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

Madani, Sina Sina.Madani at
Fri Sep 27 11:27:08 PDT 2019

Thank you very much John for the comprehensive reply.

I’ll discuss these options with the team and adopt an approach


From: John Graybeal <jgraybeal at>
Date: Friday, September 27, 2019 at 11:23 AM
To: "Madani, Sina" <Sina.Madani at>
Cc: "support at" <support at>
Subject: Re: [bioontology-support] Access to the notes in deactivated submissions

Ah, I misunderstood your request. You want to continue to be able to see the earlier submissions as first class ontologies, yes?

There is not a way to keep those submissions 'active' as a simple request. You would have two choices:
- Actually create a separate public ontology for each submission that you want to be preserved publicly
- Make a private copy of whatever submission you want to preserve (by resubmitting it as a separate ontology)

We do not encourage the first approach, because people who are looking for matching ontologies will find ALL the copies of your ontology, and will be confused about which one to choose (and annoyed at all the duplication).

Making private copies of the older submissions will avoid that problem—they can be shared with the members of BioPortal who need to see them, and you can append the version ID to the acronym of the ontology to create the new private ontology. I still wouldn't recommend creating lots of these, because people who DO have access to them will still see all those ontologies represented in the search, annotation, and recommendation tools.

Even if you do this, all the Notes will still be attached to the single public ontology, and will not be reflected in any copy.

A third option, if you strongly desire to maintain this workflow, is to use a private deployment of BioPortal (the Virtual Appliance) to store every version of your ontology separately (including the version ID in the acronym) as public ontologies. In your BioPortal deployment (which you could make public or not from your own site) the Notes would be attached to the versioned ontologies. Then you could upload to BioPortal whatever versions you want to be public in BioPortal (even by reference to your local repository).


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?

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

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

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