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[bioontology-support] [BioPortal] Feedback from Eric Deutsch

Eric Deutsch edeutsch at systemsbiology.org
Sun Oct 10 21:25:58 PDT 2021


Hi Jennifer, many thanks for fixing this. I have tested and it is good, all
up to date.



Thank you!

Eric





*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* Saturday, October 9, 2021 8:12 AM
*To:* Eric Deutsch <edeutsch at systemsbiology.org>
*Cc:* support at bioontology.org
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from Eric Deutsch



Hi Eric,



I checked our system this morning and it appears that a new version of MS
was successfully retrieved and processed.



Kind regards,

Jennifer











On Oct 8, 2021, at 11:11 AM, Eric Deutsch <edeutsch at systemsbiology.org>
wrote:



Hi Jennifer, thank you for the prompt response!

Looking forward to seeing if it will be fixed as of tomorrow.



Thanks!

Eric





*From:* Jennifer Leigh Vendetti <vendetti at stanford.edu>
*Sent:* Friday, October 8, 2021 11:00 AM
*To:* support at bioontology.org
*Cc:* edeutsch at systemsbiology.org
*Subject:* Re: [bioontology-support] [BioPortal] Feedback from Eric Deutsch



Hi Eric,





On Oct 8, 2021, at 10:28 AM, support at bioontology.org wrote:



Hi, our ontology "MS" has not been updated at your site for over a year:

https://bioportal.bioontology.org/ontologies/MS

but we have updated it over 20 times in the past year:
https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo

How we arrange it so that the MS ontology is kept up-to-date in BioPortal?







I examined the log files for our nightly ontology pull process and found an
error related to MS. Our triplestore contained a corrupt ontology
submission object that’s preventing creation of new submissions for MS:



E, [2021-10-07T18:05:48.973919 #18479] ERROR -- : Unable to create a new
submission in OntologyPull: {:proc_naming=>{:duplicate=>"There is already a
persistent resource with id `
http://data.bioontology.org/ontologies/MS/submissions/163`”}}



I’ve deleted this corrupt submission object, which should clear the way for
the nightly pull process to resume processing new versions of your ontology.



However, there’s something else to be aware of - we’re currently
troubleshooting an issue in our production system that’s been preventing
our nightly pull process from downloading new versions of a subset of
ontologies since September 30th. It’s currently documented here in our
issue tracker:



https://github.com/ncbo/bioportal_web_ui/issues/176



I’m not sure if your ontology will be affected by this issue - I’ll know
more after our pull process kicks off this evening.



Apologies for the inconvenience.



Kind regards,

Jennifer
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