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[bioontology-support] Failed to parse PSI-MS CV in BioPortal VA

Jennifer Leigh Vendetti vendetti at stanford.edu
Tue May 17 11:33:55 PDT 2016


Hello Vincent,


On May 16, 2016, at 11:57 PM, vincentguo <gjw_0418 at sina.com<mailto:gjw_0418 at sina.com>> wrote:

Dear BioPortal experts,

   I submitted PSI-MS Controlled Vocabulary (version: 3.86.2, downloaded
from HUPO official website:
https://raw.githubusercontent.com/HUPO-PSI/psi-ms-CV/master/psi-ms.obo) into
our BioPortal VA (version2.4) and got an import error.


I downloaded the OBO file from the URL you mention above and was able to parse in BioPortal without any errors.



   Then I replaced the imports with:
import: http://purl.obolibrary.org/obo/pato.obo
import: http://purl.obolibrary.org/obo/uo.obo

   I still got an import error as follows:
Error: UNKNOWN
Message: Error Could not load imported ontology:
<http://purl.obolibrary.org/obo/pato.obo> Cause: Problem parsing
http://purl.obolibrary.org/obo/pato.obo


Based on this error message from the log, I’m theorizing that this may be a more general issue with your virtual appliance not being connected to a network that would allow access to these outside import resources, e.g., http://purl.obolibrary.org/obo/pato.owl.

From your virtual appliance, are you able to ping an outside resource like Google (ping -c 5 google.com<http://google.com>)?

You could also try to see if a curl command returns any data (curl www.google.com<http://www.google.com>).

Jennifer

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