phosphoELMdb

115

Service version1.0

WSDL URLhttp://phospho.elm.eu.org/webservice/phosphoELMdb.wsdl PASSED

The phospho.ELM database contains descriptions of sets of one or more orthologous eukaryotic proteins that are annotated to be phosphorylated.
The orthology grouping allows convenient cross-species comparison.

The web-service provides the following methods to gain access to the various information in the database:

getBindingDomainList
getKinaseList
getSubstrateByIdentifier
getSubstratesByNameSearch
getSubstratesByGeneNameSearch
getInstanceByIdentifier
getInstancesByBindingDomainText
getInstancesByKinaseTextSearch
getInstancesByProteinSequenceAccessionSearchWithAllThroughputData
getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly
getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData
getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly
getInstancesByPubMedId
getInstancesWithPdbEntryAssigned

Reference:

Phospho.ELM: a database of phosphorylation sites–update 2008.
Diella, F., Gould, C.M., Chica, C., Via, A. & Gibson, T.J.
Nucleic Acids Res. (Database Issue):D240-4 (2008)

URL: phospho.ELM

A description of the WSDL service:

phosphoELMdb

Namespace: http://phospho.elm.eu.org/phosphoELMdb

This WSDL file describe the phospho.ELM database Web Service. The phospho.ELM database contains descriptions of sets of one or more orthologous proteins that are annotated to be phosphorylated. The orthology grouping allows convenient cross-species comparison. Reference: Phospho.ELM: A database of experimentally verified phosphorylation sites in eukaryotic proteins Francesca Diella, Scott Cameron, Christine Gemuend, Rune Linding, Allegra Via, Bernhard Kuster, Thomas Sicheritz-Ponten, Nikolaj Blom and Toby J Gibson (2004) BMC Bioinformatics, 5:79 URL:http://phospho.elm.eu.org

Port: phosphoELMdb
Location: http://luna.embl.de:8080/axis2/services/phosphoELMdb
Protocol: http://schemas.xmlsoap.org/soap/http
Default Style: document

Operations

getKinaseList

Retrieves all kinases present in the database.

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getKinaseList
Input Message: getKinaseListRequestMsg
- parameters
  - getKinaseList type
Output Message: getKinaseListResponseMsg
- parameters
  - getKinaseListResponse type
    - Kinase type KinaseType

getBindingDomainList

Retrieves all binding domains present in the database.

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getBindingDomainList
Input Message: getBindingDomainListRequestMsg
- parameters
  - getBindingDomainList type
Output Message: getBindingDomainListResponseMsg
- parameters
  - getBindingDomainListResponse type
    - BindingDomain type BindingDomainType

getSubstratesByNameSearch

Retrieves a list of substrates matching the specified substrate name.

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getSubstratesByNameSearch
Input Message: getSubstratesByNameSearchRequestMsg
- parameters
  - getSubstratesByNameSearch type
    - SubstrateName type string
Output Message: getSubstratesByNameSearchResponseMsg
- parameters
  - getSubstratesByNameSearchResponse type
    - Substrate type SubstrateType
      - Name type string
      - Description type string
      - Instance type string
      - Expression type string
      - Synonym type string
      - DatabaseURL type string
      - Interaction type InteractionType
        MintID type DBReferenceType
        Database type DatabaseType
        Accession type string
        InteractorReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        InteractorIdentifier type string
      - GOterm type GOtermType
        Ontology type OntologyType
        GOAccession type string
        Term type string

getSubstratesByGeneNameSearch

Retrieves a list of substrates matching the specified gene name.

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getSubstratesByGeneNameSearch
Input Message: getSubstratesByGeneNameSearchRequestMsg
- parameters
  - getSubstratesByGeneNameSearch type
    - GeneName type string
Output Message: getSubstratesByGeneNameSearchResponseMsg
- parameters
  - getSubstratesByGeneNameSearchResponse type
    - Substrate type SubstrateType
      - Name type string
      - Description type string
      - Instance type string
      - Expression type string
      - Synonym type string
      - DatabaseURL type string
      - Interaction type InteractionType
        MintID type DBReferenceType
        Database type DatabaseType
        Accession type string
        InteractorReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        InteractorIdentifier type string
      - GOterm type GOtermType
        Ontology type OntologyType
        GOAccession type string
        Term type string

getInstancesByProteinSequenceAccessionSearchWithAllThroughputData

Retrieves a list of instances by specified protein sequence accession nr for all types of throughput data

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByProteinSequenceAccessionSearchWithAllThroughputData
Input Message: getInstancesByProteinSequenceAccessionSearchWithAllThroughputDataRequestMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchWithAllThroughputData type
    - ProteinSequenceAccession type string
Output Message: getInstancesByProteinSequenceAccessionSearchWithAllThroughputDataResponseMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchWithAllThroughputDataResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly

Retrieves a list of instances by specified protein sequence accession nr for low throughput data only

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly
Input Message: getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyRequestMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly type
    - ProteinSequenceAccession type string
Output Message: getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyResponseMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData

Retrieves a list of instances by specified protein sequence accession nr for all related species for all types of throughput data

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData
Input Message: getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataRequestMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData type
    - ProteinSequenceAccession type string
Output Message: getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataResponseMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly

Retrieves a list of instances by specified protein sequence accession nr for all related species for low throughput data only

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly
Input Message: getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyRequestMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly type
    - ProteinSequenceAccession type string
Output Message: getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyResponseMsg
- parameters
  - getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getInstancesByKinaseTextSearch

Retrieves a list of instances by specified kinase(exact match only)

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByKinaseTextSearch
Input Message: getInstancesByKinaseTextSearchRequestMsg
- parameters
  - getInstancesByKinaseTextSearch type
    - QueryText type string
Output Message: getInstancesByKinaseTextSearchResponseMsg
- parameters
  - getInstancesByKinaseTextSearchResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getInstancesByBindingDomainTextSearch

Retrieves a list of instances by specified binding domain(exact match only)

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByBindingDomainTextSearch
Input Message: getInstancesByBindingDomainTextSearchRequestMsg
- parameters
  - getInstancesByBindingDomainTextSearch type
    - QueryText type string
Output Message: getInstancesByBindingDomainTextSearchResponseMsg
- parameters
  - getInstancesByBindingDomainTextSearchResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getSubstrateByIdentifier

Retrieves a Substrate by its identifier

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getSubstrateByIdentifier
Input Message: getSubstrateByIdentifierRequestMsg
- parameters
  - getSubstrateByIdentifier type
    - SubstrateIdentifier type string
Output Message: getSubstrateByIdentifierResponseMsg
- parameters
  - getSubstrateByIdentifierResponse type
    - Substrate type SubstrateType
      - Name type string
      - Description type string
      - Instance type string
      - Expression type string
      - Synonym type string
      - DatabaseURL type string
      - Interaction type InteractionType
        MintID type DBReferenceType
        Database type DatabaseType
        Accession type string
        InteractorReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        InteractorIdentifier type string
      - GOterm type GOtermType
        Ontology type OntologyType
        GOAccession type string
        Term type string
Fault Message: SubstrateByIdentifierFaultMsg
- fault
  - SubstrateByIdentifierFault type
    - FaultDescription type string

getInstanceByIdentifier

Retrieves an Instance by its identifier

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstanceByIdentifier
Input Message: getInstanceByIdentifierRequestMsg
- parameter
  - getInstanceByIdentifier type
    - InstanceIdentifier type string
Output Message: getInstanceByIdentifierResponseMsg
- parameter
  - getInstanceByIdentifierResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string
Fault Message: InstanceByIdentifierFaultMsg
- fault
  - InstanceByIdentifierFault type
    - FaultDescription type string

getInstancesWithPdbEntryAssigned

Retrieves a list of instances with a Pdb entry assigned to them

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesWithPDBEntryAssigned
Input Message: getInstancesWithPdbEntryAssignedRequestMsg
- parameter
  - getInstancesWithPdbEntryAssigned type
Output Message: getInstancesWithPdbEntryAssignedResponseMsg
- parameter
  - getInstancesWithPdbEntryAssignedResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

getInstancesByPubMedId

Retrieves a list of instances by specified PubMed id

SOAP Action: http://phospho.elm.eu.org/phosphoELMdb/getInstancesByPubMedId
Input Message: getInstancesByPubMedIdRequestMsg
- parameter
  - getInstancesByPubMedId type
    - pubmedId type string
Output Message: getInstancesByPubMedIdResponseMsg
- parameter
  - getInstancesByPubMedIdResponse type
    - Instance type InstanceType
      - Position type integer
      - Residue type string
      - Sequence type string
      - Species type string
      - SequenceReference type DBReferenceType
        Database type DatabaseType
        Accession type string
      - UniPROTIsPrimaryAcc type boolean
      - Substrate type string
      - Note type string
      - DomainReference type DomainReferenceType
        Database type DatabaseType
        Domain type string
      - ReliabilityId type ReliabilityIdType
      - Kinase type KinaseType
      - BindingDomain type BindingDomainType
      - ELMAccession type string
      - OtherAccession type DBReferenceType
        Database type DatabaseType
        Accession type string
      - PdbId type string
      - EvidenceReference type EvidenceReferenceType
        LiteratureReference type DBReferenceType
        Database type DatabaseType
        Accession type string
        Method type string
        Source type string
        CellLine type string
        MIId type string

WSDL Changes

Date	Description of Changes
8th April 2009	First Snapshot

Test #1: phosphoELM_getBindingDomainList

The results from the phosphoELM webservice method getBindingDomainList are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #2: phosphoELM_getInstanceByIdentifier

The results from the phosphoELM webservice method getInstanceByIdentifier are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #3: phosphoELM_getInstancesByBindingDomainTextSearch

The results from the phosphoELM webservice method getInstancesByBindingDomainTextSearch are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output

Test #4: phosphoELM_getInstancesByKinaseTextSearch

The results from the phosphoELM webservice method getInstancesByKinaseTextSearch are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #5: phosphoELM_getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData

The results from the phosphoELM webservice method phosphoELM_getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData.py are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #6: phosphoELM_getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly

The results from the phosphoELM webservice method
getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly
are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #7: phosphoELM_getInstancesByProteinSequenceAccessionSearchWithAllThroughputData

The results from the phosphoELM webservice method
getInstancesByProteinSequenceAccessionSearchWithAllThroughputData
are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #8: phosphoELM_getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly

The results from the phosphoELM webservice method
getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly
are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #9: phosphoELM_getInstancesByPubMedId

The results from the phosphoELM webservice method
getInstancesByPubMedId
are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #10: phosphoELM_getInstancesWithPdbEntryAssigned

The results from the phosphoELM webservice method getInstancesWithPdbEntryAssigned are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #11: phosphoELM_getKinaseList

The results from the phosphoELM webservice method getKinaseList are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #12: phosphoELM_getSubstrateByIdentifier

The results from the phosphoELM webservice method getSubstrateByIdentifier are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #13: phosphoELM_getSubstratesByGeneNameSearch

The results from the phosphoELM webservice method getSubstratesByGeneNameSearch are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Test #14: phosphoELM_getSubstratesByNameSearch

The results from the phosphoELM webservice method getSubstratesByNameSearch are deterministic(unless there is a database update which may affect the output) so the script checks for exact values in the output.

Submitted by kate on Tue, 10/14/2008 - 16:08