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

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

Gaurab Mukherjee

Hi John,

 

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 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

[hidden email]

 

 

From: John Graybeal <[hidden email]>
Date: Saturday, 21 November 2020 at 04:49
To: "[hidden email]" <[hidden email]>
Cc: Gaurab Mukherjee <[hidden email]>
Subject: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from [hidden email]

 

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, [hidden email] wrote:

 

Name: [hidden email]

[hidden email]

Location: https%3A%2F%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.

 

_______________________________________________
bioontology-support mailing list
[hidden email]
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

 

 

 

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
bioontology-support mailing list
[hidden email]
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Re: [bioontology-support] [EXTERNAL]Re: [BioPortal] Feedback from gaurab.mukherjee@jax.org

John Graybeal-2
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


From: Gaurab Mukherjee <[hidden email]>
Sent: Monday, November 23, 2020 3:43 AM
To: John Graybeal <[hidden email]>; [hidden email] <[hidden email]>
Subject: Re: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from [hidden email]
 

Hi John,

 

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 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

[hidden email]

 

 

From: John Graybeal <[hidden email]>
Date: Saturday, 21 November 2020 at 04:49
To: "[hidden email]" <[hidden email]>
Cc: Gaurab Mukherjee <[hidden email]>
Subject: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from [hidden email]

 

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, [hidden email] wrote:

 

Name: [hidden email]

[hidden email]

Location: https%3A%2F%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.

 

_______________________________________________
bioontology-support mailing list
[hidden email]
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

 

 

 

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] [EXTERNAL]Re: [BioPortal] Feedback from gaurab.mukherjee@jax.org

Gaurab Mukherjee

Thanks for your help John.

If you do add this functionality to the web browser version then I would be grateful if you could keep me in the loop.

 

Yours,

Gaurab

 

-- 

Gaurab Mukherjee

[hidden email]

 

 

From: John Graybeal <[hidden email]>
Date: Tuesday, 24 November 2020 at 04:56
To: Gaurab Mukherjee <[hidden email]>, "[hidden email]" <[hidden email]>
Subject: Re: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from [hidden email]

 

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

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 <[hidden email]>
Sent: Monday, November 23, 2020 3:43 AM
To: John Graybeal <[hidden email]>; [hidden email] <[hidden email]>
Subject: Re: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from [hidden email]

 

Hi John,

 

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 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

[hidden email]

 

 

From: John Graybeal <[hidden email]>
Date: Saturday, 21 November 2020 at 04:49
To: "[hidden email]" <[hidden email]>
Cc: Gaurab Mukherjee <[hidden email]>
Subject: [EXTERNAL]Re: [bioontology-support] [BioPortal] Feedback from [hidden email]

 

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, [hidden email] wrote:

 

Name: [hidden email]

[hidden email]

Location: https%3A%2F%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.

 

_______________________________________________
bioontology-support mailing list
[hidden email]
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

 

 

 

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support