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[bioontology-support] Issues with importing ontologies to virtual appliance

Trish Whetzel whetzel at stanford.edu
Wed Apr 3 09:11:43 PDT 2013


Hi Colin, 

I've looped in Paul, who can help with the general issues about the import script and documentation of this step, and Lian for specific questions on loading the UMLS terminologies you mention below. 

Trish 


On Apr 3, 2013, at 8:49 AM, Colin Morris wrote:

> Hi,
> 
> We have an image of the Virtual Appliance running, and are trying to import ontologies. None of our attempts have been successful so far, namely:
> 
> 1) We downloaded the MeSH ontology from http://bioportal.bioontology.org/ontologies/1351 using download link http://rest.bioontology.org/bioportal/ontologies/download/46836?apikey=4ea81d74-8960-4525-810b-fa1baab576ff&userapikey= . 
> 
> We tried to submit it to our virtual appliance through the web interface, selecting the rrf format, and uploading a local copy of the zip file downloaded from the above link. This was successful, but the next day there's a note next to the ontology entry saying " parsing error" and it shows as having 0 terms etc.
> 
> 1b) We tried the same thing using the ICD9M ontology. This time, submitting gave a generic error message ("something went wrong - this has been logged", or something like that) after the file had uploaded.
> 
> 2) We've been trying to use the import script at /srv/ncbo/rails/BioPortal/current/util/import_ontologies/import_ontologies.rb. Running it without specifying $INCLUDE_ONTOLOGIES (i.e. trying to download all ontologies) continues to give a weird ruby error:
> 
> ./bioportal/ontology_wrapper.rb:149:in `[]': can't convert String into Integer (TypeError)
> 
> 2b) Setting $INCLUDE_ONTOLOGIES to [ 1352 ] (the id of the National Drug File), gives this output:
> 
> Total onts: 1
> Retrieving ontology
> http://rest.bioontology.org/bioportal/ontologies/47101?apikey=<apikey>
> Problem: 403 Forbidden
> 
> 
> 
> errors
> 47101	National Drug File	403 Forbidden
> 
> This is truly bizarre, because if I copy-paste that url (without the api key being redacted) into my browser, I get the results fine. If I do wget on that url from the server running the appliance, I also get the expected output.
> 
> 
> Do you have any suggestions for getting past any of the above issues? We'd like to import ontologies (just 5 of them) any way we can, and as soon as possible.
> 
> Also, I'd be curious to read any error logs associated with 1) and 1b), but I'm not sure where they live on the file system.
> 
> Thanks,
> Colin
> 
> 
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> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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