[bioontology-support] [BioPortal] Feedback from Karin Colsman

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[bioontology-support] [BioPortal] Feedback from Karin Colsman

support

Name: Karin Colsman

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO


Feedback:

Dear support team,

we uploaded a TTL file, and some of the properties are missing their labels.

https://bioportal.bioontology.org/ontologies/AFO/?p=properties

I have double-checked the file, and the entities do have a skos:prefLabel defined in our source file.

http://purl.allotrope.org/voc/afo/merged/REC/2020/06/merged-and-inferred.ttl

Is there anything we can do to help fix this bug?

Kind regards

Karin Colsman


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

jvendetti
Hello Karin,


On Aug 24, 2020, at 2:24 AM, [hidden email] wrote:

Dear support team,

we uploaded a TTL file, and some of the properties are missing their labels.

https://bioportal.bioontology.org/ontologies/AFO/?p=properties

I have double-checked the file, and the entities do have a skos:prefLabel defined in our source file.

http://purl.allotrope.org/voc/afo/merged/REC/2020/06/merged-and-inferred.ttl

Is there anything we can do to help fix this bug?




I spent some time yesterday investigating the portion of the source code that sets human readable labels for ontology classes and properties. For classes, the logic is more involved and looks at several locations for label values, including rdfs:label, skos:prefLabel, and http://data.bioontology.org/metadata/def/prefLabel. However, the code for properties is more simplistic and only checks for rdfs:label values.

To see a concrete example, you can look at the property tree for the Biomedical Resource Ontology:


BioPortal displays human readable labels for each node in the tree because the source ontology stored those values in an rdfs:label for each property.

It appears that the human readable labels for your properties are stored in skos:prefLabel, which is why they aren’t getting picked up and displayed by BioPortal. I’ve entered an enhancement request in our issue tracker to add skos:prefLabel as one of the locations to check for human readable property labels:


I don’t have a definitive answer at the moment for where this issue will end up in the queue. If you have an urgent need for this functionality, a workaround would be to modify your ontology to add your labels in rdfs:label for each property.

Kind regards,
Jennifer


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

Karin Colsman

Dear Jennifer,

 

thanks for opening the issue for us!

 

Kind regards

 

Karin Colsman

 

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Tuesday, 25 August, 2020 21:22
To: NCBO User Support <[hidden email]>
Cc: Karin Colsman <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

 

Hello Karin,

 



On Aug 24, 2020, at 2:24 AM, [hidden email] wrote:

Dear support team,

we uploaded a TTL file, and some of the properties are missing their labels.

https://bioportal.bioontology.org/ontologies/AFO/?p=properties

I have double-checked the file, and the entities do have a skos:prefLabel defined in our source file.

http://purl.allotrope.org/voc/afo/merged/REC/2020/06/merged-and-inferred.ttl

Is there anything we can do to help fix this bug?

 

 

 

I spent some time yesterday investigating the portion of the source code that sets human readable labels for ontology classes and properties. For classes, the logic is more involved and looks at several locations for label values, including rdfs:label, skos:prefLabel, and http://data.bioontology.org/metadata/def/prefLabel. However, the code for properties is more simplistic and only checks for rdfs:label values.

 

To see a concrete example, you can look at the property tree for the Biomedical Resource Ontology:

 

 

BioPortal displays human readable labels for each node in the tree because the source ontology stored those values in an rdfs:label for each property.

 

It appears that the human readable labels for your properties are stored in skos:prefLabel, which is why they aren’t getting picked up and displayed by BioPortal. I’ve entered an enhancement request in our issue tracker to add skos:prefLabel as one of the locations to check for human readable property labels:

 

 

I don’t have a definitive answer at the moment for where this issue will end up in the queue. If you have an urgent need for this functionality, a workaround would be to modify your ontology to add your labels in rdfs:label for each property.

 

Kind regards,

Jennifer

 


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

Karin Colsman
In reply to this post by support

Dear support team,

 

we are getting an RDF error while trying to upload a new version of the AFO ontology at https://bioportal.bioontology.org/ontologies/AFO

 

The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?

 

I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.

 

Thank you very much for your time,

 

Karin Colsman

 

 

From: [hidden email] <[hidden email]>
Sent: Monday, 24 August, 2020 10:24
To: [hidden email]; Karin Colsman <[hidden email]>
Subject: [BioPortal] Feedback from Karin Colsman

 

Name: Karin Colsman

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO

 


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

John Graybeal-2
Karin,

Thank you for your request.

We are investigating this error and will give you more information as soon as we can. (It is not anything obvious to me, but I will forward to our experts. It may be a day or two before we have further information, due to our current staffing limits. Apologies for that.

I am not able to duplicate your issue with the support form—on my system it displays as a small pop-up form, without the footer. Is it possible you have blocked pop-ups?

John





On Apr 26, 2021, at 1:39 AM, Karin Colsman <[hidden email]> wrote:

Dear support team,
 
we are getting an RDF error while trying to upload a new version of the AFO ontology athttps://bioportal.bioontology.org/ontologies/AFO
 
The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?
 
I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.
 
Thank you very much for your time,
 
Karin Colsman
 
 
From: [hidden email] <[hidden email]> 
Sent: Monday, 24 August, 2020 10:24
To: [hidden email]; Karin Colsman <[hidden email]>
Subject: [BioPortal] Feedback from Karin Colsman
 

Name: Karin Colsman 

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO 

 

<merged-and-inferred.ttl><bioportal_support.png>_______________________________________________
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




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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

Karin Colsman

Hi John,

 

thanks for getting back to me.

 

I did not get a popup, so I guess all browsers are blocking it by default, and I did not notice them doing that.

 

Maybe you could reprogram this without using a popup, or ensure it gets the space it needs when popups are blocked?

 

Kind regards

 

Karin

 

 

From: John Graybeal <[hidden email]>
Sent: Thursday, 29 April, 2021 01:51
To: Karin Colsman <[hidden email]>
Cc: [hidden email]; Amnon Ptashek <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

 

Karin,

 

Thank you for your request.

 

We are investigating this error and will give you more information as soon as we can. (It is not anything obvious to me, but I will forward to our experts. It may be a day or two before we have further information, due to our current staffing limits. Apologies for that.

 

I am not able to duplicate your issue with the support form—on my system it displays as a small pop-up form, without the footer. Is it possible you have blocked pop-ups?

 

John

 

 

 

 



On Apr 26, 2021, at 1:39 AM, Karin Colsman <[hidden email]> wrote:

 

Dear support team,

 

we are getting an RDF error while trying to upload a new version of the AFO ontology athttps://bioportal.bioontology.org/ontologies/AFO

 

The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?

 

I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.

 

Thank you very much for your time,

 

Karin Colsman

 

 

From: [hidden email] <[hidden email]> 
Sent: Monday, 24 August, 2020 10:24
To: [hidden email]; Karin Colsman <[hidden email]>
Subject: [BioPortal] Feedback from Karin Colsman

 

Name: Karin Colsman 

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO 

 

<merged-and-inferred.ttl><bioportal_support.png>_______________________________________________
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

 

 

 


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

John Graybeal-2
Good suggestion, thank you! I’ll make a ticket for that. 


From: Karin Colsman <[hidden email]>
Sent: Thursday, April 29, 2021 12:54:19 AM
To: John Graybeal <[hidden email]>
Cc: [hidden email] <[hidden email]>
Subject: RE: [bioontology-support] [BioPortal] Feedback from Karin Colsman
 

Hi John,

 

thanks for getting back to me.

 

I did not get a popup, so I guess all browsers are blocking it by default, and I did not notice them doing that.

 

Maybe you could reprogram this without using a popup, or ensure it gets the space it needs when popups are blocked?

 

Kind regards

 

Karin

 

 

From: John Graybeal <[hidden email]>
Sent: Thursday, 29 April, 2021 01:51
To: Karin Colsman <[hidden email]>
Cc: [hidden email]; Amnon Ptashek <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

 

Karin,

 

Thank you for your request.

 

We are investigating this error and will give you more information as soon as we can. (It is not anything obvious to me, but I will forward to our experts. It may be a day or two before we have further information, due to our current staffing limits. Apologies for that.

 

I am not able to duplicate your issue with the support form—on my system it displays as a small pop-up form, without the footer. Is it possible you have blocked pop-ups?

 

John

 

 

 

 



On Apr 26, 2021, at 1:39 AM, Karin Colsman <[hidden email]> wrote:

 

Dear support team,

 

we are getting an RDF error while trying to upload a new version of the AFO ontology athttps://bioportal.bioontology.org/ontologies/AFO

 

The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?

 

I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.

 

Thank you very much for your time,

 

Karin Colsman

 

 

From: [hidden email] <[hidden email]> 
Sent: Monday, 24 August, 2020 10:24
To: [hidden email]; Karin Colsman <[hidden email]>
Subject: [BioPortal] Feedback from Karin Colsman

 

Name: Karin Colsman 

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO 

 

<merged-and-inferred.ttl><bioportal_support.png>_______________________________________________
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

 

 

 


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

John Graybeal-2
In reply to this post by Karin Colsman
Karin,

The issue we found seems to be with line 665, which declares that the IRI 'http://purl.org/dc/terms/' is an AnnotationProperty. I'm not sure why this is an error (likely because the IRI is also used as the object of all the importedFrom triples of dct:); but if we delete that line we find the ontology loads properly into BioPortal. (We have uploaded it as the latest version with this change.)  We checked the last version that loaded correctly, and it does not have this declaration.

663  ###  http://purl.org/dc/terms/
664  
665  dct: rdf:type owl:AnnotationProperty .

We suggest that you might want to remove that line from future submissions in order that they parse in BioPortal.

We found the issue when running our OWL API wrapper code against this ontology. (That's just a command line wrapper for the OWL API library.)  I'm wondering if you might be running a different version of the OWL API library, to explain why you didn't see a parsing issue?  We are running 4.5.17.

Please let us know of concerns or questions. 

John

On Apr 26, 2021, at 1:39 AM, Karin Colsman <[hidden email]> wrote:

Dear support team,
 
we are getting an RDF error while trying to upload a new version of the AFO ontology athttps://bioportal.bioontology.org/ontologies/AFO
 
The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?
 
I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.
 
Thank you very much for your time,
 
Karin Colsman
 
 
From: [hidden email] <[hidden email]> 
Sent: Monday, 24 August, 2020 10:24
To: [hidden email]; Karin Colsman <[hidden email]>
Subject: [BioPortal] Feedback from Karin Colsman
 

Name: Karin Colsman 

Email: [hidden email]

Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO 

 

<merged-and-inferred.ttl><bioportal_support.png>_______________________________________________
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




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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

jvendetti
In reply to this post by Karin Colsman
Hi Karin,

Just to clarify - the submit feedback form is presented in a modal dialog rather than a pop-up. Whether or not you’re blocking pop-ups should have no bearing on the modal dialog display. I’ve done some testing on my system with Chrome, Firefox, and Safari. Pop-ups are blocked in all 3 of the browsers and the submit feedback dialog displays properly for me in a modal dialog. 

In the original screenshot you sent, I noticed other oddities in your display. There are bullets showing up in the header and footer next to navigation links, and improper left-alignment of the “cite us” and other links at the bottom. I’ve included your screenshot again below, along with a screenshot of how BioPortal displays on my system to underline the differences. Out of curiosity, have you tried clearing the cache for BioPortal to see if these issues persist? You could selectively clear the cache for just the BioPortal website in Chrome by doing the following:

- Navigate to BioPortal
- Click the three dots menu and choose More Tools -> Developer Tools to open the developer console
- In the upper left corner of the browser window, right click on the reload icon and choose “Empty Cache and Hard Reload”

If you still see the same differences in display, could you provide more information about the version of Chrome or Firefox that you have installed, as well as what operating system you’re using?

Kind regards,
Jennifer












On Apr 29, 2021, at 12:54 AM, Karin Colsman <[hidden email]> wrote:

Hi John,
 
thanks for getting back to me.
 
I did not get a popup, so I guess all browsers are blocking it by default, and I did not notice them doing that.
 
Maybe you could reprogram this without using a popup, or ensure it gets the space it needs when popups are blocked?
 
Kind regards
 
Karin
 
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, 29 April, 2021 01:51
To: Karin Colsman <[hidden email]>
Cc: [hidden email]; Amnon Ptashek <[hidden email]>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman
 
Karin, 
 
Thank you for your request.
 
We are investigating this error and will give you more information as soon as we can. (It is not anything obvious to me, but I will forward to our experts. It may be a day or two before we have further information, due to our current staffing limits. Apologies for that. 
 
I am not able to duplicate your issue with the support form—on my system it displays as a small pop-up form, without the footer. Is it possible you have blocked pop-ups?
 
John
 
<image001.png>
 
 
 


On Apr 26, 2021, at 1:39 AM, Karin Colsman <[hidden email]> wrote:
 
Dear support team,
 
we are getting an RDF error while trying to upload a new version of the AFO ontology athttps://bioportal.bioontology.org/ontologies/AFO
 
The ttl file can be opened both with the OWL API and the JENA API (Java versions) without any errors. Can you see from your server logs what the problem might be?
 
I am also attaching a screenshot of the support form which is unusable, because the site footer is overlapping the form fields. My screen resolution is 1920x1080. I have tried Firefox, Chrome and Internet Explorer and the problem is present on all of them.
 
Thank you very much for your time,
 
Karin Colsman
 
 
From: [hidden email] <[hidden email]> 
Sent: Monday, 24 August, 2020 10:24
To: [hidden email]; Karin Colsman <[hidden email]>
Subject: [BioPortal] Feedback from Karin Colsman
 
Name: Karin Colsman 
Location: https%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FAFO 
 
<merged-and-inferred.ttl><bioportal_support.png>_______________________________________________
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
 
 
 
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bioontology-support mailing list
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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Re: [bioontology-support] [BioPortal] Feedback from Karin Colsman

jvendetti
Hi Karin,

OK - glad to hear the modal dialog is functioning for you.

With regard to the footer layout, I’m not sure how to reproduce what you’re seeing. I used the BrowserStack cross-browser testing application with the inputs you gave (Windows, Chrome 90, resolutions 1920x1080), and the footer displays as intended:




I also used BrowserStack to look at the 1920x1080 resolution for the latest versions of tSafari, Edge, and Firefox, and they all looked OK.

Are you running Windows 10?

Kind regards,
Jennifer



On May 6, 2021, at 10:54 AM, Karin Colsman <[hidden email]> wrote:

Hi Jennifer,
 
I’m getting the modal dialog now without any issues, in all my browsers (Firefox, Chrome, IE, Edge). No idea what went wrong at the time and why it is fixed now – I didn’t do anything.
 
The footer layout looks broken now though – I am attaching a screenshot from Chrome Version 90.0.4430.93 (64-Bit) on Windows. A hard refresh doesn’t fix it.
 
Thank you very much for spending time on this!
 
Kind regards
 
Karin
 







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