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[bioontology-support] Access to the notes in deactivated submissions

Michael Dorf mdorf at
Thu Sep 26 15:26:13 PDT 2019

Hi Sina,

I am just confirming John’s earlier statement about notes being attached to the global ontology rather than an individual submission artifact. You should be able to see ALL notes by navigating to the Notes tab on the ontology page:



On Sep 26, 2019, at 12:27 PM, Madani, Sina <Sina.Madani at<mailto:Sina.Madani at>> wrote:

Thank you John & ppreciate your prompt response.
The use case is that we have created several versions of a locally defined ontology as it evolves (in our local instance of BioPortal) based on SMEs feedback (documented as “Notes” in the ontology).
In some instances, we’d like to be able to go back, browse, and see previous submissions and examines the notes that were documented on a given class. However, as soon as a new version/submission of an ontology is loaded, the previous submission becomes inactive/archived (in the example below, Sep 10 and Sep 11).



From: John Graybeal <jgraybeal at<mailto:jgraybeal at>>
Date: Thursday, September 26, 2019 at 1:26 PM
To: "Madani, Sina" <Sina.Madani at<mailto:Sina.Madani at>>
Cc: "support at<mailto:support at>" <support at<mailto:support at>>
Subject: Re: [bioontology-support] Access to the notes in deactivated submissions


My suspicion is that the notes are associated with the ontology artifact, not with a specific submission artifact. One of the team can be more authoritative about that.

Regarding your second question, can you tell me the use case you are concerned about?

I am pretty sure there is no automated way to delete older submissions. Part of the reason for this is that people who have used older submissions in research, or been affected by possible changes, then have no way to replicate their research or go back to confirm the exact change, or history of changes.

If there is a specific submission that is sensitive in some way (has something that should not be publicly accessible), we are happy to work with you to remove it from public access. You can contact me directly with confidential requests like that.


On Sep 26, 2019, at 8:25 AM, Madani, Sina <Sina.Madani at<mailto:Sina.Madani at>> wrote:

Good morning all,

Is there a way to access notes places on the previous versions of submissions (that are de-activated)? Where are those notes typically stored?
Also, is it possible to prevent OntoPortal from archiving older submissions when a new one is loaded?

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John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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