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

Jennifer Leigh Vendetti vendetti at stanford.edu
Sat Oct 9 08:11:36 PDT 2021


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


[cid:F1661DE5-BABC-4CB9-B2AF-294D137DEF87 at lan]



On Oct 8, 2021, at 11:11 AM, Eric Deutsch <edeutsch at systemsbiology.org<mailto: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<mailto:vendetti at stanford.edu>>
Sent: Friday, October 8, 2021 11:00 AM
To: support at bioontology.org<mailto:support at bioontology.org>
Cc: edeutsch at systemsbiology.org<mailto: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<mailto: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`<http://data.bioontology.org/ontologies/MS/submissions/163%60>”}}

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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