The ELM Resource Structure Filter

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Service version1.0

WSDL URLhttp://structurefilter.embl.de/webservice/structureFilter.wsdl PASSED

This web service is useful for evaluating the location of candidate short regulatory sequences in proteins (linear motifs) which need to be accessible to interact with their ligand domains. The StructureFilter web-service calculates an accessibility score, secondary structure score and total score (as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. (If a regular expression match is determined as having no associated structural information available, no reference is made to this match in the result set.)

the web service consists of three methods:

RunJob
GetStatus
GetResult

Reference:

A structure filter for the Eukaryotic Linear Motif Resource
Allegra Via, Cathryn M Gould, Christine Gemuend, Toby J Gibson and Manuela Helmer-Citterich
BMC Bioinformatics, 2009 (in review)

A description of the WSDL service:

StructureFilter

Namespace: http://structureFilter.embl.de/StructureFilter

This WSDL file describe the Structure Filter Web Service. It calculates an accessibility score, secondary structure score and total score(as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. If a regular expression match is determined as having no associated structural information available no reference is made to this match in the result set. Via et al. 2008 http://structurefilter.embl.de/webservice/clients/structureFilterClient.txt

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

Operations

RunJob

This operation is the initial operation in a stateful interaction with the Structure Filter service.

SOAP Action: http://structureFilter.embl.de/StructureFilter/RunJob
Input Message: RunJobMsg
- parameters
  - RunJob type
    - identifier type string
    - querySequence type
      - restriction type string
    - regularExpression type
      - restriction type string
    - elmIdentifierName type
      - restriction type string
    - includeSecondaryStructureRecords type
      - restriction type string
    - includeAccessibilityRecords type
      - restriction type string
Output Message: RunJobResponseMsg
- parameters
  - RunJobResponse type
    - JobIdentifier type string

GetStatus

This operation returns the status of a job identified by its job identifier. A client should use this operation to be aware when/if the results are available.

SOAP Action: http://structureFilter.embl.de/StructureFilter/GetStatus
Input Message: GetStatusMsg
- parameters
  - GetStatus type
    - JobIdentifier type string
Output Message: GetStatusResponseMsg
- parameters
  - GetStatusResponse type
    - Status type string
    - StatusDetails type string
Fault Message: JobIdentifierFaultMsg
- fault
  - JobIdentifierFault type
    - FaultDescription type string

GetResult

This operation returns the resulting predictions.

SOAP Action: http://structureFilter.embl.de/StructureFilter/GetResult
Input Message: GetResultMsg
- parameters
  - GetResult type
    - JobIdentifier type string
Output Message: GetResultResponseMsg
- parameters
  - GetResultResponse type
    - sequence type SequenceType
      - identifier type
        restriction type string
      - sequence type
        restriction type string
    - structureFilterRecord type StructureFilterRecordType
      - ELMIdentifier type string
      - regularExpression type string
      - start type integer
      - end type integer
      - accessibilityScore type decimal
      - accessibilityScorePValue type decimal
      - secondaryStructureScore type decimal
      - secondaryStructureScorePValue type decimal
      - totalScore type decimal
      - totalScorePValue type decimal
      - targetDomainStructure type string
      - percentageIdentity type decimal
      - benchmarkAssignment type string
      - individualResidueValues type IndividualResidueValuesType
        position type integer
        targetDomainStructure type string
        accessibility type decimal
        secondaryStructure type string
    - secondaryStructureRecord type SecondaryStructureRecordType
      - start type integer
      - end type integer
      - secondaryStructure type string
      - targetDomainStructure type string
    - accessibilityRecord type AccessibilityRecordType
      - position type integer
      - accessibility type decimal
      - targetDomainStructure type string
Fault Message: JobIdentifierFaultMsg
- fault
  - JobIdentifierFault type
    - FaultDescription type string

WSDL Changes

Date	Description of Changes
22nd April 2009	First Snapshot

Test #1: StructureFilter_test

The StructureFilter web-service consists of the following three methods:

RunJob
GetStatus
GetResult

the runStructureFilterWS.py script tests the functionality of all three methods of this web-service.
The results from the Strucuture Filter web-service are deterministic so the script checks for exact values for the output.

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