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

Colin Morris colin at
Wed Apr 3 08:49:48 PDT 2013


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 using download link

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<apikey>
Problem: 403 Forbidden

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

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

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.

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