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] Adding a group to an ontology

Madani, Sina Sina.Madani at vumc.org
Tue Dec 10 17:23:51 PST 2019


Thank you very much John for the comprehensive reply.
I did contact BioMixer few months ago but they referred me back to OntoPortal team!

We’ve just started testing the mapping functionality of OntoPortal, so we can certainly wait until OntoPortal’s DevOps person returns.
And in terms of funding, we are still in the evaluation phase and if our end users/SMEs decide to adopt OntiolPortal we will definitely get back to you to formalize a collaborative agreement.

Regards,

Sina

From: John Graybeal <jgraybeal at stanford.edu>
Date: Tuesday, December 10, 2019 at 4:51 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

Sina,

Thanks for your followup on these BioMixer issues.  As you may know, because we have very limited ability to support BioMixer, we are considering our options to replace it at some point. Please read on for further thoughts on that, as well as your specific situation.

I am not sure there is an easy way forward here. Just to give a hypothetical approach, the first step for anyone to fix to the code is for the developer to be familiar with the Typescript and javascript development and installation stack for BioMixer, and to be able to work with that stack in the BioPortal environment and Virtual Appliance environment. While one of our developers has touched some of the BioMixer code, no BioMixer code on GitHub has been touched by anyone in 4 years. Meanwhile, Typescript and javascript processors have evolved since then, so we'd be starting from scratch to get this going.

That said, I appreciate your sense that the authentication line may be something simple. The problem here may be in the configuration of our system, or in the need to have a login already configured in the deployed BIomixer service. I have not been able to identify any obvious discrepancies but posted a note for further checking by our DevOps expert. Similarly there may be a configuration issue in the second ticket as well.

I've posted a few notes that our DevOps person can follow up on when he returns, but unfortunately he is out until after the new year. I do not think it would be good use of anyone else's time in our group to play with this; we would have to invest a very large amount of time to come up to speed.

If you have a really good DevOps person in your group, they might be able to follow and diagnose the calls that are made from the front end "Visualize" button through to the BioMixer REST service, and using the BioMixer GItHub repository (https://github.com/thechiselgroup/biomixer/<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fthechiselgroup%2Fbiomixer%2F&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792110454&sdata=OK7l7BrQLVoIPJD%2FmOWcIHvKVZo8eKaWzwJ5LtdNJBA%3D&reserved=0> and e.g., https://github.com/thechiselgroup/biomixer/wiki/BioMixer-Dev-Setup<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fthechiselgroup%2Fbiomixer%2Fwiki%2FBioMixer-Dev-Setup&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792110454&sdata=7qyJ28UNUfdOP5Oxo4KNqS%2BSNKwAxqPZYH90i5XR388%3D&reserved=0>), the BioPortal Virtual Appliance documentation (https://www.bioontology.org/wiki/Category:NCBO_Virtual_Appliance<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bioontology.org%2Fwiki%2FCategory%3ANCBO_Virtual_Appliance&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792120446&sdata=9CpFTanW7T9%2Ffa1ZB73AgK15vDMBC7su4TIUthHln7E%3D&reserved=0> and https://www.bioontology.org/wiki/Advanced_Administration<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bioontology.org%2Fwiki%2FAdvanced_Administration&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792120446&sdata=sTRtFff3hPDkE7i3gB1QZEmRb87aTVHXAMhEnoJTTdc%3D&reserved=0>), and the BioMixer video I mentioned (https://www.youtube.com/watch?v=tA5LLmMzlTs<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.youtube.com%2Fwatch%3Fv%3DtA5LLmMzlTs&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792120446&sdata=GJHL6ZJj7xBzcOQMj1WUNC0L3TDaKxLZ0I%2BhdJgyajQ%3D&reserved=0>) to dive in to the details of these interconnections to understand where the problem arises.

If you do not have such a person, and you can afford to wait, our DevOps person has a decent chance of sorting those issues, but we can't make any promises.

There are two other options you could pursue if these options are not suitable. One is to pay for someone to do this work; although there are very few people with the appropriate expertise, we might be able to free someone on our team to at least explore these issues, if funding is available to support them.

A second option is to contact the original providers of the BioMixer software to see if they have any advice. I am pretty sure they are not available for any work on the system, but there might be someone willing to share knowledge briefly with regard to specific issues, such as the ones in GitHub. You could try contacting them through GitHub, or via contacts from the published paper on BioMixer.

I hope something in that response proves helpful.

john


On Dec 9, 2019, at 12:22 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Forwarding to the support list so the team can respond.



Begin forwarded message:

From: "Madani, Sina" <Sina.Madani at vumc.org<mailto:Sina.Madani at vumc.org>>
Subject: Re: [bioontology-support] Adding a group to an ontology
Date: December 9, 2019 at 11:52:46 AM PST
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>

Hi Michael,

Speaking of github issue, there are two issue related to Biomixer since April on github that I haven’t seen any activity on them. Can you give us a hint how possibly we can fix it in our local instance or perhaps who can I follow up from your side?
The first issue  (“BioMixer missing top menu bar”) seems to me can be fixed easily since it’s apparently an authentication issue: I see below response in Chrome developer console after clicking on any class

POST http://biblio.ontoportal.org/BioMixer/org.thechiselgroup.biomixer.BioMixerWorkbench/authentication<https://nam05.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiblio.ontoportal.org%2FBioMixer%2Forg.thechiselgroup.biomixer.BioMixerWorkbench%2Fauthentication&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792130441&sdata=FIBk%2BGne3pK3Nqaf8pUviNdQxFhPxT4JXUZvFnyuVN0%3D&reserved=0> 500 (Internal Server Error)

The second issue (expanding concept mapping) might be a little more complex

https://github.com/ncbo/virtual_appliance/issues/6<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fvirtual_appliance%2Fissues%2F6&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792130441&sdata=RDGGr1O8rfIllgliTtt7P1PAeheRdSwanBbnQFrLGlo%3D&reserved=0>
https://github.com/ncbo/virtual_appliance/issues/7<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fncbo%2Fvirtual_appliance%2Fissues%2F7&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792140430&sdata=nazfukgnVNdmY%2Bs9z7clKUgMSrNoFFFTkzNDe2lCoBA%3D&reserved=0>


Thanks!
Sina











From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Date: Wednesday, December 4, 2019 at 1:42 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,

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%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792140430&sdata=lDl2321QPGuVv3rcSXYMZhcq6IFF%2Fx1Ss6A4VftIcTM%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
_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support<https://nam05.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.stanford.edu%2Fmailman%2Flistinfo%2Fbioontology-support&data=02%7C01%7CSina.Madani%40vumc.org%7C91e580f847974c75bb6d08d77dc37391%7Cef57503014244ed8b83c12c533d879ab%7C0%7C0%7C637116150792150432&sdata=ZobJ78zpd4G5dz3DaoVHxb23tJ%2BByIlMId01bRHwjVw%3D&reserved=0>

_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20191211/a8512215/attachment-0001.html>


More information about the bioontology-support mailing list