fetchProDom

PASSED
113
Service version1.0
Contributor URLhttp://prodom.prabi.fr/prodom/current/documentation/fetchProDom.html
WSDL URLhttp://prodom.prabi.fr/prodom/current/wsdl/fetchProDom.wsdlPASSED

fetchProDom is a set of five different webservices that interrogates the ProDom database.

  • fetchdom: Enter one or several (separated by spaces) ProDom AC (eg PD000039) and it returns the family(ies) description in prodom format.
  • fetchdom_fasta: same as above with the results given in fasta format.
  • fetchdom_align: from one ProDom AC gives two output: one is the alignment of the proteins of the ProDom family and the other is the consensus sequence. This particular webservice is made to work with blastProDom.
  • fetchdom_keyword: Enter one or several keyword(s)(separated by a blank space) and a “boolean”: and/or and it returns the ProDom familiy(ies) which have the keyword(s) in the description field in prodom format and a file with only their AC.
  • fetchProt: Enter one Protein AC (SWISS-Prot or TREmbl) and it returns the domain composition of this protein.

Please see ProDom help page and data file format help page if needed.
We have a perl script available to run this webservice from your computer. Please install SOAP Lite before.

A description of the WSDL service:

FetchProDomService

Namespace: http://prodom.prabi.fr/fetchProDom

  • Port: FetchProDomPort
  • Location: http://prodom.prabi.fr/prodom/2006.1/cgi-bin/fetchProDom.cgi
  • Protocol: http://schemas.xmlsoap.org/soap/http
  • Default Style: document

Operations

runFetchDom

Takes a ProDom AC and returns the domain in ProDom Format

  • SOAP Action: http://prodom.prabi.fr/fetchProDom#runFetchDom
  • Input Message: FetchDomRequestMsg
    • inputWrapper
      • runFetchDom type
        • ProdomAC type string
    • Output Message: FetchDomResponseMsg
      • outputWrapper
        • runFetchDomResponse type
          • output_in_fetchdom_format type string

      runFetchProt

      Takes a Protein ID (Swiss-prot/trembl) and returns the domains of this protein

      • SOAP Action: http://prodom.prabi.fr/fetchProDom#runFetchProt
      • Input Message: FetchProtRequestMsg
        • inputWrapper
          • runFetchProt type
            • Protein_ID type string
        • Output Message: FetchProtResponseMsg
          • outputWrapper
            • runFetchProtResponse type
              • protein_domains type string

          runFetchFasta

          Takes a ProDom AC and returns the domain in FASTA Format

          • SOAP Action: http://prodom.prabi.fr/fetchProDom#runFetchFasta
          • Input Message: FetchFastaRequestMsg
            • inputWrapper
              • runFetchFasta type
                • ProdomAC type string
            • Output Message: FetchFastaResponseMsg
              • outputWrapper
                • runFetchFastaResponse type
                  • output_in_fasta_format type string

              runFetchAlign

              Takes a ProDom AC and returns the alignment-with consensus- and the consensus sequence

              • SOAP Action: http://prodom.prabi.fr/fetchProDom#runFetchAlign
              • Input Message: FetchAlignRequestMsg
                • inputWrapper
                  • runFetchAlign type
                    • ProdomAC type string
                • Output Message: FetchAlignResponseMsg
                  • outputWrapper
                    • runFetchAlignResponse type
                      • output_as_alignment type string
                        • output_as_consensus type string

                    runFetchKW

                    Takes one or several keywords(separated by a space) and a boolean (and or or) and gives out the domain families (complete output or only ids)

                    • SOAP Action: http://prodom.prabi.fr/fetchProDom#runFetchKW
                    • Input Message: FetchKWRequestMsg
                      • inputWrapper
                        • runFetchKW type
                          • boolean type string
                            • keyword type string
                        • Output Message: FetchKWResponseMsg
                          • outputWrapper
                            • runFetchKWResponse type
                              • complete_output type string
                                • output_ids type string

                            runFetchKWscript

                            only for script use, not for Taverna

                            • SOAP Action: http://prodom.prabi.fr/fetchProDom#runFetchKWscript
                            • Input Message: FetchKWscriptRequestMsg
                              • inputWrapper
                                • runFetchKWscript type
                                  • boolean type string
                                    • keyword type string
                                • Output Message: FetchKWscriptResponseMsg
                                  • outputWrapper
                                    • runFetchKWscriptResponse type
                                      • complete_output type string

                                  WSDL Changes

                                  DateDescription of Changes
                                  8th April 2009First Snapshot
                                  PASSED

                                  Test #1: fetchProDom Test (perl SOAP::Lite)

                                  Perl script to test each of the 5 services composing fetchProDom : fetchdom, fetchfasta, fetchprot, fetchalign and fetchkw.
                                  Uses SOAP::Lite.

                                  PASSED

                                  Test #2: fetchProDom Test (perl XML::Compile::WSDL11)

                                  Perl script testing simply each of the five services composing fetchProDom : fetchDom, fetchFasta, fetchProt, fetchAlign and fetchKW.
                                  Uses XML::Compile::WSDL11.

                                  Submitted by lauranne.duquenne on Mon, 10/13/2008 - 16:25
                                  »