by hierarchy." ,
"required": false,
"allowableValues": {
"values": [
"chebi",
"go"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/classificationsForTargets" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Classification of Targets for Compound" ,
"description": "The hierarchy of classes for the different Targets that interact with a given Compound. Currently supported hierarchies are the Enzyme Classification, the ChEMBL Target Tree and the Gene Ontology.
Response template:
?ops_item skos:exactMatch ?chembl_compound_uri ;
skos:exactMatch ?cw_compound_uri .
?chembl_compound_uri ops:interactsWithTargetOfClass ?class ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?cw_compound_uri skos:prefLabel ?cw_label ;
void:inDataset <http://www.conceptwiki.org> .
?class skos:prefLabel ?class_label ;
void:inDataset ?g .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI." ,
"defaultValue": "http://ops.rsc.org/OPS6958",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "tree" ,
"description": "Restrict results by hierarchy. Currently one of 'chembl', 'enzyme', 'go'" ,
"required": false,
"allowableValues": {
"values": [
"chembl",
"enzyme",
"go"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/pharmacology/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Pharmacology: Count" ,
"description": "Returns the total number of activity values in the linked data cache (LDC) for a user specified compound. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc.
Response template:
?ops_item ops:compoundPharmacologyTotalResults ?count .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/pharmacology/pages" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Pharmacology: List" ,
"description": "Returns a variety of pharmacological data, including assay and activity information, for a user specified compound. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc.
Response template:
?item chembl:hasMolecule ?chembl_compound_uri ;
chembl:standardType ?activity_type ;
chembl:standardRelation ?activity_relation ;
chembl:standardValue ?activity_value ;
chembl:hasQUDT ?qudt_uri ;
chembl:publishedType ?published_type ;
chembl:publishedRelation ?published_relation ;
chembl:publishedValue ?published_value ;
chembl:publishedUnits ?published_unit ;
chembl:pChembl ?pChembl ;
chembl:activityComment ?act_comment ;
chembl:hasAssay ?assay_uri ;
chembl:hasDocument ?doi ;
bibo:pmid ?pmid ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?qudt_uri skos:prefLabel ?activity_unit .
?assay_uri chembl:hasTarget ?target_uri ;
chembl:assayOrganismName ?assay_organism ;
chembl:assayTestType ?assay_type ;
dcterms:description ?assay_description ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?target_uri dcterms:title ?target_name ;
chembl:targetOrganismName ?target_organism ;
chembl:hasTargetComponent ?protein ;
a ?target_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_compound_uri skos:exactMatch ?cw_compound_uri .
?protein skos:exactMatch ?cw_target .
?cw_target skos:prefLabel ?protein_name ;
void:inDataset <http://www.conceptwiki.org> .
?cw_compound_uri skos:prefLabel ?compound_name ;
void:inDataset <http://www.conceptwiki.org> .
?chembl_compound_uri skos:exactMatch ?ocrs_compound_uri .
?ocrs_compound_uri ops:smiles ?smiles ;
ops:inchi ?inchi ;
ops:inchikey ?inchiKey ;
ops:molweight ?molweight ;
ops:ro5_violations ?num_ro5_violations ;
void:inDataset <http://ops.rsc.org> .
?chembl_compound_uri skos:exactMatch ?db_compound_uri ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?db_compound_uri drugbank:drugType ?drugType ;
drugbank:genericName ?drug_name ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal assay organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?act_comment",
"DESC(?act_comment)",
"?activity_relation",
"DESC(?activity_relation)",
"?activity_type",
"DESC(?activity_type)",
"?activity_unit",
"DESC(?activity_unit)",
"?activity_value",
"DESC(?activity_value)",
"?assay_description",
"DESC(?assay_description)",
"?assay_organism",
"DESC(?assay_organism)",
"?assay_type",
"DESC(?assay_type)",
"?assay_uri",
"DESC(?assay_uri)",
"?chembl_compound_uri",
"DESC(?chembl_compound_uri)",
"?compound_name",
"DESC(?compound_name)",
"?cw_compound_uri",
"DESC(?cw_compound_uri)",
"?cw_target",
"DESC(?cw_target)",
"?db_compound_uri",
"DESC(?db_compound_uri)",
"?doc_uri",
"DESC(?doc_uri)",
"?doi",
"DESC(?doi)",
"?drug_name",
"DESC(?drug_name)",
"?drugType",
"DESC(?drugType)",
"?inchi",
"DESC(?inchi)",
"?inchiKey",
"DESC(?inchiKey)",
"?item",
"DESC(?item)",
"?molweight",
"DESC(?molweight)",
"?num_ro5_violations",
"DESC(?num_ro5_violations)",
"?ocrs_compound_uri",
"DESC(?ocrs_compound_uri)",
"?pChembl",
"DESC(?pChembl)",
"?pmid",
"DESC(?pmid)",
"?protein",
"DESC(?protein)",
"?protein_name",
"DESC(?protein_name)",
"?published_relation",
"DESC(?published_relation)",
"?published_type",
"DESC(?published_type)",
"?published_unit",
"DESC(?published_unit)",
"?published_value",
"DESC(?published_value)",
"?qudt_uri",
"DESC(?qudt_uri)",
"?smiles",
"DESC(?smiles)",
"?standard_value",
"DESC(?standard_value)",
"?target_name",
"DESC(?target_name)",
"?target_organism",
"DESC(?target_organism)",
"?target_type",
"DESC(?target_type)",
"?target_uri",
"DESC(?target_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/tree/pharmacology/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Class Pharmacology: Count" ,
"description": "Returns the total number of activity values in the linked data cache (LDC) for a user specified compound class. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc. Currently only the ChEBI Ontology is supported.
Response template:
?ops_item ops:compoundPharmacologyTotalResults ?count .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A ChEBI Class URI." ,
"defaultValue": "http://purl.obolibrary.org/obo/CHEBI_100",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/compound/tree/pharmacology/pages" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Compound Class Pharmacology: List" ,
"description": "Returns a list of activity types, values and units in the linked data cache (LDC) for a user specified compound class. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc. Currently only the ChEBI Ontology is supported.
Response template:
?item chembl:hasMolecule ?chembl_compound ;
chembl:standardType ?activity_type ;
chembl:standardRelation ?activity_relation ;
chembl:standardValue ?activity_value ;
chembl:hasQUDT ?qudt_uri ;
chembl:publishedType ?published_type ;
chembl:publishedRelation ?published_relation ;
chembl:publishedValue ?published_value ;
chembl:publishedUnits ?published_unit ;
chembl:hasAssay ?assay_uri ;
chembl:pChembl ?pChembl ;
chembl:activityComment ?act_comment ;
chembl:hasDocument ?doi ;
bibo:pmid ?pmid ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?qudt_uri skos:prefLabel ?activity_unit .
?assay_uri chembl:hasTarget ?target_uri ;
chembl:assayOrganismName ?assay_organism ;
dcterms:description ?assay_description ;
chembl:assayTestType ?assay_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?target_uri dcterms:title ?target_name ;
chembl:organismName ?target_organism ;
chembl:hasTargetComponent ?protein ;
a ?target_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?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> .
?ims_ocrs_compound_uri ops:smiles ?smiles ;
ops:inchi ?inchi ;
ops:inchikey ?inchiKey ;
ops:ro5_violations ?num_ro5_violations ;
ops:molweight ?molweight ;
void:inDataset <http://ops.rsc.org> .
?chembl_compound void:inDataset <http://www.ebi.ac.uk/chembl> ;
skos:exactMatch ?ocrs_compound ;
skos:exactMatch ?cw_compound .
",
"group": "Compound" ,
"parameters": [
{
"name": "uri" ,
"description": "A ChEBI Class URI." ,
"defaultValue": "http://purl.obolibrary.org/obo/CHEBI_100",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?act_comment",
"DESC(?act_comment)",
"?activity_relation",
"DESC(?activity_relation)",
"?activity_type",
"DESC(?activity_type)",
"?activity_unit",
"DESC(?activity_unit)",
"?activity_value",
"DESC(?activity_value)",
"?assay_description",
"DESC(?assay_description)",
"?assay_organism",
"DESC(?assay_organism)",
"?assay_type",
"DESC(?assay_type)",
"?assay_uri",
"DESC(?assay_uri)",
"?chebi_compound",
"DESC(?chebi_compound)",
"?chembl_compound",
"DESC(?chembl_compound)",
"?class",
"DESC(?class)",
"?compound_name",
"DESC(?compound_name)",
"?cw_compound",
"DESC(?cw_compound)",
"?cw_target",
"DESC(?cw_target)",
"?document",
"DESC(?document)",
"?doi",
"DESC(?doi)",
"?ims_cw_compound_uri",
"DESC(?ims_cw_compound_uri)",
"?ims_ocrs_compound_uri",
"DESC(?ims_ocrs_compound_uri)",
"?inchi",
"DESC(?inchi)",
"?inchi_key",
"DESC(?inchi_key)",
"?inchiKey",
"DESC(?inchiKey)",
"?item",
"DESC(?item)",
"?molweight",
"DESC(?molweight)",
"?node_uri",
"DESC(?node_uri)",
"?num_ro5_violations",
"DESC(?num_ro5_violations)",
"?ocrs_compound",
"DESC(?ocrs_compound)",
"?pChembl",
"DESC(?pChembl)",
"?pmid",
"DESC(?pmid)",
"?protein",
"DESC(?protein)",
"?protein_name",
"DESC(?protein_name)",
"?published_relation",
"DESC(?published_relation)",
"?published_type",
"DESC(?published_type)",
"?published_unit",
"DESC(?published_unit)",
"?published_value",
"DESC(?published_value)",
"?qudt_uri",
"DESC(?qudt_uri)",
"?smiles",
"DESC(?smiles)",
"?std_value",
"DESC(?std_value)",
"?target_name",
"DESC(?target_name)",
"?target_organism",
"DESC(?target_organism)",
"?target_type",
"DESC(?target_type)",
"?target_uri",
"DESC(?target_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/structure" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Chemical Structure Conversion: Inchi to URI" ,
"description": "Converts a user specified InChI string into a ChemSpider URI. Driven by ChemSpider. Driven by ChemSpider.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic cheminf:CHEMINF_000396 ?inchi .
",
"group": "ChemSpider structure search" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "inchi" ,
"description": "An InChI string." ,
"defaultValue": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)",
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/structure" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Chemical Structure Conversion: InchiKey to URI" ,
"description": "Converts a user specified InChIKey into a ChemSpider URI. Driven by ChemSpider.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic cheminf:CHEMINF_000399 ?inchi_key .
",
"group": "ChemSpider structure search" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "inchi_key" ,
"description": "An InChIKey string." ,
"defaultValue": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/structure" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Chemical Structure Conversion: SMILES to URI" ,
"description": "Converts a user specified SMILES string into a ChemSpider URI. Driven by ChemSpider.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic cheminf:CHEMINF_000018 ?smiles .
",
"group": "ChemSpider structure search" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "smiles" ,
"description": "A SMILES string." ,
"defaultValue": "CC(=O)Oc1ccccc1C(=O)O",
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/structure/similarity" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Chemical Structure Search: Similarity" ,
"description": "A list of ChemSpider URIs for compounds similar to the input molecule will be returned. Tanimoto, Tversky and Euclidian similarities are available along with a parameter to specify the similarity threshold. Driven by ChemSpider.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic rdf:type ?searchType ;
ops_api_search:Molecule ?moleculeSmiles ;
ops_api:result ?result ;
ops_api_search:Threshold ?searchThreshold ;
ops_api_search:Alph a ?searchAlpha ;
ops_api_search:Bet a ?searchBeta ;
ops_api_search:SimilarityType ?searchSimilarityType ;
ops_api_common:Complexity ?complexity ;
ops_api_common:Isotopic ?isotopic ;
ops_api_common:HasSpectr a ?hasSpectra ;
ops_api_common:HasPatents ?hasPatents ;
ops_api_result:Start ?start ;
ops_api_result:Count ?count .
?result ops_api:relevance ?relevance .
",
"group": "ChemSpider structure search" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "searchOptions.Molecule",
"description": "A SMILES string." ,
"defaultValue": "CC(=O)Oc1ccccc1C(=O)O",
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "searchOptions.SimilarityType",
"description": "0: Tanimoto ; 1: Tversky ; 2: Euclidian" ,
"required": true,
"allowableValues": {
"values": [
"0",
"1",
"2"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "integer"
},
{
"name": "searchOptions.Threshold",
"description": "Double <= 1.0" ,
"required": true,
"minimum": "0.75",
"maximum": "1",
"defaultValue": "0.95",
"paramType": "query",
"dataType": "double"
},
{
"name": "searchOptions.Alpha",
"description": "Value in [0,1] ; Default=0.5 ; available only for Tversky metric (for the other types it will be ignored) " ,
"paramType": "query",
"minimum": "0",
"maximum": "1",
"dataType": "double"
},
{
"name": "searchOptions.Beta",
"description": "Value in [0,1] ; Default=0.5 ; available only for Tversky metric (for the other types it will be ignored) " ,
"paramType": "query",
"minimum": "0",
"maximum": "1",
"dataType": "double"
},
{
"name": "resultOptions.Start",
"description": "Integer. Return results starting the index. Default value: 0" ,
"paramType": "query",
"dataType": "integer"
},
{
"name": "resultOptions.Count",
"description": "Integer. How many results should be returned starting from Start index. Default value: -1 (returns all results)." ,
"paramType": "query",
"dataType": "integer"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/structure/substructure" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Chemical Structure Search: Substructure" ,
"description": "A list of ChemSpider URLs for compounds containing the specified structure will be returned. Specifying the parameter “searchOptions.MolType” allows either SMILES or SMARTS to be given as input. Driven by ChemSpider.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic rdf:type ?searchType ;
ops_api_search:Molecule ?moleculeSmiles ;
ops_api_search:MolType ?searchMolType ;
ops_api:result ?result ;
ops_api_search:MatchTautomers ?searchMatchTautomers ;
ops_api_common:Complexity ?complexity ;
ops_api_common:Isotopic ?isotopic ;
ops_api_common:HasSpectr a ?hasSpectra ;
ops_api_common:HasPatents ?hasPatents ;
ops_api_result:Start ?start ;
ops_api_result:Count ?count .
?result ops_api:relevance ?relevance .
",
"group": "ChemSpider structure search" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "searchOptions.Molecule",
"description": "A SMILES or SMARTS string." ,
"defaultValue": "CC(=O)Oc1ccccc1C(=O)O",
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "searchOptions.MolType",
"description": "0: SMILES ; 1: SMARTS" ,
"required": true,
"allowableValues": {
"values": [
"0",
"1"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "integer"
},
{
"name": "resultOptions.Start",
"description": "Integer. Return results starting from this index value. Default value: 0" ,
"paramType": "query",
"dataType": "integer"
},
{
"name": "resultOptions.Count",
"description": "Integer. How many results should be returned starting from Start index. Default value: -1. (Returns all results)" ,
"paramType": "query",
"dataType": "integer"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/structure/exact" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Chemical Structure Search: Exact" ,
"description": "Returns a ChemSpider URI corresponding to the input SMILES string. The optional parameter “searchOptions.MatchType” is available in order to match other forms of the input molecule such as tautomeric equivalents.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic rdf:type ?searchType ;
ops_api_search:Molecule ?moleculeSmiles ;
ops_api_search:MatchType ?searchMatchType ;
ops_api:result ?result ;
ops_api_common:Complexity ?complexity ;
ops_api_common:Isotopic ?isotopic ;
ops_api_common:HasSpectr a ?hasSpectra ;
ops_api_common:HasPatents ?hasPatents .
",
"group": "ChemSpider structure search" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "searchOptions.Molecule",
"description": "A SMILES string." ,
"defaultValue": "CNC(=O)c1cc(ccn1)Oc2ccc(cc2)NC(=O)Nc3ccc(c(c3)C(F)(F)F)Cl",
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "searchOptions.MatchType",
"description": "0: ExactMatch ; 1: AllTautomers ; 2: SameSkeletonIncludingH ; 3: SameSkeletonExcludingH ; 4: AllIsomers" ,
"required": true,
"allowableValues": {
"values": [
"0",
"1",
"2",
"3",
"4"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "integer"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Information" ,
"description": "Returns information about a single target including (but not limited to): function, alternative names, list of drugs for the target and the cellular location of the target.
Response template:
?ops_item skos:exactMatch ?cw_target_uri ;
skos:exactMatch ?uniprot_target_uri ;
skos:exactMatch ?chembl_target_uri ;
skos:exactMatch ?db_target_uri .
?cw_target_uri skos:prefLabel ?target_name ;
void:inDataset <http://www.conceptwiki.org> .
?uniprot_target_uri uniprot:existence ?existence ;
uniprot:organism ?organism ;
uniprot:sequence ?sequence ;
uniprot:Function_Annotation ?function ;
ops:interactsWith ?inter_prot ;
uniprot:classifiedWith ?class ;
uniprot:alternativeName ?alt_name ;
uniprot:mass ?mass ;
ops:molecularWeight ?mass ;
rdfs:seeAlso ?target_pdb ;
rdfs:seeAlso ?ppi ;
void:inDataset <http://purl.uniprot.org> .
?inter_prot rdfs:label ?inter_label .
?chembl_target_uri chembl:hasTargetComponent ?target_component ;
a ?target_type ;
rdfs:label ?synonym ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?target_component dcterms:description ?description ;
skos:exactMatch ?cw_target ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?cw_target skos:prefLabel ?protein_name ;
void:inDataset <http://www.conceptwiki.org> .
?db_target_uri drugbank:cellularLocation ?cellularLocation ;
drugbank:molecularWeight ?molecularWeight ;
drugbank:numberOfResidues ?numberOfResidues ;
drugbank:theoreticalPi ?theoreticalPi ;
ops:targetForDrug ?db_compound ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
?db_compound drugbank:genericName ?drug_name ;
drugbank:drugType ?drugType ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "drug_type" ,
"description": "One of: 'approved', 'experimental', 'illicit', 'investigational', 'nutraceutical', 'withdrawn'" ,
"required": false,
"allowableValues": {
"values": [
"approved",
"experimental",
"illicit",
"investigational",
"nutraceutical",
"withdrawn"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/batch" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Information: Batch" ,
"description": "Information about a list of targets, separated by '|'.
Response template:
?ims_cw_target_uri skos:prefLabel ?target_name ;
void:inDataset <http://www.conceptwiki.org> .
?ims_uniprot_target_uri uniprot:existence ?existence ;
uniprot:organism ?organism ;
uniprot:sequence ?sequence ;
uniprot:Function_Annotation ?function ;
ops:interactsWith ?inter_prot ;
uniprot:classifiedWith ?class ;
uniprot:alternativeName ?alt_name ;
uniprot:mass ?mass ;
ops:molecularWeight ?mass ;
rdfs:seeAlso ?target_pdb ;
rdfs:seeAlso ?ppi ;
void:inDataset <http://purl.uniprot.org> .
?inter_prot rdfs:label ?inter_label .
?ims_chembl_target_uri chembl:hasTargetComponent ?target_component ;
a ?target_type ;
rdfs:label ?synonym ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?target_component dcterms:description ?description ;
skos:exactMatch ?cw_target ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?ims_db_target_uri drugbank:cellularLocation ?cellularLocation ;
drugbank:molecularWeight ?molecularWeight ;
drugbank:numberOfResidues ?numberOfResidues ;
drugbank:theoreticalPi ?theoreticalPi ;
ops:targetForDrug ?db_compound ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
?db_compound drugbank:genericName ?drug_name ;
drugbank:drugType ?drugType ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
",
"group": "Target" ,
"parameters": [
{
"name": "uri_list" ,
"description": "A list of target URIs. e.g.: http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291|http://www.conceptwiki.org/concept/7b21c06f-0343-4fcc-ab0f-a74ffe871ade" ,
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "drug_type" ,
"description": "One of: 'approved', 'experimental', 'illicit', 'investigational', 'nutraceutical', 'withdrawn'" ,
"required": false,
"allowableValues": {
"values": [
"approved",
"experimental",
"illicit",
"investigational",
"nutraceutical",
"withdrawn"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/members/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Class Members: Count" ,
"description": "The number 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.
Response template:
?ops_item ops:memberCount ?count .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.uniprot.org/enzyme/6.2.-.-",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "target_organism_uri" ,
"description": "An organism URI from Uniprot. e.g. http://purl.uniprot.org/taxonomy/386043" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/members/pages" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Class Members: List" ,
"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.
Response 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 .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.uniprot.org/enzyme/6.2.-.-",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "target_organism_uri" ,
"description": "An organism URI from Uniprot. e.g. http://purl.uniprot.org/taxonomy/386043" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?chembl_name",
"DESC(?chembl_name)",
"?chembl_organism",
"DESC(?chembl_organism)",
"?chembl_target",
"DESC(?chembl_target)",
"?child_node",
"DESC(?child_node)",
"?g",
"DESC(?g)",
"?g2",
"DESC(?g2)",
"?ims_chembl_target_uri",
"DESC(?ims_chembl_target_uri)",
"?ims_uniprot_target_uri",
"DESC(?ims_uniprot_target_uri)",
"?item",
"DESC(?item)",
"?mapping",
"DESC(?mapping)",
"?mapping_dataset",
"DESC(?mapping_dataset)",
"?mapping_name",
"DESC(?mapping_name)",
"?mapping_org",
"DESC(?mapping_org)",
"?mapping_org_uri",
"DESC(?mapping_org_uri)",
"?mapping_type",
"DESC(?mapping_type)",
"?node_uri",
"DESC(?node_uri)",
"?target_type",
"DESC(?target_type)",
"?uniprot_name",
"DESC(?uniprot_name)",
"?uniprot_organism",
"DESC(?uniprot_organism)",
"?uniprot_target",
"DESC(?uniprot_target)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/classifications" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Classifications" ,
"description": "The classes the given target URI has been classified with. Currently supported hierarchies are the Enzyme Classification, the ChEMBL Target Tree and the Gene Ontology.
Response template:
?ops_item skos:exactMatch ?chembl_target_uri ;
skos:exactMatch ?uniprot_target_uri .
?chembl_target_uri chembl:hasProteinClassification ?chembl_class ;
dcterms:title ?target_name ;
a ?target_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?uniprot_target_uri ops:hasGoComponent ?go_component ;
ops:hasGoFunction ?go_function ;
ops:hasGoProcess ?go_process ;
ops:hasEnzymeClassification ?enzyme_class ;
skos:prefLabel ?uniprot_name ;
void:inDataset ?dataset .
?chembl_class skos:prefLabel ?chembl_label ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?enzyme_class skos:prefLabel ?enzyme_label ;
void:inDataset <http://purl.uniprot.org/enzyme> .
?go_component skos:prefLabel ?go_c_label ;
void:inDataset <http://www.geneontology.org> .
?go_function skos:prefLabel ?go_f_label ;
void:inDataset <http://www.geneontology.org> .
?go_process skos:prefLabel ?go_p_label ;
void:inDataset <http://www.geneontology.org> .
<http://purl.uniprot.org/enzyme> skos:prefLabel 'Enzyme Classification' .
<http://www.ebi.ac.uk/chembl/target> skos:prefLabel 'ChEMBL Target Hierarchy' .
<http://www.geneontology.org> skos:prefLabel 'GeneOntology' .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/P14756",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "tree" ,
"description": "Restrict results by hierarchy." ,
"required": false,
"allowableValues": {
"values": [
"chembl",
"enzyme",
"go"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/classificationsForCompounds" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Classification of Compounds for Target" ,
"description": "The hierarchy classes for the different Compounds that interact with a given Target. Currently only the ChEBI Ontology is supported.
Response template:
?ops_item skos:exactMatch ?chembl_target_uri ;
skos:exactMatch ?cw_target_uri .
?chembl_target_uri ops:interactsWithMoleculeOfClass ?chebi_class ;
ops:interactsWithMoleculeOfClass ?chebi_other_class ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?cw_target_uri skos:prefLabel ?cw_label .
?chebi_class skos:prefLabel ?chebi_label ;
void:inDataset <http://www.ebi.ac.uk/chebi> .
?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 .
<http://www.ebi.ac.uk/chebi> skos:prefLabel 'ChEBI Ontology' .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/P00918",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/pharmacology/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Pharmacology: Count" ,
"description": "Returns the total number of activity values in the linked data cache (LDC) for a user specified target. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc.
Response template:
?ops_item ops:targetPharmacologyTotalResults ?count .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal assay organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/pharmacology/pages" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Pharmacology: List" ,
"description": "Returns a variety of pharmacological data, including assay and activity information, for a user specified target. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc.
Response 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:assayTestType ?assay_type ;
chembl:pChembl ?pChembl ;
chembl:activityComment ?act_comment ;
bibo:pmid ?pmid ;
chembl:hasDocument ?doi ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?qudt_uri skos:prefLabel ?activity_unit .
?assay_uri chembl:assayOrganismName ?assay_organism ;
chembl:hasTarget ?chembl_target_uri ;
dcterms:description ?assay_description ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_target_uri dcterms:title ?target_name_chembl ;
chembl:targetOrganismName ?target_organism ;
chembl:hasTargetComponent ?protein ;
a ?target_type ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?protein skos:exactMatch ?cw_target .
?chembl_compound skos:exactMatch ?ocrs_compound ;
void:inDataset <http://www.ebi.ac.uk/chembl> ;
skos:exactMatch ?cw_compound .
?cw_target skos:prefLabel ?protein_name ;
void:inDataset <http://www.conceptwiki.org> .
?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://ops.rsc.org> .
?ims_cw_compound_uri skos:prefLabel ?compound_name ;
void:inDataset <http://www.conceptwiki.org> .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?act_comment",
"DESC(?act_comment)",
"?activity_relation",
"DESC(?activity_relation)",
"?activity_type",
"DESC(?activity_type)",
"?activity_unit",
"DESC(?activity_unit)",
"?activity_value",
"DESC(?activity_value)",
"?assay_description",
"DESC(?assay_description)",
"?assay_organism",
"DESC(?assay_organism)",
"?assay_type",
"DESC(?assay_type)",
"?assay_uri",
"DESC(?assay_uri)",
"?chembl_compound",
"DESC(?chembl_compound)",
"?chembl_target_uri",
"DESC(?chembl_target_uri)",
"?compound_name",
"DESC(?compound_name)",
"?cw_compound",
"DESC(?cw_compound)",
"?cw_target",
"DESC(?cw_target)",
"?doc_uri",
"DESC(?doc_uri)",
"?doi",
"DESC(?doi)",
"?ims_cw_compound_uri",
"DESC(?ims_cw_compound_uri)",
"?ims_ocrs_compound_uri",
"DESC(?ims_ocrs_compound_uri)",
"?inchi",
"DESC(?inchi)",
"?inchi_key",
"DESC(?inchi_key)",
"?item",
"DESC(?item)",
"?molweight",
"DESC(?molweight)",
"?num_ro5_violations",
"DESC(?num_ro5_violations)",
"?ocrs_compound",
"DESC(?ocrs_compound)",
"?pChembl",
"DESC(?pChembl)",
"?pmid",
"DESC(?pmid)",
"?protein",
"DESC(?protein)",
"?protein_name",
"DESC(?protein_name)",
"?published_relation",
"DESC(?published_relation)",
"?published_type",
"DESC(?published_type)",
"?published_unit",
"DESC(?published_unit)",
"?published_value",
"DESC(?published_value)",
"?qudt_uri",
"DESC(?qudt_uri)",
"?smiles",
"DESC(?smiles)",
"?standard_value",
"DESC(?standard_value)",
"?target_name_chembl",
"DESC(?target_name_chembl)",
"?target_organism",
"DESC(?target_organism)",
"?target_type",
"DESC(?target_type)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/tree/pharmacology/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Class Pharmacology: Count" ,
"description": "Returns the total number of activity values in the linked data cache (LDC) for a user specified target class. Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc. Currently supported hierarchies are the Enzyme Classification, the ChEMBL Target Tree, and the Gene Ontology.
Response template:
?ops_item ops:targetPharmacologyTotalResults ?count .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.uniprot.org/enzyme/6.2.-.-",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/tree/pharmacology/pages" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Class Pharmacology: List " ,
"description": "Returns a variety of pharmacological information, such as assay information, Filtering of results is possible via a variety of options such as: target organism, activity type, activity value, etc. Currently supported hierarchies are the Enzyme Classification, the ChEMBL Target Tree, and the Gene Ontology.
Response 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 ;
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:assayOrganismName ?assay_organism ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?chembl_target dcterms:title ?target_name ;
chembl:organismName ?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://ops.rsc.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> .
",
"group": "Target" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.uniprot.org/enzyme/6.2.-.-",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "target_organism" ,
"description": "A literal target organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_value" ,
"description": "Return activity values equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-activity_value" ,
"description": "Return activity values greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-activity_value" ,
"description": "Return activity values greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-activity_value" ,
"description": "Return activity values less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-activity_value" ,
"description": "Return activity values less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "activity_relation" ,
"description": "The relation reported. e.g. '>' for IC50 > X" ,
"required": false,
"allowableValues": {
"values": [
">",
">=",
"=",
"<",
"<="
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "assay_organism" ,
"description": "A literal organism in ChEMBL." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "pChembl" ,
"description": "Return activities with a pChembl value equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "min-pChembl" ,
"description": "Return activities with a pChembl value greater than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "minEx-pChembl" ,
"description": "Return activities with a pChembl value greater than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "max-pChembl" ,
"description": "Return activities with a pChembl value less than or equal to this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "maxEx-pChembl" ,
"description": "Return activities with a pChembl value less than this number." ,
"dataType": "double",
"paramType": "query"
},
{
"name": "target_type" ,
"description": "One of the types listed at /target/types." ,
"required": false,
"allowableValues": {
"values": [
"admet",
"chimeric_protein",
"nucleic_acid",
"organism",
"phenotype",
"ppi",
"protein_complex",
"protein_complex_group",
"protein_family",
"protein_selectivity_group",
"single_protein",
"sub_cellular",
"tissue",
"unclassified",
"unknown"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?act_comment",
"DESC(?act_comment)",
"?activity_relation",
"DESC(?activity_relation)",
"?activity_type",
"DESC(?activity_type)",
"?activity_unit",
"DESC(?activity_unit)",
"?activity_value",
"DESC(?activity_value)",
"?assay_description",
"DESC(?assay_description)",
"?assay_organism",
"DESC(?assay_organism)",
"?assay_type",
"DESC(?assay_type)",
"?assay_uri",
"DESC(?assay_uri)",
"?chembl_compound",
"DESC(?chembl_compound)",
"?chembl_target",
"DESC(?chembl_target)",
"?class",
"DESC(?class)",
"?compound_name",
"DESC(?compound_name)",
"?cw_compound",
"DESC(?cw_compound)",
"?cw_target",
"DESC(?cw_target)",
"?document",
"DESC(?document)",
"?doi",
"DESC(?doi)",
"?g",
"DESC(?g)",
"?ims_cw_compound_uri",
"DESC(?ims_cw_compound_uri)",
"?ims_ocrs_compound_uri",
"DESC(?ims_ocrs_compound_uri)",
"?inchi",
"DESC(?inchi)",
"?inchi_key",
"DESC(?inchi_key)",
"?item",
"DESC(?item)",
"?molweight",
"DESC(?molweight)",
"?node_uri",
"DESC(?node_uri)",
"?num_ro5_violations",
"DESC(?num_ro5_violations)",
"?ocrs_compound",
"DESC(?ocrs_compound)",
"?pChembl",
"DESC(?pChembl)",
"?pmid",
"DESC(?pmid)",
"?protein",
"DESC(?protein)",
"?protein_name",
"DESC(?protein_name)",
"?published_relation",
"DESC(?published_relation)",
"?published_type",
"DESC(?published_type)",
"?published_unit",
"DESC(?published_unit)",
"?published_value",
"DESC(?published_value)",
"?qudt_uri",
"DESC(?qudt_uri)",
"?smiles",
"DESC(?smiles)",
"?std_value",
"DESC(?std_value)",
"?target_name",
"DESC(?target_name)",
"?target_organism",
"DESC(?target_organism)",
"?target_type",
"DESC(?target_type)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/target/types" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Target Types" ,
"description": "Returns a list of ChEMBL target types, along with the number of each type.
Response template:
<http://www.ebi.ac.uk/chembl> ops:hasTargetType ?target_type .
?target_type ops:targetCount ?target_count .
<http://rdf.ebi.ac.uk/terms/chembl#SingleProtein> rdfs:label 'single_protein' .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinComplexGroup> rdfs:label 'protein_complex_group' .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinFamily> rdfs:label 'protein_family' .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinSelectivityGroup> rdfs:label 'protein_selectivity_group' .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinComplex> rdfs:label 'protein_complex' .
<http://rdf.ebi.ac.uk/terms/chembl#Organism> rdfs:label 'organism' .
<http://rdf.ebi.ac.uk/terms/chembl#CellLine> rdfs:label 'cell_line' .
<http://rdf.ebi.ac.uk/terms/chembl#Tissue> rdfs:label 'tissue' .
<http://rdf.ebi.ac.uk/terms/chembl#ProteinProteinInteraction> rdfs:label 'ppi' .
<http://rdf.ebi.ac.uk/terms/chembl#UnknownTarget> rdfs:label 'unknown' .
<http://rdf.ebi.ac.uk/terms/chembl#NucleicAcid> rdfs:label 'nucleic_acid' .
<http://rdf.ebi.ac.uk/terms/chembl#SubCellular> rdfs:label 'sub_cellular' .
<http://rdf.ebi.ac.uk/terms/chembl#UnclassifiedTarget> rdfs:label 'unclassified' .
<http://rdf.ebi.ac.uk/terms/chembl#ADMET> rdfs:label 'admet' .
<http://rdf.ebi.ac.uk/terms/chembl#ChimericProtein> rdfs:label 'chimeric_protein' .
<http://rdf.ebi.ac.uk/terms/chembl#Phenotype> rdfs:label 'phenotype' .
",
"group": "Target" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways: Count" ,
"description": "Returns the total number of pathways stored in the linked data cache (LDC). When the optional parameter “pathway_organism” is specified, only the number of pathways stored in the LDC for that organism will be returned.
Response template:
<http://www.wikipathways.org> ops:pathway_count ?count .
",
"group": "Pathway" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways: List" ,
"description": "Returns a list of the pathways stored in the linked data cache (LDC). Specifying the optional parameter “pathway_organism” returns only the pathways for that organism.
Response template:
?item dc:title ?title ;
wp:organism ?organism_uri ;
foaf:page ?page ;
dc:identifier ?identifier ;
dcterms:description ?description ;
wp:pathwayOntology ?ontology ;
void:inDataset <http://www.wikipathways.org> .
?organism_uri rdfs:label ?organism .
",
"group": "Pathway" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?description",
"DESC(?description)",
"?identifier",
"DESC(?identifier)",
"?item",
"DESC(?item)",
"?ontology",
"DESC(?ontology)",
"?organism",
"DESC(?organism)",
"?organism_uri",
"DESC(?organism_uri)",
"?page",
"DESC(?page)",
"?title",
"DESC(?title)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathway" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathway Information" ,
"description": "Returns information about a single pathway.
Response template:
?ops_item skos:exactMatch ?pw_uri .
?pw_uri sioc:latest_version ?rev ;
void:inDataset <http://www.wikipathways.org> .
?rev dc:title ?title ;
wp:organism ?organism_uri ;
foaf:page ?page ;
dcterms:description ?description ;
wp:pathwayOntology ?ontology ;
dcterms:hasPart ?part ;
void:inDataset <http://www.wikipathways.org> .
?organism_uri rdfs:label ?organism .
?part a ?type .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A Pathway URI." ,
"defaultValue": "http://identifiers.org/wikipathways/WP1019",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathway/getCompounds" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathway Information: Get Compounds" ,
"description": "Returns a list of compounds that are explicitly mentioned in the user specified pathway such as metabolites or drugs.
Response template:
?ops_item skos:exactMatch ?pw_uri .
?pw_uri sioc:latest_version ?rev .
?rev dc:title ?title ;
dcterms:hasPart ?metabolite ;
void:inDataset <http://www.wikipathways.org> .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A Pathway URI." ,
"defaultValue": "http://identifiers.org/wikipathways/WP1002",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathway/getTargets" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathway Information: Get Targets" ,
"description": "Returns a list of targets which are part of the user specified pathway.
Response template:
?ops_item skos:exactMatch ?pw_uri .
?pw_uri sioc:latest_version ?rev .
?rev dc:title ?title ;
dcterms:hasPart ?gene_product ;
void:inDataset <http://www.wikipathways.org> .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A Pathway URI." ,
"defaultValue": "http://identifiers.org/wikipathways/WP1008",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathway/getReferences" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathway Information: Get Publications" ,
"description": "Returns publication(s) containing information, such as evidence for a specific interaction, for a user specified pathway.
Response template:
?ops_item skos:exactMatch ?pw_uri .
?pw_uri sioc:latest_version ?rev .
?rev dc:title ?title ;
dcterms:hasPart ?reference ;
void:inDataset <http://www.wikipathways.org> .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A Pathway URI." ,
"defaultValue": "http://identifiers.org/wikipathways/WP1015",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/byCompound/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways for Compound: Count" ,
"description": "Returns the total number of pathways in which the user specified compound, usually a metabolite, plays a role.
Response template:
<http://www.wikipathways.org> ops:pathway_count ?count .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/83931753-9e3f-4e90-b104-e3bcd0b4d833",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/byCompound" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways for Compound: List" ,
"description": "Returns a list of pathways in which the user specified compound, usually a metabolite, plays a role.
Response template:
?item dc:title ?title ;
wp:organism ?organism_uri ;
foaf:page ?page ;
dc:identifier ?identifier ;
dcterms:description ?description ;
wp:pathwayOntology ?ontology ;
dcterms:hasPart ?pw_uri ;
void:inDataset <http://www.wikipathways.org> .
?organism_uri rdfs:label ?organism .
?pw_uri a wp:Metabolite ;
skos:exactMatch ?cw_uri .
?cw_uri skos:prefLabel ?prefLabel ;
void:inDataset <http://www.conceptwiki.org> .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A compound URI." ,
"defaultValue": "http://www.conceptwiki.org/concept/83931753-9e3f-4e90-b104-e3bcd0b4d833",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?cw_uri",
"DESC(?cw_uri)",
"?description",
"DESC(?description)",
"?identifier",
"DESC(?identifier)",
"?item",
"DESC(?item)",
"?metabolite",
"DESC(?metabolite)",
"?ontology",
"DESC(?ontology)",
"?organism",
"DESC(?organism)",
"?organism_uri",
"DESC(?organism_uri)",
"?page",
"DESC(?page)",
"?prefLabel",
"DESC(?prefLabel)",
"?pw_uri",
"DESC(?pw_uri)",
"?title",
"DESC(?title)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/byTarget/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways for Target: Count" ,
"description": "Returns the total number of pathways which contain a user specified target.
Response template:
<http://www.wikipathways.org> ops:pathway_count ?count .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://identifiers.org/ncbigene/282478",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/byTarget" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways for Target: List" ,
"description": "Returns a list of pathways which contain a user specified target.
Response template:
?item dc:title ?title ;
wp:organism ?organism_uri ;
foaf:page ?page ;
dc:identifier ?identifier ;
dcterms:description ?description ;
wp:pathwayOntology ?ontology ;
dcterms:hasPart ?pw_uri ;
void:inDataset <http://www.wikipathways.org> .
?organism_uri rdfs:label ?organism .
?pw_uri a wp:GeneProduct ;
skos:exactMatch ?cw_uri .
?cw_uri skos:prefLabel ?prefLabel .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI. e.g.: http://identifiers.org/ncbigene/282478" ,
"defaultValue": "http://identifiers.org/ncbigene/282478",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?cw_uri",
"DESC(?cw_uri)",
"?description",
"DESC(?description)",
"?gene_product",
"DESC(?gene_product)",
"?identifier",
"DESC(?identifier)",
"?item",
"DESC(?item)",
"?ontology",
"DESC(?ontology)",
"?organism",
"DESC(?organism)",
"?organism_uri",
"DESC(?organism_uri)",
"?page",
"DESC(?page)",
"?prefLabel",
"DESC(?prefLabel)",
"?pw_uri",
"DESC(?pw_uri)",
"?title",
"DESC(?title)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/byReference/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways for Publication: Count" ,
"description": "Returns the total number of pathways which cite a user given publication.
Response template:
<http://www.wikipathways.org> ops:pathway_count ?count .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A reference URI." ,
"defaultValue": "http://identifiers.org/pubmed/9789062",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/byReference" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathways for Publication: List" ,
"description": "Returns a list of pathways which cite a user given publication.
Response template:
?item dc:title ?title ;
wp:organism ?organism_uri ;
foaf:page ?page ;
dc:identifier ?identifier ;
dcterms:description ?description ;
wp:pathwayOntology ?ontology ;
dcterms:hasPart ?pw_uri ;
void:inDataset <http://www.wikipathways.org> .
?organism_uri rdfs:label ?organism .
?pw_uri a wp:PublicationReference .
",
"group": "Pathway" ,
"parameters": [
{
"name": "uri" ,
"description": "A reference URI." ,
"defaultValue": "http://identifiers.org/pubmed/9789062",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "pathway_organism" ,
"description": "The rdfs:label for the pathway organism (URL encode). e.g.: Homo sapiens." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?description",
"DESC(?description)",
"?identifier",
"DESC(?identifier)",
"?item",
"DESC(?item)",
"?ontology",
"DESC(?ontology)",
"?organism",
"DESC(?organism)",
"?organism_uri",
"DESC(?organism_uri)",
"?page",
"DESC(?page)",
"?pw_uri",
"DESC(?pw_uri)",
"?title",
"DESC(?title)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pathways/organisms" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Pathway Organisms" ,
"description": "Returns a list of URIs for all organisms which have pathway data available along with the organism label and how many pathways are available for each.
Response template:
<http://www.wikipathways.org> ops:pathway_organism ?item .
?item rdfs:label ?label ;
ops:pathway_count ?count .
",
"group": "Pathway" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?count",
"DESC(?count)",
"?item",
"DESC(?item)",
"?label",
"DESC(?label)",
"?pathway",
"DESC(?pathway)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/byTarget/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Diseases for Target: Count" ,
"description": "The total number of diseases which correspond to the target {uri}.
Response template:
?ops_item ops:diseaseCount ?count .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/Q9Y5Y9",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/byTarget" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Diseases for Target: List" ,
"description": "A list of diseases which correspond to {uri}.
Response template:
?item foaf:name ?diseaseName ;
ops:forGene ?dg_gene_uri ;
void:inDataset ?diseaseDataset .
?dg_gene_uri ops:encodes ?uniprot_target_uri ;
void:inDataset ?geneDataset .
?uniprot_target_uri skos:exactMatch ?cw_target_uri ;
void:inDataset <http://purl.uniprot.org> .
?cw_target_uri skos:prefLabel ?cw_prefLabel ;
void:inDataset <http://www.conceptwiki.org> .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/Q9Y5Y9",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?cw_prefLabel",
"DESC(?cw_prefLabel)",
"?cw_target_uri",
"DESC(?cw_target_uri)",
"?dg_gene_uri",
"DESC(?dg_gene_uri)",
"?diseaseDataset",
"DESC(?diseaseDataset)",
"?diseaseName",
"DESC(?diseaseName)",
"?existence",
"DESC(?existence)",
"?geneDataset",
"DESC(?geneDataset)",
"?gene_disease_assoc",
"DESC(?gene_disease_assoc)",
"?item",
"DESC(?item)",
"?uniprot_target_uri",
"DESC(?uniprot_target_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/getTargets/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Targets for Disease: Count" ,
"description": "A list of targets which correspond to the disease {uri}.
Response template:
?ops_item ops:targetCount ?count .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A disease URI." ,
"defaultValue": "http://linkedlifedata.com/resource/umls/id/C0004238",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/getTargets" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Targets for Disease: List" ,
"description": "A list of targets which correspond to the disease {uri}.
Response template:
?umls_disease_uri foaf:name ?diseaseName ;
void:inDataset ?diseaseDataset .
?item ops:forDisease ?umls_disease_uri ;
void:inDataset ?geneDataset .
?ims_uniprot_target_uri void:inDataset <http://purl.uniprot.org> .
?ims_cw_target_uri skos:prefLabel ?prefLabel ;
void:inDataset <http://www.conceptwiki.org> .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A disease URI." ,
"defaultValue": "http://linkedlifedata.com/resource/umls/id/C0004238",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?diseaseDataset",
"DESC(?diseaseDataset)",
"?diseaseName",
"DESC(?diseaseName)",
"?existence",
"DESC(?existence)",
"?geneDataset",
"DESC(?geneDataset)",
"?gene_disease_assoc",
"DESC(?gene_disease_assoc)",
"?ims_cw_target_uri",
"DESC(?ims_cw_target_uri)",
"?ims_uniprot_target_uri",
"DESC(?ims_uniprot_target_uri)",
"?item",
"DESC(?item)",
"?prefLabel",
"DESC(?prefLabel)",
"?umls_disease_uri",
"DESC(?umls_disease_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/assoc/byTarget/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Associations for Target: Count" ,
"description": "Total count of disease-target associations which correspond to a target {uri}.
Response template:
?ops_item ops:associationsCount ?count .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/Q9Y5Y9",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "assoc_type" ,
"description": "One of the following association type URIs: http://semanticscience.org/resource/SIO_001119 (gene-disease association linked with causal mutation), http://semanticscience.org/resource/SIO_001120 (therapeutic gene-disease association), http://semanticscience.org/resource/SIO_001121 (gene-disease biomarker association), http://semanticscience.org/resource/SIO_001122 (gene-disease association linked with genetic variation), http://semanticscience.org/resource/SIO_001123 (gene-disease association linked with altered gene expression), http://semanticscience.org/resource/SIO_001124 (gene-disease association linked with post-translational modification)" ,
"required": false,
"allowableValues": {
"values": [
"http://semanticscience.org/resource/SIO_001119",
"http://semanticscience.org/resource/SIO_001120",
"http://semanticscience.org/resource/SIO_001121",
"http://semanticscience.org/resource/SIO_001122",
"http://semanticscience.org/resource/SIO_001123",
"http://semanticscience.org/resource/SIO_001124"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/assoc/byTarget" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Associations for Target: List" ,
"description": "A list of disease-target associations which correspond to a target {uri}.
Response template:
?item ops:disease ?disease ;
ops:gene ?dg_gene_uri ;
rdf:type ?type ;
dcterms:description ?description ;
ops:pmid ?pubmed_id ;
ops:primarySource ?primarySource ;
void:inDataset ?assocDataset .
?type rdfs:label ?type_label .
?disease foaf:name ?diseaseName ;
ops:diseaseClass ?diseaseClass ;
void:inDataset ?diseaseDataset .
?diseaseClass foaf:name ?diseaseClassName ;
void:inDataset ?diseaseClassDataset .
?dg_gene_uri ops:encodes ?uniprot_target_uri ;
void:inDataset ?geneDataset .
?uniprot_target_uri skos:exactMatch ?cw_target_uri ;
void:inDataset <http://purl.uniprot.org> .
?cw_target_uri skos:prefLabel ?cw_prefLabel ;
void:inDataset <http://www.conceptwiki.org> .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A target URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/Q9Y5Y9",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "assoc_type" ,
"description": "One of the following association type URIs: http://semanticscience.org/resource/SIO_001119 (gene-disease association linked with causal mutation), http://semanticscience.org/resource/SIO_001120 (therapeutic gene-disease association), http://semanticscience.org/resource/SIO_001121 (gene-disease biomarker association), http://semanticscience.org/resource/SIO_001122 (gene-disease association linked with genetic variation), http://semanticscience.org/resource/SIO_001123 (gene-disease association linked with altered gene expression), http://semanticscience.org/resource/SIO_001124 (gene-disease association linked with post-translational modification)" ,
"required": false,
"allowableValues": {
"values": [
"http://semanticscience.org/resource/SIO_001119",
"http://semanticscience.org/resource/SIO_001120",
"http://semanticscience.org/resource/SIO_001121",
"http://semanticscience.org/resource/SIO_001122",
"http://semanticscience.org/resource/SIO_001123",
"http://semanticscience.org/resource/SIO_001124"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?assocDataset",
"DESC(?assocDataset)",
"?cw_prefLabel",
"DESC(?cw_prefLabel)",
"?cw_target_uri",
"DESC(?cw_target_uri)",
"?description",
"DESC(?description)",
"?dg_gene_uri",
"DESC(?dg_gene_uri)",
"?disease",
"DESC(?disease)",
"?diseaseClass",
"DESC(?diseaseClass)",
"?diseaseClassDataset",
"DESC(?diseaseClassDataset)",
"?diseaseClassName",
"DESC(?diseaseClassName)",
"?diseaseDataset",
"DESC(?diseaseDataset)",
"?diseaseName",
"DESC(?diseaseName)",
"?existence",
"DESC(?existence)",
"?geneDataset",
"DESC(?geneDataset)",
"?item",
"DESC(?item)",
"?primarySource",
"DESC(?primarySource)",
"?pubmed_id",
"DESC(?pubmed_id)",
"?type",
"DESC(?type)",
"?type_label",
"DESC(?type_label)",
"?uniprot_target_uri",
"DESC(?uniprot_target_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/assoc/byDisease/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Associations for Disease: Count" ,
"description": "A list of associations which correspond to the disease {uri}.
Response template:
?ops_item ops:associationsCount ?count .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A disease URI." ,
"defaultValue": "http://linkedlifedata.com/resource/umls/id/C0004238",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/assoc/byDisease" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Associations for Disease: List" ,
"description": "A list of associations which correspond to the disease {uri}.
Response template:
?item ops:disease ?umls_disease_uri ;
ops:gene ?gene_uri ;
rdf:type ?type ;
dcterms:description ?description ;
ops:pmid ?pubmed_id ;
ops:primarySource ?primarySource ;
void:inDataset ?assocDataset .
?type rdfs:label ?type_label .
?umls_disease_uri foaf:name ?diseaseName ;
ops:diseaseClass ?diseaseClass ;
void:inDataset ?diseaseDataset .
?diseaseClass foaf:name ?diseaseClassName ;
void:inDataset ?diseaseClassDataset .
?gene_uri void:inDataset ?geneDataset .
?ims_uniprot_target_uri void:inDataset <http://purl.uniprot.org> .
?ims_cw_target_uri skos:prefLabel ?prefLabel ;
void:inDataset <http://www.conceptwiki.org> .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A disease URI." ,
"defaultValue": "http://linkedlifedata.com/resource/umls/id/C0004238",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?assocDataset",
"DESC(?assocDataset)",
"?description",
"DESC(?description)",
"?dg_uniprot_uri",
"DESC(?dg_uniprot_uri)",
"?diseaseClass",
"DESC(?diseaseClass)",
"?diseaseClassDataset",
"DESC(?diseaseClassDataset)",
"?diseaseClassName",
"DESC(?diseaseClassName)",
"?diseaseDataset",
"DESC(?diseaseDataset)",
"?diseaseName",
"DESC(?diseaseName)",
"?existence",
"DESC(?existence)",
"?geneDataset",
"DESC(?geneDataset)",
"?gene_uri",
"DESC(?gene_uri)",
"?ims_cw_target_uri",
"DESC(?ims_cw_target_uri)",
"?ims_uniprot_target_uri",
"DESC(?ims_uniprot_target_uri)",
"?item",
"DESC(?item)",
"?prefLabel",
"DESC(?prefLabel)",
"?primarySource",
"DESC(?primarySource)",
"?pubmed_id",
"DESC(?pubmed_id)",
"?type",
"DESC(?type)",
"?type_label",
"DESC(?type_label)",
"?umls_disease_uri",
"DESC(?umls_disease_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Disease Information" ,
"description": "Information about a single disease.
Response template:
?ops_item skos:exactMatch ?umls_disease_uri .
?umls_disease_uri foaf:name ?diseaseName ;
ops:diseaseClass ?diseaseClass ;
rdfs:seeAlso ?mesh_uri ;
void:inDataset ?diseaseDataset .
?diseaseClass foaf:name ?diseaseClassName ;
void:inDataset ?diseaseClassDataset .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri" ,
"description": "A disease URI." ,
"defaultValue": "http://linkedlifedata.com/resource/umls/id/C0004238",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/disease/batch" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Disease Information: Batch" ,
"description": "Information about a list of diseases, separated by '|'.
Response template:
?ims_umls_disease_uri foaf:name ?diseaseName ;
ops:diseaseClass ?diseaseClass ;
rdfs:seeAlso ?mesh_uri ;
void:inDataset ?diseaseDataset .
?diseaseClass foaf:name ?diseaseClassName ;
void:inDataset ?diseaseClassDataset .
",
"group": "Disease" ,
"parameters": [
{
"name": "uri_list" ,
"description": "A list of disease URIs, separated by '|' characters." ,
"defaultValue": "http://linkedlifedata.com/resource/umls/id/C0004238|http://linkedlifedata.com/resource/umls/id/C0018794",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tissue" ,
"operations": [
{
"httpMethod": "GET",
"summary": "[PREVIEW] Tissue Information" ,
"description": "Information about a single tissue.
Response template:
?ops_item rdfs:label ?tissue_label ;
ops:definition ?tissue_def ;
oboowl:hasDbXref ?tissue_xref ;
void:inDataset <http://www.nextprot.org/caloha> .
",
"group": "Tissue" ,
"parameters": [
{
"name": "uri" ,
"description": "A tissue URI." ,
"defaultValue": "ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo#TS-0171",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tissue/batch" ,
"operations": [
{
"httpMethod": "GET",
"summary": "[PREVIEW] Tissue Information: Batch" ,
"description": "Information about a list of tissues.
Response template:
?ims_caloha_tissue_uri rdfs:label ?tissue_label ;
ops:definition ?tissue_def ;
oboowl:hasDbXref ?tissue_xref ;
void:inDataset <http://www.nextprot.org/caloha> .
",
"group": "Tissue" ,
"parameters": [
{
"name": "uri_list" ,
"description": "A list of tissue URIs, separated by '|' characters." ,
"defaultValue": "ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo#TS-0171|ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo#TS-0173",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tissue/byProtein/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "[PREVIEW] Tissues for Protein: Count" ,
"description": "The total number of assertions in the LDC that a given protein is expressed in a tissue.
Response template:
?ops_item ops:tissueExpressionTotalResults ?count .
",
"group": "Tissue" ,
"parameters": [
{
"name": "uri" ,
"description": "A protein URI." ,
"defaultValue": "http://purl.uniprot.org/uniprot/P55795",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "evidence" ,
"description": "'gold' or 'silver'" ,
"required": false,
"allowableValues": {
"values": [
"gold",
"silver"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "quality" ,
"description": "One of: none, moderate, high, low, medium, negative, positive, strong, weak." ,
"required": false,
"allowableValues": {
"values": [
"none",
"moderate",
"high",
"low",
"medium",
"negative",
"positive",
"strong",
"weak"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tissue/byProtein" ,
"operations": [
{
"httpMethod": "GET",
"summary": "[PREVIEW] Tissues for Protein: List" ,
"description": "A page of items corresponding to assertions that a given protein is expressed in a tissue.
Response template:
terms:tissue ?tissue ;
terms:protein ?nextprot_uri ;
rel:has_quality ?quality ;
a ?evidence_type ;
prv:usedDat a ?data_used ;
wi:evidence ?evidence_qual_uri ;
prov:wasDerivedFrom ?derived_from ;
prov:wasGeneratedBy ?generated_by ;
void:inDataset <http://www.nextprot.org> .
?nextprot_uri skos:exactMatch ?uniprot_target_uri .
?uniprot_target_uri void:inDataset <http://purl.uniprot.org> .
?tissue rdfs:label ?tissue_label ;
void:inDataset <http://www.nextprot.org/caloha> .
?evidence_qual_uri rdfs:label ?evidence_qual_label ;
void:inDataset <http://www.nextprot.org> .
",
"group": "Tissue" ,
"parameters": [
{
"name": "uri" ,
"description": "A protein URI.http://purl.uniprot.org/uniprot/P55795" ,
"defaultValue": "http://purl.uniprot.org/uniprot/P55795",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "evidence" ,
"description": "'gold' or 'silver'" ,
"required": false,
"allowableValues": {
"values": [
"gold",
"silver"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "quality" ,
"description": "One of: none, moderate, high, low, medium, negative, positive, strong, weak." ,
"required": false,
"allowableValues": {
"values": [
"none",
"moderate",
"high",
"low",
"medium",
"negative",
"positive",
"strong",
"weak"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?data_used",
"DESC(?data_used)",
"?derived_from",
"DESC(?derived_from)",
"?evidence_qual_label",
"DESC(?evidence_qual_label)",
"?evidence_qual_uri",
"DESC(?evidence_qual_uri)",
"?evidence_type",
"DESC(?evidence_type)",
"?generated_by",
"DESC(?generated_by)",
"?item",
"DESC(?item)",
"?nanopub",
"DESC(?nanopub)",
"?nextprot_uri",
"DESC(?nextprot_uri)",
"?prov",
"DESC(?prov)",
"?quality",
"DESC(?quality)",
"?tissue",
"DESC(?tissue)",
"?tissue_label",
"DESC(?tissue_label)",
"?uniprot_target_uri",
"DESC(?uniprot_target_uri)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tissue/getProteins/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "[PREVIEW] Proteins for Tissue: Count" ,
"description": "The total number of assertions in the LDC that a protein is expressed in a given tissue.
Response template:
?ops_item ops:tissueExpressionTotalResults ?count .
",
"group": "Tissue" ,
"parameters": [
{
"name": "uri" ,
"description": "A tissue URI." ,
"defaultValue": "ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo#TS-0016",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "evidence" ,
"description": "'gold' or 'silver'" ,
"required": false,
"allowableValues": {
"values": [
"gold",
"silver"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "quality" ,
"description": "One of: none, moderate, high, low, medium, negative, positive, strong, weak." ,
"required": false,
"allowableValues": {
"values": [
"none",
"moderate",
"high",
"low",
"medium",
"negative",
"positive",
"strong",
"weak"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tissue/getProteins" ,
"operations": [
{
"httpMethod": "GET",
"summary": "[PREVIEW] Proteins for Tissue: List" ,
"description": "A page of items corresponding to assertions that a protein is expressed in a given tissue.
Response template:
terms:tissue ?ops_item ;
terms:protein ?nextprot_uri ;
rel:has_quality ?quality ;
a ?evidence_type ;
prv:usedDat a ?data_used ;
wi:evidence ?evidence_qual_uri ;
prov:wasDerivedFrom ?derived_from ;
prov:wasGeneratedBy ?generated_by ;
void:inDataset <http://www.nextprot.org> .
?nextprot_uri skos:exactMatch ?uniprot_target .
?uniprot_target void:inDataset <http://purl.uniprot.org> .
?ops_item rdfs:label ?tissue_label ;
void:inDataset <http://www.nextprot.org/caloha> .
?evidence_qual_uri rdfs:label ?evidence_qual_label ;
void:inDataset <http://www.nextprot.org> .
",
"group": "Tissue" ,
"parameters": [
{
"name": "uri" ,
"description": "A tissue URI." ,
"defaultValue": "ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo#TS-0016",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "evidence" ,
"description": "'gold' or 'silver'" ,
"required": false,
"allowableValues": {
"values": [
"gold",
"silver"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "quality" ,
"description": "One of: none, moderate, high, low, medium, negative, positive, strong, weak." ,
"required": false,
"allowableValues": {
"values": [
"none",
"moderate",
"high",
"low",
"medium",
"negative",
"positive",
"strong",
"weak"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?data_used",
"DESC(?data_used)",
"?derived_from",
"DESC(?derived_from)",
"?evidence_qual_label",
"DESC(?evidence_qual_label)",
"?evidence_qual_uri",
"DESC(?evidence_qual_uri)",
"?evidence_type",
"DESC(?evidence_type)",
"?generated_by",
"DESC(?generated_by)",
"?item",
"DESC(?item)",
"?nanopub",
"DESC(?nanopub)",
"?nextprot_uri",
"DESC(?nextprot_uri)",
"?ops_item",
"DESC(?ops_item)",
"?prov",
"DESC(?prov)",
"?quality",
"DESC(?quality)",
"?tissue_label",
"DESC(?tissue_label)",
"?uniprot_target",
"DESC(?uniprot_target)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pharmacology/filters/activities/count" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Activity Types: Count" ,
"description": "The total number of activity types available will be returned. Specifying the parameter “activity_unit” returns the number of activity types that use the given unit. See “Activity Units: List” for allowed activity units (e.g. nanomolar).
Response template:
<http://www.ebi.ac.uk/chembl> ops:activity_type_count ?count
",
"group": "Pharmacology Filters" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pharmacology/filters/activities" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Activity Types: List" ,
"description": "Returns a list of available activity types. Specifying the parameter “activity_unit” returns only the activity types that use the given parameter. See “Activity Units: List” for allowed activity units (e.g. nanomolar).
Response template:
<http://www.ebi.ac.uk/chembl> ops:normalised_activity_type ?item .
?item rdfs:label ?type_label ;
ops:activity_count ?count .
",
"group": "Pharmacology Filters" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "activity_unit" ,
"required": false,
"allowableValues": {
"values": [
"centimeter",
"day",
"degree_celsius",
"gram",
"gram_per_liter",
"hour",
"international_unit_per_liter",
"kilogram",
"liter",
"microgram_per_milliliter",
"micrometer",
"micromolar",
"milligram_per_deciliter",
"milligram_per_milliliter",
"millimeter",
"millimolar",
"milli_second",
"minute_time",
"molar",
"nanogram_per_milliliter",
"nanomolar",
"percent",
"picogram_per_milliliter",
"picomolar",
"second_time"
],
"valueType": "LIST"
},
"description": "The unit in which {activity_value} is given. See /pharmacology/filters/units/{activity_type} for allowed values. For e.g. IC50: /pharmacology/filters/units/IC50" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?activity",
"DESC(?activity)",
"?count",
"DESC(?count)",
"?item",
"DESC(?item)",
"?standard_type",
"DESC(?standard_type)",
"?type_label",
"DESC(?type_label)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pharmacology/filters/count_units" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Activity Units: Count" ,
"description": "The total number of activity units that are available will be returned. Specifying the parameter “activity_type” returns the number of activity types that use the given unit. See “Activity Types: List” for allowed activity units (e.g. nanomolar).
Response template:
<http://www.ebi.ac.uk/chembl> ops:normalised_activity_unit_count ?count .
",
"group": "Pharmacology Filters" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "activity_type" ,
"description": "One of the activity types listed at /pharmacology/filters/activities" ,
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pharmacology/filters/units" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Activity Units: List" ,
"description": "Returns a list of available activity units.
Response template:
<http://www.ebi.ac.uk/chembl> ops:normalised_activity_unit ?item .
?item rdfs:label ?qudt_label ;
ops:activity_count ?count .
",
"group": "Pharmacology Filters" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_page",
"description": "A number; the page that should be viewed",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"dataType": "integer",
"paramType": "query"
},
{
"name": "_pageSize",
"description": "The desired page size. Set to all to retrieve all results in a single page. Default: 10.",
"allowableValues": {
"values": [
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_orderBy",
"description": "The desired variable to sort by. Multiple values can be specified seperated by spaces. Direction of sort can be specified with ASC(?var) and DESC(?var). Default is ascending",
"allowableValues": {
"values": [
"?activity",
"DESC(?activity)",
"?count",
"DESC(?count)",
"?item",
"DESC(?item)",
"?qudt_label",
"DESC(?qudt_label)"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/pharmacology/filters/units/{act_type}" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Activity Units for Type" ,
"description": "Returns a list of activity units for the user specified activity type.
Response template:
?item qudt:unit ?unit ;
rdfs:label ?act_label .
?unit rdfs:label ?unit_label .
",
"group": "Pharmacology Filters" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "act_type" ,
"description": "http://www.openphacts.org/terms/chembl#{act_type}" ,
"required": true,
"paramType": "path",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tree" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Hierarchies: Root Nodes" ,
"description": "A representation of the root classes in each hierarchy. The ChEBI Ontology, the Gene Ontology, the Enzyme Classification, and the ChEMBL Target Tree are currently supported.
Response template:
ops:conceptHierarchy dcterms:hasPart ?g_short .
?g_short ops:rootNode ?root_node .
?root_node skos:prefLabel ?name ;
skos:prefLabel ?label .
<http://purl.uniprot.org/enzyme> skos:prefLabel 'Enzyme Classification' .
<http://www.ebi.ac.uk/chembl/target> skos:prefLabel 'ChEMBL Target Hierarchy' .
<http://www.ebi.ac.uk/chebi> skos:prefLabel 'ChEBI Ontology' .
<http://www.geneontology.org> skos:prefLabel 'GeneOntology' .
",
"group": "Concept Class Hierarchies" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "root" ,
"description": "Restrict results by hierarchy. Currently one of 'chembl', 'chebi', 'enzyme', 'go'" ,
"required": false,
"allowableValues": {
"values": [
"chembl",
"chebi",
"enzyme",
"go"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tree/children" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Hierarchies: Child Nodes" ,
"description": "A representation of all child nodes of the given class in the supportted hierarchies. The ChEBI Ontology, the Gene Ontology, the Enzyme Classification, and the ChEMBL Target Tree are currently supported.
Response template:
?ops_item skos:exactMatch ?node_uri .
?node_uri ops:childNode ?child_node ;
skos:prefLabel ?label ;
void:inDataset ?g_short .
?child_node skos:prefLabel ?child_label .
<http://purl.uniprot.org/enzyme> skos:prefLabel 'Enzyme Classification' .
<http://www.ebi.ac.uk/chembl/target> skos:prefLabel 'ChEMBL Target Hierarchy' .
<http://www.ebi.ac.uk/chebi> skos:prefLabel 'ChEBI Ontology' .
<http://www.geneontology.org> skos:prefLabel 'GeneOntology' .
",
"group": "Concept Class Hierarchies" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.uniprot.org/enzyme/6.2.-.-",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/tree/parents" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Hierarchies: Parent Nodes" ,
"description": "A representation of all parent nodes of the given class in the supportted hierarchies. The ChEBI Ontology, the Gene Ontology, the Enzyme Classification, and the ChEMBL Target Tree are currently supported.
Response template:
?ops_item skos:exactMatch ?node_uri .
?node_uri ops:parentNode ?parent_node ;
skos:prefLabel ?label ;
void:inDataset ?g_short .
?parent_node skos:prefLabel ?parent_label ;
skos:prefLabel ?parent_name .
<http://purl.uniprot.org/enzyme> skos:prefLabel 'Enzyme Classification' .
<http://www.ebi.ac.uk/chembl/target> skos:prefLabel 'ChEMBL Target Hierarchy' .
<http://www.ebi.ac.uk/chebi> skos:prefLabel 'ChEBI Ontology' .
<http://www.geneontology.org> skos:prefLabel 'GeneOntology' .
",
"group": "Concept Class Hierarchies" ,
"parameters": [
{
"name": "uri" ,
"description": "A class URI from one of the supported hierarchies." ,
"defaultValue": "http://purl.uniprot.org/enzyme/6.2.-.-",
"dataType": "string",
"required": true,
"paramType": "query"
},
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/search/freetext" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Free Text to Concept" ,
"description": "Returns a list of ConceptWiki URIs for a user specified free text search term (e.g. water, aspirin etc). Driven by ConceptWiki.
Response template:
?primaryTopic rdf:type ?searchType ;
ops_api:searchTerm ?searchTerm ;
ops_api:result ?uuidURL ;
ops_api:limit ?resultsLimit .
?uuidURL skos:prefLabel ?conceptPrefLabel ;
ops_api:match ?match ;
skos:altLabel ?conceptAltLabel ;
ops_api:semanticTag ?tagBNode ;
skos:exactMatch ?urlBNode .
?tagBNode cw:uuid tagUUID ;
skos:prefLabel ?tagPrefLabel ;
cw:deleted ?deletedFromWikiMarker .
skos:altLabel ?tagAltLabel ;
?urlBNode cw:url ?url ;
cw:matchType ?matchType .
",
"group": "Concept Wiki services" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "q" ,
"description": "Query; required. Mininum length is 3 characters." ,
"defaultValue": "aspirin",
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "limit" ,
"description": "Limits the number of results; optional. Minimum value is 1, default value is 10." ,
"minimum": "1",
"paramType": "query",
"dataType": "integer"
},
{
"name": "branch" ,
"description": "The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = Computer Inferred, 6 = Pathway Ontology, 7 = WikiPathways" ,
"required": false,
"allowableValues": {
"values": [
"1",
"2",
"3",
"4",
"5",
"6",
"7"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "integer"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/search/byTag" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Free Text to Concept for Semantic Tag" ,
"description": "Returns a list of ConceptWiki URIs for a user specified free text search term. The results are limited by a user specified UUID for an input tag that specifies a semantic type. Driven by ConceptWiki.
Response template:
?primaryTopic rdf:type ?searchType ;
ops_api:searchTerm ?searchTerm ;
ops_api:tagUUID ?inputTagUUID ;
ops_api:result ?uuidURL ;
ops_api:limit ?resultsLimit .
?uuidURL skos:prefLabel ?conceptPrefLabel ;
ops_api:match ?match ;
ops_api:semanticTag ?tagBNode ;
skos:altLabel ?conceptAltLabel ;
skos:exactMatch ?urlBNode .
?tagBNode cw:uuid tagUUID ;
skos:prefLabel ?tagPrefLabel ;
cw:deleted ?deletedFromWikiMarker ;
skos:altLabel ?tagAltLabel .
?urlBNode cw:url ?url ;
cw:matchType ?matchType .
",
"group": "Concept Wiki services" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "q" ,
"description": "Query; required. Minimum length is 3 characters." ,
"defaultValue": "aspirin",
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "limit" ,
"description": "Limits the number of results; optional. Minimum value is 1, default value is 10." ,
"minimum": "1",
"paramType": "query",
"dataType": "integer"
},
{
"name": "uuid" ,
"description": "UUID of the tag concept; required. Specifies the 'semantic type' required for the search results. E.g. 07a84994-e464-4bbf-812a-a4b96fa3d197 for 'Chemical Viewed Structurally', eda73945-b112-407e-811a-88448966834f for 'Disease or Syndrome', or eeaec894-d856-4106-9fa1-662b1dc6c6f1 for 'Amino Acid, Peptide, or Protein'" ,
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "branch" ,
"description": "The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = Computer Inferred, 6 = Pathway Ontology, 7 = WikiPathways" ,
"required": false,
"allowableValues": {
"values": [
"1",
"2",
"3",
"4",
"5",
"6",
"7"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "integer"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/getConceptDescription" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Concept Description" ,
"description": "Returns the description of a concept stored in the ConceptWiki based on a UUID. Driven by ConceptWiki.
Response template:
?conceptURL skos:prefLabel ?conceptPrefLabel ;
skos:altLabel ?conceptAltLabel ;
ops_api:semanticTag ?tagBNode ;
skos:exactMatch ?urlBNode ;
skos:definition ?definitionText .
?tagBNode cw:uuid tagUUID ;
skos:prefLabel ?tagPrefLabel ;
cw:deleted ?deletedFromWikiMarker .
skos:altLabel ?tagAltLabel ;
?urlBNode cw:url ?url ;
cw:matchType ?matchType ;
void:inDataset ?sourceURL ;
?sourceURL skos:prefLabel ?sourcePrefLabel ;
cw:deleted ?deletedFromWikiMarker .
",
"group": "Concept Wiki services" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "uuid" ,
"description": "UUID of the concept; required." ,
"defaultValue": "8e3a87ae-345d-4c25-bd7a-5b3221c6e3fa",
"paramType": "query",
"required": true,
"dataType": "string"
},
{
"name": "branch" ,
"description": "The search results will be filtered by this source authority; optional. Possible values: 1 = Community, 2 = UMLS, 3 = SwissProt, 4 = ChemSpider, 5 = Computer Inferred, 6 = Pathway Ontology, 7 = WikiPathways" ,
"required": false,
"allowableValues": {
"values": [
"1",
"2",
"3",
"4",
"5",
"6",
"7"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "integer"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/sources" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Data Sources" ,
"description": "(UNDER DEVELOPMENT) Returns a list of data sources used by Open PHACTS along with a variety of information about each one.
Response template:
<http://www.openphacts.org/linked_data_cache> a void:Dataset ;
void:subset ?top_dataset .
?top_dataset foaf:isPrimaryTopicOf ?description .
?dataset dcterms:title ?title .
?dataset dcterms:description ?dctDescription .
?dataset dcterms:license ?license .
?dataset void:subset ?subset .
?dataset prov:wasDerivedFrom ?derivedFrom .
?dataset prov:hadPrimarySource ?primarySource .
?dataset prov:wasQuotedFrom ?quotedFrom .
?dataset prov:wasRevisionOf ?revisionOf .
?dataset void:triples ?tripleNo .
?dataset void:dataDump ?dataDump .
?dataset dcat:landingPage ?landingPage .
?dataset foaf:homepage ?homepage .
?dataset a void:Dataset .
",
"group": "Data Sources" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
},
{
"path": "/mapUri" ,
"operations": [
{
"httpMethod": "GET",
"summary": "Map URL" ,
"description": "Returns a list of URIs associated to the input URI.
Response template:
foaf:primaryTopic ?primaryTopic .
?primaryTopic foaf:isPrimaryTopicOf .
?primaryTopic skos:exactMatch ?url .
",
"group": "Mapping service betweem URLs" ,
"parameters": [
{
"name": "app_id",
"description": "Your access application id",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_ids"
},
{
"name": "app_key",
"description": "Your access application key",
"required": true,
"dataType": "string",
"paramType": "query",
"threescale_name": "app_keys"
},
{
"name": "Uri" ,
"description": "An input Uri to be mapped." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "targetUriPattern" ,
"description": "List of URI patterns (text only, no regex support) separated by '|' characters. Limits the results to URIs which start with the given pattern. Example: http://identifiers.org returns all identifiers.org URIs." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "graph" ,
"description": "Limits the results to ones required for this OpenRdf context/graph." ,
"paramType": "query",
"dataType": "string"
},
{
"name": "lensUri" ,
"description": "Lens URI." ,
"required": false,
"allowableValues": {
"values": [
"Default",
"DefaultCW",
"tautomerCW",
"tautomer",
"stereochemistryCW",
"stereochemistry",
"isotopeCW",
"isotope",
"child_child",
"chargeCW",
"charge",
"ConceptWikiGene",
"CHEMINF_parent_child",
"CHEMINF_parent",
"CHEMINF_child_parent",
"CHEMINF_000514",
"CHEMINF_000499",
"CHEMINF_000498",
"CHEMINF_000497",
"CHEMINF_000495",
"CHEMINF_000494",
"CHEMINF_000492",
"CHEMINF_000491",
"CHEMINF_000489",
"CHEMINF_000480",
"CHEMINF_000461",
"CHEMINF_000460",
"CHEMINF_000459",
"CHEMINF_000458",
"CHEMINF_000456",
"CHEMINF_000455",
"All"
],
"valueType": "LIST"
},
"paramType": "query",
"dataType": "string"
},
{
"name": "_format",
"description": "The desired result format.",
"allowableValues": {
"values": [
"json",
"tsv",
"ttl",
"xml",
"rdf",
"rdfjson",
"html"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
},
{
"name": "_callback",
"description": "For JSONP",
"dataType": "string",
"paramType": "query"
},
{
"name": "_metadata",
"description": "Additional metadata to be included with response.",
"allowableValues": {
"values": [
"execution",
"site",
"formats",
"views",
"all"
],
"valueType": "LIST"
},
"dataType": "string",
"required": false,
"paramType": "query"
}
]
}
]
}
]
}