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[bioontology-support] [EXTERNAL]Re: [BioPortal] Feedback from gaurab.mukherjee at jax.org

John Graybeal jgraybeal at stanford.edu
Mon Nov 23 20:56:26 PST 2020


I'm sorry that didn't work for you. It appears to be a bug in our handling of custom ontology requests.

I've written up ticket https://github.com/ncbo/bioportal-project/issues/195 to address it. Unfortunately we won't be able to investigate this further any time soon, so at the moment I think we're out of options using BioPortal.

Another option that some people have chosen is to install OntoPortal on their own computer or server, and only install the ontologies they want to search through. I realize that may be more work that you want to invest.

I'm sorry we can't do more for you at the present time. If we get a chance to address this problem we will try to let you know, or you can subscribe to the GitHub ticket if you want notifications of changes to its status.

John
[https://avatars2.githubusercontent.com/u/317926?s=400&v=4]<https://github.com/ncbo/bioportal-project/issues/195>
can't create custom ontologies · Issue #195 · ncbo/bioportal-project<https://github.com/ncbo/bioportal-project/issues/195>
User wrote: Thank you for your quick response. I did go back into my account and tried to create in Account Settings à Custom Ontology Set à select ontologies. I then picked three ontologies from t...
github.com

________________________________
From: Gaurab Mukherjee <Gaurab.Mukherjee at jax.org>
Sent: Monday, November 23, 2020 3:43 AM
To: John Graybeal <jgraybeal at stanford.edu>; support at bioontology.org <support at bioontology.org>
Subject: Re: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from gaurab.mukherjee at jax.org


Hi John,



Thank you for your quick response. I did go back into my account and tried to create in Account Settings --> Custom Ontology Set --> select ontologies. I then picked three ontologies from the pick list, for details see the screenshot.



But when I hit ‘Save custom ontologies’ it returns the below error message:

The page you are looking for wasn't found. Please try again.



I am using Firefox 78.0.3esr on Mac OS 10.13.6



Yours,

Gaurab



--

Gaurab Mukherjee

gaurab.mukherjee at jax.org<mailto:gaurab.mukherjee at jax.org>





From: John Graybeal <jgraybeal at stanford.edu>
Date: Saturday, 21 November 2020 at 04:49
To: "support at bioontology.org" <support at bioontology.org>
Cc: Gaurab Mukherjee <Gaurab.Mukherjee at jax.org>
Subject: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from gaurab.mukherjee at jax.org



Hello,



Thank you for this input. I created an issue (https://github.com/ncbo/bioportal-project/issues/1910) to capture it.



BioPortal has an obscure feature that might meet your needs. When you are logged in, visit Account Settings (the drop-down under your account name). If you scroll to the end of that page, you will see a link under Custom Ontology Set that reads 'select ontologies'. If you click on this link, you will be able to see only the ontologies that you have selected.



There are a few documented side effects of using this setting: Any ontology with a view (ontology views are listed in the lower left of the ontology's summary page) is no longer viewable in the UI (https://github.com/ncbo/bioportal_web_ui/issues/36),. And once you set the list of custom ontologies you can't modify it; you can only delete all the ontologies and start over (https://github.com/ncbo/bioportal_web_ui/issues/51).



For your needs, this might be a good fit (or you could create a separate account just for this task and set its Custom Ontology Set).



John







On Nov 20, 2020, at 7:09 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:



Name: gaurab.mukherjee at jax.org<mailto:gaurab.mukherjee at jax.org>

Email: gaurab.mukherjee at jax.org<mailto:gaurab.mukherjee at jax.org>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2Fsearch%3Fopt%3Dadvanced

Feedback:

Hi. This is a great tool. I have created a login account. I use advanced search to search for terms in only three ontologies, which are mouse adult anatomy (MA), Mammalian Phenotype (MP) and Vertebrate trait (VT). It would be much easier If I could save this set of three ontologies as a term, that I could pick to then search within this for my specific terms.



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========================

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







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