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Open PHACTS

Obsolete
Connect to the Open PHACTS API using the Wolfram Language to explore a variety of pharmacological data resources.

Connecting & Authenticating

ServiceConnect["OpenPHACTS"] creates a connection to the Open PHACTS API. If a previously saved connection can be found, it will be used; otherwise, a new authentication request will be launched.

Requests

ServiceExecute["OpenPHACTS","request",params] sends a request to the Open PHACTS API, using parameters params. The following give possible requests.

Compound Information

Request:

"CompoundInformation" — information about one or more compounds

Parameters:
  • "URI"(required)a compound URI or List of URIs
    "InChI"NoneInChI compound identifier
    "InChIKey"NoneInChIKey compound identifier
    "SMILES"NoneSMILES compound identifier

    • Number of Class Members from a Compound

    Request:

    "CompoundClassMembersCount" — the number of compounds classified with the given class in the supported hierarchies. Currently, the only supported hierarchy is the ChEBI Ontology.

    Parameters:
  • "URI"(required)a compound URI or List of URIs
    "InChI"NoneInChI string
    "InChIKey"NoneInChIKey string
    "SMILES"NoneSMILES string

    • List of Class Members from a Compound

    Request:

    "CompoundClassMembersList" — a list of compounds classified with the given class in the supported hierarchies. Currently, the only supported hierarchy is the ChEBI Ontology.

    Parameters:
  • "URI"(required)a compound URI or List of URIs
    "InChI"NoneInChI string
    "InChIKey"NoneInChIKey string
    "SMILES"NoneSMILES string
    "StartIndex"1start index
    MaxItems10number of elements to return
    "SortBy"Nonevariable to sort by

    • Classes of a Compound

    Request:

    "CompoundClassifications" — the classes the given compound URI has been classified with. Currently supported hierarchies are the ChEBI Ontology and the Gene Ontology.

    Parameters:
  • "URI"(required)a compound URI or List of URIs
    "InChI"NoneInChI string
    "InChIKey"NoneInChIKey string
    "SMILES"NoneSMILES string

    • Compound URI from InChI, InChiKey or SMILES

    Request:

    "GetURI" — a ChemSpider URI corresponding to the given InChI, InChIKey, or SMILES string

    Parameters:
  • "InChI"NoneInChI string
    "InChIKey"NoneInChIKey string
    "SMILES"NoneSMILES string

    • Only one type of identifier can be used as an input.

    Target Information

    Request:

    "TargetInformation" — information about one or more targets

    Parameters:
  • "URI"(required)a compound URI or List of URIs

    • Number of Class Members from a Target

    Request:

    "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.

    Parameters:
  • "URI"(required)a compound URI or List of URIs
    "TargetOrganism"Nonea literal organism in ChEMBL
    "TargetOrganismURI"Nonean organism URI from Uniprot

    • List of Class Members from a Target

    Request:

    "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.

    Parameters:
  • "URI"(required)a compound URI or List of URIs
    "TargetOrganism"Nonea literal organism in ChEMBL
    "TargetOrganismURI"Nonean organism URI from Uniprot
    "StartIndex"1start index
    MaxItems10number of elements to return
    "SortBy"Nonethe desired variable to sort by

    • List of Target Types

    Request:

    "TargetTypes" — a list of target types in the LDC

    Pathway Information

    Request:

    "PathwayInformation" — information about a single pathway

    Parameters:
  • "URI"(required)a pathway URI

    • List of Compounds from a Pathway

    Request:

    "PathwayCompounds" — a list of compounds that are part of the pathway specified

    Parameters:
  • "URI"(required)a pathway URI

    • Pathway Organisms

    Request:

    "PathwayOrganisms" — a list of organism URIs and labels for which pathway data is available

    Parameters:
  • "StartIndex"1start index
    MaxItems10number of elements to return
    "SortBy"Nonethe desired variable to sort by

    • Search by Similarity

    Request:

    "StructureSearchBySimilarity" — a set of ChemSpider compound URLs similar to the input molecule according to the specified algorithm and threshold

    Parameters:
  • "Molecule"(required)a SMILES string
    "SimilarityType"None"Tanimoto", "Tversky", or "Euclidian"
    "Threshold"Nonereal number from 0 to 1
    "Alpha"Nonereal number from 0 to 1 (available only for Tversky metric)
    "Beta"Nonereal number from 0 to 1 (available only for Tversky metric)
    "StartIndex"1start index
    MaxItems10number of elements to return

    • Search by Substructure

    Request:

    "StructureSearchBySubstructure" — a set of ChemSpider compound URLs that contain the specified structure

    Parameters:
  • "Molecule"(required)a SMILES string
    "MolType"Noneeither "SMILES" or "SMARTS"
    "StartIndex"1start index
    MaxItems10number of elements to return

    • Parameter details

    Possible values for "SortBy" in the request "CompoundClassMembersList" include:
  • "ChildNode"child node
    "CompoundName"compound name
    "CWCompound"cW compound
    "Item"item
    "NodeURI"node URI
    "OCRSCompound"OCRS compound
    • Possible values for "SortBy" in the request "TargetClassMembersList" include:
  • "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
    • Possible values for "SortBy" in the request "PathwayOrganisms" include:
  • "Count"count
    "Item"item
    "Label"label
    "Pathway"pathway

    • Examples

    Basic Examples  (5)

    Create a new connection by launching an authentication dialog:

    Wolfram Language code: op = ServiceConnect["OpenPHACTS"]

    Find the compound URI that corresponds to a given identifier:

    Wolfram Language code: op["GetURI", "SMILES" -> "CCCC(C(N=C(N1)C2=C(OCC)C=CC(S(N3CCN(CC3)C)(=O)=O)=C2)=C4C1=O)=NN4C"]
    Wolfram Language code: op["GetURI", "InChI" -> "InChI=1S/C8H9NO2/c1-6(10)9-7-2-4-8(11)5-3-7/h2-5,11H,1H3,(H,9,10)"]

    Find URIs for structures containing a given substructure:

    Wolfram Language code: op["StructureSearchBySubstructure", {"Molecule" -> "ClC1=CC=C(Cl)C=C1", MaxItems -> 5}]

    Find similar structures within a given threshold:

    Wolfram Language code: op["StructureSearchBySimilarity", {"Molecule" -> "ClC(C=C1)=CC=C1C(C(Cl)(Cl)Cl)C2=CC=C(Cl)C=C2", "SimilarityType" -> "Tanimoto", "Threshold" -> 0.75, MaxItems -> 5}]

    Get detailed information about a compound:

    Wolfram Language code: sorafenib = ServiceExecute["OpenPHACTS", "CompoundInformation", "URI" -> "http://www.conceptwiki.org/concept/38932552-111f-4a4e-a46a-4ed1d7bdf9d5"];
    Wolfram Language code: Keys[sorafenib]//Normal
    Wolfram Language code: sorafenib[[3]]

    Get the number of compounds in a given class:

    Wolfram Language code: ServiceExecute["OpenPHACTS", "CompoundClassMembersCount", "URI" -> "http://purl.obolibrary.org/obo/CHEBI_24431"]

    Get a list of compounds in a given class:

    Wolfram Language code: ServiceExecute["OpenPHACTS", "CompoundClassMembersList", {"URI" -> "http://purl.obolibrary.org/obo/CHEBI_24431", MaxItems -> 5}]

    Get a list of ChEMBL target types and counts for each type:

    Wolfram Language code: ServiceExecute["OpenPHACTS", "TargetTypes"]

    Get a list of targets in a given class:

    Wolfram Language code: ServiceExecute["OpenPHACTS", "TargetClassMembersList", "URI" -> "http://purl.uniprot.org/enzyme/6.2.-.-"]

    Get a list of pathways stored in the linked data cache (LDC):

    Wolfram Language code: ServiceExecute["OpenPHACTS", "PathwayOrganisms"]

    Get a list of compounds that are explicitly mentioned in the specified pathway:

    Wolfram Language code: ServiceExecute["OpenPHACTS", "PathwayCompounds", "URI" -> "http://identifiers.org/wikipathways/WP1002"]