Problems with Generic Web Service Client

Hey folks,

today I wanted to try the Generic Web Service Client node for the first time. Unfortunately I am not able to load the NCBI webservice description file(s) into the node. Here are the WSDL files:

http://www.ncbi.nlm.nih.gov/books/NBK43082/#_chapter5_WSDL_Files_for_the_Current_Vers_

Please see the attached file showing the error message. Can you please help?

Best,
Marc

*bump*

Hi Marc, 

Unfortunately, the NCBI web services don't seem to work with Apache CXF and up to now, I have been unable to discover why.  

For now, there are a couple of potential options for workarounds.  The most promising are the KNIME4Bio nodes which have some specific NCBI webservice wrappers.  See here for more information:

https://code.google.com/p/knime4bio/

Big caveat, these nodes *seem* to work well, but they aren't part of our official community contributions, so I have no idea how well they are tested, etc. etc. 

Alternatively, we may be able to just scrape the information you need from their site. Specifically, what sort of information are you looking to get at?

Hey Aaron,

thank you for your help. I will give the knime4bio nodes a try.

I use the NCBI Gene Reports as a starting point for all kinds of useful and not-so-useful analysis. E.g. to find the UniProtKB ID or the Gene Ontologies associated with a Gene ID.

Unfortunately requesting these reports via the REST client is very slow and very error-prone. That means requesting 20k reports as XML takes 5 to 7 days. No joke, no exaggeration! Requesting 20k reports as XML via UniProt takes 1 hour. No joke, no exaggeration!

I expected to solve both problems using the web service client node...

Best,
Marc