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[bioontology-support] Adding a group to an ontology

Madani, Sina Sina.Madani at vumc.org
Wed Dec 4 14:39:30 PST 2019


Thank you very much again Michael,

I have another question about automatic & manual mapping function in OntoPortal but I will post it under a separate email thread.

Sina

From: Michael Dorf <mdorf at stanford.edu>
Date: Wednesday, December 4, 2019 at 1:42 PM
To: "Madani, Sina" <Sina.Madani at vumc.org>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] Adding a group to an ontology

Hi Sina,

Agreed, that functionality would indeed be very useful. I’ve created a Github issue for it so that, at the very least, we keep track of it and possibly prioritize it for some near future development:

https://github.com/ncbo/bioportal_web_ui/issues/117<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fbioportal_web_ui%2Fissues%2F117&data=02%7C01%7CSina.Madani%40vumc.org%7C4ff69b9dbe0e422064cb08d778f20c1d%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637110853298907526&sdata=OZRXVhI9rs2cD8m%2BJUNMBaNGScd6Tp%2FpOyusPBgCyhw%3D&reserved=0>

My colleague tells me that our reason for not publishing that functionality may have been intentional to prevent ontology authors to randomly assign their ontologies to special groups like “OBO Foundry”. That makes sense, though it should still be available, possibly in the “Admin” mode for VM users.

As far as removing a group from an ontology, this code should do the trick:

Remove Ontology from Group
--------------------------
gr_to_remove = LinkedData::Models::Group.find("TESTGROUP").first
ont = LinkedData::Models::Ontology.find("MYONT").first
ont.bring_remaining
groups = ont.group.dup
groups.delete_if { |gr| gr.id.to_s === gr_to_remove.id.to_s }
ont.group = groups
ont.valid?
ont.save

Let me know if you require further assistance.

Thanks!

Michael



On Dec 4, 2019, at 9:31 AM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Thank you very much Michael

It did the trick!
Is there a way to “un-assign” a “Group” for a given ontology as well?
A graphical interface like the one used for “categories” under Edit Ontology Information panel would be very practical for “groups” as well ☺

Thanks!
Sina

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Tuesday, December 3, 2019 at 10:12 PM
To: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Cc: "support at bioontology.org<mailto:support at bioontology.org>" <support at bioontology.org<mailto:support at bioontology.org>>
Subject: Re: [bioontology-support] Adding a group to an ontology

Hi Sina,

Thank you for contacting us. You were on the right track, it just requires a little more code. Group is an object rather than a string, and an ontology may belong to multiple groups. Here is the code for both creating a group and assigning ontology to it:

Create Group
------------
gr = LinkedData::Models::Group.new({acronym: "TESTGROUP", name: "Test Group", description: "Test Group Description", created: DateTime.parse("2019-12-03T09:26:30-08:00")})
gr.valid?
gr.save

gr = LinkedData::Models::Group.find("TESTGROUP").first
gr.bring_remaining

Assign Ontology to Group
------------------------
ont = LinkedData::Models::Ontology.find("MYONT").first
ont.bring_remaining
groups = ont.group.dup
groups << gr
ont.group = groups
ont.valid?
ont.save

Let me know if this works for you.

Thanks,

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------





On Dec 3, 2019, at 4:27 PM, Madani, Sina <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>> wrote:

Hi,

How can we add a “group” to an ontology in our local OntoPortal instance?
I tried below commands within ruby console but it was unsuccessful:

ontology  = LinkedData::Models::Ontology.find("MyOntology").first
ontology.group = ”MyGroup”

“MyGroup” group already exists in our BioPortal instance (created in ruby console)

I tried ontology.save command at the end as well as but no success.


Thanks!

Sina
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