2

all,

I do not have good understanding of the Web Services. However, following the instructions on BRENDA (enzyme database) web site, I can use their SOAP service in perl programs. Then I tried to use the web service directly from Mathematica, but I got the following result:

In[182]:= << WebServices`

In[185]:= \
InstallService["http://www.brenda-enzymes.org/soap/brenda.wsdl"]

During evaluation of In[185]:= InstallService::elementschema: The element schema cannot be found for xsd:string. >>
During evaluation of In[185]:= InstallService::elementschema: The element schema cannot be found for xsd:string. >>
During evaluation of In[185]:= InstallService::elementschema: The element schema cannot be found for xsd:string. >>
During evaluation of In[185]:= General::stop: Further output of InstallService::elementschema will be suppressed during this calculation. >>
During evaluation of In[185]:= InstallService::bindinginput: There is not a valid input element in the getEcNumbersFromReference binding operation. >>
During evaluation of In[185]:= InstallService::use: Use not supported:  >>
During evaluation of In[185]:= Part::partd: Part specification Null[[2]] is longer than depth of object. >>
During evaluation of In[185]:= Part::partd: Part specification Null[[2]] is longer than depth of object. >>
During evaluation of In[185]:= InstallService::messagename: There is not a valid message name attribute on the Null input element in this WSDL. >>
During evaluation of In[185]:= InstallService::bindinginput: There is not a valid input element in the getOrganismsFromReference binding operation. >>
During evaluation of In[185]:= InstallService::use: Use not supported:  >>
During evaluation of In[185]:= Part::partd: Part specification Null[[2]] is longer than depth of object. >>
During evaluation of In[185]:= General::stop: Further output of Part::partd will be suppressed during this calculation. >>
During evaluation of In[185]:= InstallService::messagename: There is not a valid message name attribute on the Null input element in this WSDL. >>
During evaluation of In[185]:= InstallService::bindinginput: There is not a valid input element in the getEcNumbersFromSequence binding operation. >>
During evaluation of In[185]:= General::stop: Further output of InstallService::bindinginput will be suppressed during this calculation. >>
During evaluation of In[185]:= InstallService::use: Use not supported:  >>
During evaluation of In[185]:= General::stop: Further output of InstallService::use will be suppressed during this calculation. >>
During evaluation of In[185]:= InstallService::messagename: There is not a valid message name attribute on the Null input element in this WSDL. >>
During evaluation of In[185]:= General::stop: Further output of InstallService::messagename will be suppressed during this calculation. >>

Out[185]= {getOrganismSynonyms}

Notice that the method "getOrganismSynonyms" cannot be used correctly, either. Could anybody help to confirm whether it is my own problem or BRENDA simply does not work well with Mathematica by far?

Thanks a lot in advance.

梁國淦
  • 392
  • 1
  • 8
  • Mathematica WebService Technology is very outdated. It still works with WSDL 1.0 where the current technology is WSDL 2.0 (from 2007, reference here). I don't know if this has some influence in your case. I have exchanged some mails with support, but I didn't get any implementation forecast. – Murta Feb 21 '15 at 17:14
  • Thank you for sharing this information. It does seem that some of the features used in BRENDA were not supported. It is annoying that such information is not clearly stated in the documents. – 梁國淦 Feb 22 '15 at 00:56

1 Answers1

2

The following worked for me:

InstallService["https://www.brenda-enzymes.org/soap/brenda_zeep.wsdl", "Brenda`"]

{getReferenceById, getReferenceByPubmedId,... getEnzymeNames,... , getPdb}


?Brenda`getEnzymeNames


{___enzymeNames} getEnzymeNames["email_String","password_String","ecNumber_String","organism_String","synonyms_String"
]


Brenda`getEnzymeNames["username", Hash["password", "SHA256", "HexString"], "ecNumber3.6.1.5", "organism", "synonyms*"]


{enzymeNames["synonyms" -> "3.6.1.5", "ecNumber" -> "3.6.1.5"], 
 enzymeNames["synonyms" -> "5'-nucleotidase", 
  "ecNumber" -> "3.6.1.5"],... }
SergeyR
  • 21
  • 2