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"UniProt" (Service Connection)

Connect to the UniProt API using the Wolfram Language to get information about protein sequences and functions.

Connecting & Authenticating

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

Requests

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

Protein Sequence and Functional Information

"ProteinDetails" — get detailed information about protein sequence and function from UniProt

Parameters:
  • "UniProtID"NoneUniProt ID

    • List of Relevant Proteins

    "ProteinSearch" — get detailed information proteins related to specific search query

    Parameters:
  • "Query"Nonesearch query
    MaxItems10total number of output structures
    "IncludeIsoforms"Falseinclude isoforms

    • Examples

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    Basic Examples  (1)

    Create a new connection to UniProt:

    Wolfram Language code: uniprot = ServiceConnect["UniProt"]

    Get details about protein sequence and function by providing the UniProt ID through an ExternalIdentifier:

    Wolfram Language code: uniprot["ProteinDetails", <|"UniProtID" -> ExternalIdentifier["UniProtKBAccessionNumber", "P05193"]|>]

    Pass the identifier in as a string:

    Wolfram Language code: uniprot["ProteinDetails", <|"UniProtID" -> "Q5VSL9"|>]

    Scope  (2)

    Get information about proteins related to a query:

    Wolfram Language code: ServiceExecute["UniProt", "ProteinSearch", <|"Query" -> "Receptor Tyrosine Kinase"|>]

    Specify the number of outputs:

    Wolfram Language code: ServiceExecute["UniProt", "ProteinSearch", <|"Query" -> "Receptor Tyrosine Kinase", MaxItems -> 30|>]

    Visualize the first protein related to receptor tyrosine kinase using the "AlphaFoldDatabase" service:

    Wolfram Language code: BioMoleculePlot3D[ServiceExecute["AlphaFoldDatabase", "BioMolecule", <|"UniProtID" -> First[%]|>]]