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See Also
- ServiceExecute
- ServiceConnect
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- Service Connections
- ChemSpider
- PubChem
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See Also
- ServiceExecute
- ServiceConnect
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- Service Connections
- ChemSpider
- PubChem
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See Also
Open PHACTS
Connecting & Authenticating
Requests
Compound Information
"CompoundInformation" — information about one or more compounds
| "URI" | (required) | a compound URI or List of URIs | |
| "InChI" | None | InChI compound identifier | |
| "InChIKey" | None | InChIKey compound identifier | |
| "SMILES" | None | SMILES compound identifier |
Number of Class Members from a Compound
"CompoundClassMembersCount" — the number of compounds classified with the given class in the supported hierarchies. Currently, the only supported hierarchy is the ChEBI Ontology.
| "URI" | (required) | a compound URI or List of URIs | |
| "InChI" | None | InChI string | |
| "InChIKey" | None | InChIKey string | |
| "SMILES" | None | SMILES string |
List of Class Members from a Compound
"CompoundClassMembersList" — a list of compounds classified with the given class in the supported hierarchies. Currently, the only supported hierarchy is the ChEBI Ontology.
| "URI" | (required) | a compound URI or List of URIs | |
| "InChI" | None | InChI string | |
| "InChIKey" | None | InChIKey string | |
| "SMILES" | None | SMILES string | |
| "StartIndex" | 1 | start index | |
| MaxItems | 10 | number of elements to return | |
| "SortBy" | None | variable to sort by |
Classes of a Compound
"CompoundClassifications" — the classes the given compound URI has been classified with. Currently supported hierarchies are the ChEBI Ontology and the Gene Ontology.
| "URI" | (required) | a compound URI or List of URIs | |
| "InChI" | None | InChI string | |
| "InChIKey" | None | InChIKey string | |
| "SMILES" | None | SMILES string |
Compound URI from InChI, InChiKey or SMILES
"GetURI" — a ChemSpider URI corresponding to the given InChI, InChIKey, or SMILES string
| "InChI" | None | InChI string | |
| "InChIKey" | None | InChIKey string | |
| "SMILES" | None | SMILES string |
Only one type of identifier can be used as an input.
Target Information
"TargetInformation" — information about one or more targets
| "URI" | (required) | a compound URI or List of URIs |
Number of Class Members from a Target
"TargetClassMembersCount" — 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.
| "URI" | (required) | a compound URI or List of URIs | |
| "TargetOrganism" | None | a literal organism in ChEMBL | |
| "TargetOrganismURI" | None | an organism URI from Uniprot |
List of Class Members from a Target
"TargetClassMembersList" — 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.
| "URI" | (required) | a compound URI or List of URIs | |
| "TargetOrganism" | None | a literal organism in ChEMBL | |
| "TargetOrganismURI" | None | an organism URI from Uniprot | |
| "StartIndex" | 1 | start index | |
| MaxItems | 10 | number of elements to return | |
| "SortBy" | None | the desired variable to sort by |
List of Target Types
"TargetTypes" — a list of target types in the LDC
Pathway Information
"PathwayInformation" — information about a single pathway
| "URI" | (required) | a pathway URI |
List of Compounds from a Pathway
"PathwayCompounds" — a list of compounds that are part of the pathway specified
| "URI" | (required) | a pathway URI |
Pathway Organisms
"PathwayOrganisms" — a list of organism URIs and labels for which pathway data is available
| "StartIndex" | 1 | start index | |
| MaxItems | 10 | number of elements to return | |
| "SortBy" | None | the desired variable to sort by |
Search by Similarity
"StructureSearchBySimilarity" — a set of ChemSpider compound URLs similar to the input molecule according to the specified algorithm and threshold
| "Molecule" | (required) | a SMILES string | |
| "SimilarityType" | None | "Tanimoto", "Tversky", or "Euclidian" | |
| "Threshold" | None | real number from 0 to 1 | |
| "Alpha" | None | real number from 0 to 1 (available only for Tversky metric) | |
| "Beta" | None | real number from 0 to 1 (available only for Tversky metric) | |
| "StartIndex" | 1 | start index | |
| MaxItems | 10 | number of elements to return |
Search by Substructure
"StructureSearchBySubstructure" — a set of ChemSpider compound URLs that contain the specified structure
| "Molecule" | (required) | a SMILES string | |
| "MolType" | None | either "SMILES" or "SMARTS" | |
| "StartIndex" | 1 | start index | |
| MaxItems | 10 | number of elements to return |
Parameter details
| "ChildNode" | child node | |
| "CompoundName" | compound name | |
| "CWCompound" | cW compound | |
| "Item" | item | |
| "NodeURI" | node URI | |
| "OCRSCompound" | OCRS compound |
| "ChildNode" | child node | |
| "Item" | item | |
| "NodeURI" | node URI | |
| "ChEMBLName" | ChEMBL name | |
| "ChEMBLOrganism" | ChEMBL organism | |
| "ChEMBLTarget" | ChEMBL target | |
| "G" | G | |
| "G2" | G2 | |
| "IMSUniprotTargetURI" | IMS uniprot target URI | |
| "Mapping" | mapping | |
| "MappingDataset" | mapping dataset | |
| "MappingName" | mapping name | |
| "MappingOrg" | mapping org | |
| "MappingOrgURI" | mapping org URI | |
| "MappingType" | mapping type | |
| "TargetType" | target type | |
| "UniprotName" | Uniprot name | |
| "UniprotOrganism" | Uniprot organism | |
| "UniprotTarget" | Uniprot target |
| "Count" | count | |
| "Item" | item | |
| "Label" | label | |
| "Pathway" | pathway |
Examples
Basic Examples (5)
Create a new connection by launching an authentication dialog:
Find the compound URI that corresponds to a given identifier:
Find URIs for structures containing a given substructure:
Find similar structures within a given threshold:
Get detailed information about a compound:
Get the number of compounds in a given class:
Get a list of compounds in a given class:
Get a list of ChEMBL target types and counts for each type:
Get a list of targets in a given class:
Get a list of pathways stored in the linked data cache (LDC):
Get a list of compounds that are explicitly mentioned in the specified pathway: