Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Eric Deutsch edeutsch at
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!


*From:* Jennifer Leigh Vendetti <vendetti at>
*Sent:* Saturday, October 9, 2021 8:12 AM
*To:* Eric Deutsch <edeutsch at>
*Cc:* support at
*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,


On Oct 8, 2021, at 11:11 AM, Eric Deutsch <edeutsch at>

Hi Jennifer, thank you for the prompt response!

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



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

Hi Eric,

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

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

but we have updated it over 20 times in the past year:

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 ``”}}

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:

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,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 122158 bytes
Desc: not available
URL: <>

More information about the bioontology-support mailing list