RCSB web services

PASSED
305
Contributor URLhttp://www.pdb.org/robohelp/webservices/pdbwebservice.html
WSDL URLhttp://www.pdb.org/pdb/services/pdbws?wsdlPASSED

The RCSB-PDB provides a number of different SOAP based web services. RESTful services are in preparation.

A description of the WSDL service:

PdbWebServiceService

Namespace: webservices.pdb.org

  • Port: pdbws
  • Location: http://www.pdb.org/pdb/services/pdbws
  • Protocol: http://schemas.xmlsoap.org/soap/http
  • Default Style: rpc

Operations

getAnnotations

  • SOAP Action:
  • Input Message: getAnnotationsRequest
    • in0
      • string
  • Output Message: getAnnotationsResponse
    • getAnnotationsReturn
      • string

getEntities

  • SOAP Action:
  • Input Message: getEntitiesRequest
    • in0
      • string
  • Output Message: getEntitiesResponse
    • getEntitiesReturn
      • ArrayOf_xsd_int

blastPDB

  • SOAP Action:
  • Input Message: blastPDBRequest
    • in0
      • string
    • in1
      • string
    • in2
      • double
    • in3
      • string
    • in4
      • string
  • Output Message: blastPDBResponse
    • blastPDBReturn
      • string

blastPDB

  • SOAP Action:
  • Input Message: blastPDBRequest
    • in0
      • string
    • in1
      • string
    • in2
      • double
    • in3
      • string
    • in4
      • string
  • Output Message: blastPDBResponse
    • blastPDBReturn
      • string

getIdStatus

  • SOAP Action:
  • Input Message: getIdStatusRequest
    • in0
      • string
  • Output Message: getIdStatusResponse
    • getIdStatusReturn
      • string

getAtomSite

  • SOAP Action:
  • Input Message: getAtomSiteRequest
    • in0
      • string
  • Output Message: getAtomSiteResponse
    • getAtomSiteReturn
      • Atom_siteWS

getAtomSites

  • SOAP Action:
  • Input Message: getAtomSitesRequest
    • in0
      • string
  • Output Message: getAtomSitesResponse
    • getAtomSitesReturn
      • ArrayOfAtom_siteWS

fastaStructureIdQuery

  • SOAP Action:
  • Input Message: fastaStructureIdQueryRequest
    • in0
      • string
    • in1
      • string
    • in2
      • double
  • Output Message: fastaStructureIdQueryResponse
    • fastaStructureIdQueryReturn
      • ArrayOf_soapenc_string

fastaQuery

  • SOAP Action:
  • Input Message: fastaQueryRequest
    • in0
      • string
    • in1
      • double
  • Output Message: fastaQueryResponse
    • fastaQueryReturn
      • ArrayOf_soapenc_string

keywordQuery

  • SOAP Action:
  • Input Message: keywordQueryRequest
    • in0
      • string
    • in1
      • boolean
    • in2
      • boolean
  • Output Message: keywordQueryResponse
    • keywordQueryReturn
      • ArrayOf_soapenc_string

pubmedAbstractQuery

  • SOAP Action:
  • Input Message: pubmedAbstractQueryRequest
    • in0
      • string
  • Output Message: pubmedAbstractQueryResponse
    • pubmedAbstractQueryReturn
      • ArrayOf_soapenc_string

getSpaceGroupForStructure

  • SOAP Action:
  • Input Message: getSpaceGroupForStructureRequest
    • in0
      • string
  • Output Message: getSpaceGroupForStructureResponse
    • getSpaceGroupForStructureReturn
      • string

getPubmedIdForAllStructures

  • SOAP Action:
  • Input Message: getPubmedIdForAllStructuresRequest
    • Output Message: getPubmedIdForAllStructuresResponse
      • getPubmedIdForAllStructuresReturn
        • ArrayOf_soapenc_string

    getStructureGenomicsPdbIds

    • SOAP Action:
    • Input Message: getStructureGenomicsPdbIdsRequest
      • Output Message: getStructureGenomicsPdbIdsResponse
        • getStructureGenomicsPdbIdsReturn
          • ArrayOf_soapenc_string

      getSwissProtIds

      • SOAP Action:
      • Input Message: getSwissProtIdsRequest
        • Output Message: getSwissProtIdsResponse
          • getSwissProtIdsReturn
            • ArrayOf_soapenc_string

        getGenomeDetails

        • SOAP Action:
        • Input Message: getGenomeDetailsRequest
          • Output Message: getGenomeDetailsResponse
            • getGenomeDetailsReturn
              • ArrayOf_soapenc_string

          getPubmedIdForStructure

          • SOAP Action:
          • Input Message: getPubmedIdForStructureRequest
            • in0
              • string
          • Output Message: getPubmedIdForStructureResponse
            • getPubmedIdForStructureReturn
              • string

          getSequenceForStructureAndChain

          • SOAP Action:
          • Input Message: getSequenceForStructureAndChainRequest
            • in0
              • string
            • in1
              • string
          • Output Message: getSequenceForStructureAndChainResponse
            • getSequenceForStructureAndChainReturn
              • string

          getPrimaryCitationTitle

          • SOAP Action:
          • Input Message: getPrimaryCitationTitleRequest
            • in0
              • string
          • Output Message: getPrimaryCitationTitleResponse
            • getPrimaryCitationTitleReturn
              • string

          isStructureIdObsolete

          • SOAP Action:
          • Input Message: isStructureIdObsoleteRequest
            • in0
              • string
          • Output Message: isStructureIdObsoleteResponse
            • isStructureIdObsoleteReturn
              • int

          getSnpInfo

          • SOAP Action:
          • Input Message: getSnpInfoRequest
            • in0
              • string
          • Output Message: getSnpInfoResponse
            • getSnpInfoReturn
              • ArrayOfSnpInfo

          getLigandInfo

          • SOAP Action:
          • Input Message: getLigandInfoRequest
            • in0
              • ArrayOf_soapenc_string
          • Output Message: getLigandInfoResponse
            • getLigandInfoReturn
              • ArrayOfLigandInfo

          smilesQuery

          • SOAP Action:
          • Input Message: smilesQueryRequest
            • in0
              • string
            • in1
              • int
            • in2
              • float
          • Output Message: smilesQueryResponse
            • smilesQueryReturn
              • ArrayOfLigandInfo

          getSnps

          • SOAP Action:
          • Input Message: getSnpsRequest
            • Output Message: getSnpsResponse
              • getSnpsReturn
                • ArrayOf_soapenc_string

            getReleaseDates

            • SOAP Action:
            • Input Message: getReleaseDatesRequest
              • in0
                • ArrayOf_soapenc_string
            • Output Message: getReleaseDatesResponse
              • getReleaseDatesReturn
                • ArrayOf_soapenc_string

            getEcNumsForStructures

            • SOAP Action:
            • Input Message: getEcNumsForStructuresRequest
              • in0
                • ArrayOf_soapenc_string
            • Output Message: getEcNumsForStructuresResponse
              • getEcNumsForStructuresReturn
                • ArrayOf_soapenc_string

            getEcNums

            • SOAP Action:
            • Input Message: getEcNumsRequest
              • Output Message: getEcNumsResponse
                • getEcNumsReturn
                  • ArrayOf_soapenc_string

              getCifChain

              • SOAP Action:
              • Input Message: getCifChainRequest
                • in0
                  • string
                • in1
                  • string
              • Output Message: getCifChainResponse
                • getCifChainReturn
                  • string

              getCifResidue

              • SOAP Action:
              • Input Message: getCifResidueRequest
                • in0
                  • string
                • in1
                  • string
                • in2
                  • string
              • Output Message: getCifResidueResponse
                • getCifResidueReturn
                  • int

              getChains

              • SOAP Action:
              • Input Message: getChainsRequest
                • in0
                  • string
              • Output Message: getChainsResponse
                • getChainsReturn
                  • ArrayOf_soapenc_string

              getCifChains

              • SOAP Action:
              • Input Message: getCifChainsRequest
                • in0
                  • string
              • Output Message: getCifChainsResponse
                • getCifChainsReturn
                  • ArrayOf_soapenc_string

              getChainLength

              • SOAP Action:
              • Input Message: getChainLengthRequest
                • in0
                  • string
                • in1
                  • string
              • Output Message: getChainLengthResponse
                • getChainLengthReturn
                  • int

              getCifChainLength

              • SOAP Action:
              • Input Message: getCifChainLengthRequest
                • in0
                  • string
                • in1
                  • string
              • Output Message: getCifChainLengthResponse
                • getCifChainLengthReturn
                  • int

              getKabschSander

              • SOAP Action:
              • Input Message: getKabschSanderRequest
                • in0
                  • string
                • in1
                  • string
              • Output Message: getKabschSanderResponse
                • getKabschSanderReturn
                  • string

              getDisorder

              • SOAP Action:
              • Input Message: getDisorderRequest
                • in0
                  • string
                • in1
                  • string
              • Output Message: getDisorderResponse
                • getDisorderReturn
                  • string

              getDbRefIds

              • SOAP Action:
              • Input Message: getDbRefIdsRequest
                • in0
                  • string
                • in1
                  • string
                • in2
                  • string
              • Output Message: getDbRefIdsResponse
                • getDbRefIdsReturn
                  • ArrayOf_soapenc_string

              getPdbChain

              • SOAP Action:
              • Input Message: getPdbChainRequest
                • in0
                  • string
                • in1
                  • string
              • Output Message: getPdbChainResponse
                • getPdbChainReturn
                  • string

              runXmlQuery

              • SOAP Action:
              • Input Message: runXmlQueryRequest
                • in0
                  • string
              • Output Message: runXmlQueryResponse
                • runXmlQueryReturn
                  • ArrayOf_soapenc_string

              getCurrentPdbIds

              • SOAP Action:
              • Input Message: getCurrentPdbIdsRequest
                • Output Message: getCurrentPdbIdsResponse
                  • getCurrentPdbIdsReturn
                    • ArrayOf_soapenc_string

                getObsoletePdbIds

                • SOAP Action:
                • Input Message: getObsoletePdbIdsRequest
                  • Output Message: getObsoletePdbIdsResponse
                    • getObsoletePdbIdsReturn
                      • ArrayOf_soapenc_string

                  getDomainFragments

                  • SOAP Action:
                  • Input Message: getDomainFragmentsRequest
                    • in0
                      • string
                    • in1
                      • string
                    • in2
                      • string
                  • Output Message: getDomainFragmentsResponse
                    • getDomainFragmentsReturn
                      • ArrayOfDomainFragmentWS

                  blastQueryXml

                  • SOAP Action:
                  • Input Message: blastQueryXmlRequest
                    • in0
                      • string
                    • in1
                      • double
                  • Output Message: blastQueryXmlResponse
                    • blastQueryXmlReturn
                      • string

                  blastStructureIdQueryXml

                  • SOAP Action:
                  • Input Message: blastStructureIdQueryXmlRequest
                    • in0
                      • string
                    • in1
                      • string
                    • in2
                      • double
                  • Output Message: blastStructureIdQueryXmlResponse
                    • blastStructureIdQueryXmlReturn
                      • string

                  WSDL Changes

                  DateDescription of Changes
                  8th April 2009First Snapshot
                  27th May 2009Operation named getFirstStructSheetRange has been removed.
                  Operation named getStructSheetRanges has been removed.
                  Operation named getFirstStructConf has been removed.
                  Operation named getStructConfs has been removed.
                  Operation named homologyReductionQuery has been removed.
                  PASSED

                  Test #1: test XML query

                  the tests posts

                  <orgPdbQuery>
                  <queryType>org.pdb.query.simple.UpAccessionIdQuery</queryType>
                  <description>Simple query for a list of Uniprot Accession IDs: P50225</description>
                  <accessionIdList>P50225</accessionIdList>
                  </orgPdbQuery>

                  against the web services. The response should be a list of at least 3 PDB ids.

                  Submitted by andreas on Fri, 03/13/2009 - 23:24
                  »