[bioontology-support] metadata treeview error message

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[bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen,

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

Human_Ontology_Treeview_1.xrdf (16K) Download Attachment
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Re: [bioontology-support] metadata treeview error message

John Graybeal-2
Hi Helen,

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

John


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message
 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen,

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pete Rivett
In reply to this post by Pan, Huaqin (Helen)

Helen,

The message means you’ve used a namespace prefix “metadata:” without defining it. For example at line 253 you have:

        <metadata:treeView rdf:resource="http://www.lungmap.net/ontologies/human_anatomy#LMHA0000000211"/>

 

To fix it, add the following line in the block of namespace definitions, e.g. line 14:

     xmlns:metadata="http://data.bioontology.org/metadata/"

 

It then seemed to load OK into Protégé (I’m on 5.2).

 

Pete

 

 

Pete  Rivett ([hidden email])

CTO, Adaptive Inc

65 Enterprise, Aliso Viejo, CA 92656

cell: +1 949 338 3794

Follow me on Twitter @rivettp or http://twitter.com/rivettp

 

 

 

 

 

From: bioontology-support <[hidden email]> On Behalf Of Pan, Huaqin (Helen)
Sent: Wednesday, March 13, 2019 8:40 PM
To: John Graybeal <[hidden email]>
Cc: [hidden email]
Subject: [bioontology-support] metadata treeview error message

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen,

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)
In reply to this post by John Graybeal-2

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen,

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)
In reply to this post by Pete Rivett

Worked like a charm. Thank you, Pete!

 

Helen

 

From: Pete Rivett <[hidden email]>
Sent: Thursday, March 14, 2019 6:02 AM
To: Pan, Huaqin (Helen) <[hidden email]>; John Graybeal <[hidden email]>
Cc: [hidden email]
Subject: RE: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Helen,

The message means you’ve used a namespace prefix “metadata:” without defining it. For example at line 253 you have:

        <metadata:treeView rdf:resource="http://www.lungmap.net/ontologies/human_anatomy#LMHA0000000211"/>

 

To fix it, add the following line in the block of namespace definitions, e.g. line 14:

     xmlns:metadata="http://data.bioontology.org/metadata/"

 

It then seemed to load OK into Protégé (I’m on 5.2).

 

Pete

 

 

Pete  Rivett ([hidden email])

CTO, Adaptive Inc

65 Enterprise, Aliso Viejo, CA 92656

cell: +1 949 338 3794

Follow me on Twitter @rivettp or http://twitter.com/rivettp

 

 

 

 

 

From: bioontology-support <[hidden email]> On Behalf Of Pan, Huaqin (Helen)
Sent: Wednesday, March 13, 2019 8:40 PM
To: John Graybeal <[hidden email]>
Cc: [hidden email]
Subject: [bioontology-support] metadata treeview error message

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen,

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)
In reply to this post by Pan, Huaqin (Helen)

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john



On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

jvendetti
Hi Helen,

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

Kind regards,
Jennifer







On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

Hi John,
 
I think this question is for your team 😊
 
I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.
 
 
Thank you!
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
Just the ontologies ones. Everything about your BioPortal experience still comes to us!
 
Best wishes.
 
john


On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Thanks, John! I will send questions to [hidden email] moving forward.
 
Best regards,
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.
 
Hi Helen,
 
This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 
 
John
 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 
 
Hi John,
 
I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?
 
Thank you for your help!
 
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!
 
Helen, 
 
I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.
 
Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.
 
I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.
 
When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.
 
Thanks,
 
John
 
[1]  Results of submission:
 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at [hidden email]
 
On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hello,
 
Hello, I tried several times to submit an ontology:
 
initial submission always got 
<image002.jpg>
Another try always got 
<image004.jpg>
 
It repeats that when I tried different name/acronyms on different web browsers.
 
Would you please help me create the ontology? 
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy
 
Owl is attached.
 
Thanks!
Helen
 
 
<Human_bioportal.owl>_______________________________________________
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

 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed in http://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view.

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

 

 



On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

jvendetti
Hi Helen,

OK - thank you for the clarification.

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

1). For OWL ontologies we use “subClassOf".
2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.
3). For SKOS ontologies we use “broader”.

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

Kind regards,
Jennifer





On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

Hi Jennifer,
 
I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 
 
I am available for a phone call or web conference if that’s helpful.
 
I appreciate your help!
 
Helen
919-434-4665
 
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?
 
I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.
 
Kind regards,
Jennifer
 
 
 
 
<image001.png>
 
 


On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi John,
 
I think this question is for your team 😊
 
I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.
 
 
Thank you!
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
Just the ontologies ones. Everything about your BioPortal experience still comes to us!
 
Best wishes.
 
john



On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Thanks, John! I will send questions to [hidden email] moving forward.
 
Best regards,
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.
 
Hi Helen,
 
This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 
 
John
 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 
 
Hi John,
 
I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?
 
Thank you for your help!
 
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!
 
Helen, 
 
I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.
 
Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.
 
I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.
 
When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.
 
Thanks,
 
John
 
[1]  Results of submission:
 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at [hidden email]
 
On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hello,
 
Hello, I tried several times to submit an ontology:
 
initial submission always got 
<image002.jpg>
Another try always got 
<image004.jpg>
 
It repeats that when I tried different name/acronyms on different web browsers.
 
Would you please help me create the ontology? 
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy
 
Owl is attached.
 
Thanks!
Helen
 
 
<Human_bioportal.owl>_______________________________________________
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

 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
Open this post in threaded view
|

Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 



On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
Reply | Threaded
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|

Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Hi Jennifer,

 

We tried 2 approaches: 1) converting the file into OBO format, and 2) adding “subclass_of” in the place of “part_of”, both seem to work. However, I am having issues display the parsed uploads, after I tried different browsers (Firefox, Chrome) at different dates/times. Would you please help me take a look?

 

Thank you!

Helen

 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message

 

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 



On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

jvendetti
Hi Helen,

Apologies, I’m not sure how to reproduce your problem. I looked at both ontologies and I’m able to view the class trees in BioPortal without errors.

Are you still experiencing issues? If so, could you be more specific?

Thanks,
Jennifer


On Mar 21, 2019, at 7:31 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

Hi Jennifer,
 
We tried 2 approaches: 1) converting the file into OBO format, and 2) adding “subclass_of” in the place of “part_of”, both seem to work. However, I am having issues display the parsed uploads, after I tried different browsers (Firefox, Chrome) at different dates/times. Would you please help me take a look?
 
Thank you!
Helen
 
From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message
 
Hi Jennifer,
 
Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.
 
I appreciate your help!
 
Helen
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
OK - thank you for the clarification.
 
The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:
 
1). For OWL ontologies we use “subClassOf".
2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.
3). For SKOS ontologies we use “broader”.
 
There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.
 
As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].
 
Kind regards,
Jennifer
 
 
 
 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi Jennifer,
 
I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 
 
I am available for a phone call or web conference if that’s helpful.
 
I appreciate your help!
 
Helen
919-434-4665
 
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?
 
I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.
 
Kind regards,
Jennifer
 
 
 
 
<image001.png>
 
 



On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi John,
 
I think this question is for your team 😊
 
I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.
 
 
Thank you!
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
Just the ontologies ones. Everything about your BioPortal experience still comes to us!
 
Best wishes.
 
john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Thanks, John! I will send questions to [hidden email] moving forward.
 
Best regards,
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.
 
Hi Helen,
 
This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 
 
John
 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 
 
Hi John,
 
I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?
 
Thank you for your help!
 
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!
 
Helen, 
 
I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.
 
Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.
 
I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.
 
When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.
 
Thanks,
 
John
 
[1]  Results of submission:
 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at [hidden email]
 
On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hello,
 
Hello, I tried several times to submit an ontology:
 
initial submission always got 
<image002.jpg>
Another try always got 
<image004.jpg>
 
It repeats that when I tried different name/acronyms on different web browsers.
 
Would you please help me create the ontology? 
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy
 
Owl is attached.
 
Thanks!
Helen
 
 
<Human_bioportal.owl>_______________________________________________
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

 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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|

Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Yes, I am still having the same issues. I got this when I click on “version 1.0.1” link under Submission.

 

 

 

I got this when I click on the “Classes” tab

 

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Thursday, March 21, 2019 6:08 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

Apologies, I’m not sure how to reproduce your problem. I looked at both ontologies and I’m able to view the class trees in BioPortal without errors.

 

Are you still experiencing issues? If so, could you be more specific?

 

Thanks,

Jennifer

 



On Mar 21, 2019, at 7:31 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

We tried 2 approaches: 1) converting the file into OBO format, and 2) adding “subclass_of” in the place of “part_of”, both seem to work. However, I am having issues display the parsed uploads, after I tried different browsers (Firefox, Chrome) at different dates/times. Would you please help me take a look?

 

Thank you!

Helen

 

From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message

 

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Never mind, this one just loaded 😊 it must know that you are looking into it 😊

 

Thanks, Jennifer!

 

Helen

 

From: bioontology-support <[hidden email]> On Behalf Of Pan, Huaqin (Helen)
Sent: Thursday, March 21, 2019 6:12 PM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Yes, I am still having the same issues. I got this when I click on “version 1.0.1” link under Submission.

 

 

 

I got this when I click on the “Classes” tab

 

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Thursday, March 21, 2019 6:08 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

Apologies, I’m not sure how to reproduce your problem. I looked at both ontologies and I’m able to view the class trees in BioPortal without errors.

 

Are you still experiencing issues? If so, could you be more specific?

 

Thanks,

Jennifer

 

 

On Mar 21, 2019, at 7:31 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

We tried 2 approaches: 1) converting the file into OBO format, and 2) adding “subclass_of” in the place of “part_of”, both seem to work. However, I am having issues display the parsed uploads, after I tried different browsers (Firefox, Chrome) at different dates/times. Would you please help me take a look?

 

Thank you!

Helen

 

From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message

 

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 



On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)
In reply to this post by Pan, Huaqin (Helen)

Hi Jennifer,

 

I uploaded an ontology file a few days ago and it hasn’t been parsed yet. Usually it doesn’t take this long. Would you please take a look ?

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

 

Thanks a lot!

Helen

 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message

 

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 



On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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|

Re: [bioontology-support] metadata treeview error message

Michael Dorf
Hi Helen,

Apologies, our ontology processing engine was disabled for a few days due to an issue. I’ve re-processed your ontology, and it’s now visible in BioPortal.


Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

Hi Jennifer,
 
I uploaded an ontology file a few days ago and it hasn’t been parsed yet. Usually it doesn’t take this long. Would you please take a look ?
 
Thanks a lot!
Helen
 
From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message
 
Hi Jennifer,
 
Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.
 
I appreciate your help!
 
Helen
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
OK - thank you for the clarification.
 
The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:
 
1). For OWL ontologies we use “subClassOf".
2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.
3). For SKOS ontologies we use “broader”.
 
There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.
 
As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].
 
Kind regards,
Jennifer
 
 
 
 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi Jennifer,
 
I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 
 
I am available for a phone call or web conference if that’s helpful.
 
I appreciate your help!
 
Helen
919-434-4665
 
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?
 
I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.
 
Kind regards,
Jennifer
 
 
 
 
<image001.png>
 
 



On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi John,
 
I think this question is for your team 😊
 
I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.
 
 
Thank you!
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
Just the ontologies ones. Everything about your BioPortal experience still comes to us!
 
Best wishes.
 
john




On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Thanks, John! I will send questions to [hidden email] moving forward.
 
Best regards,
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.
 
Hi Helen,
 
This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 
 
John
 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 
 
Hi John,
 
I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?
 
Thank you for your help!
 
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!
 
Helen, 
 
I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.
 
Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.
 
I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.
 
When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.
 
Thanks,
 
John
 
[1]  Results of submission:
 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at [hidden email]
 
On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hello,
 
Hello, I tried several times to submit an ontology:
 
initial submission always got 
<image002.jpg>
Another try always got 
<image004.jpg>
 
It repeats that when I tried different name/acronyms on different web browsers.
 
Would you please help me create the ontology? 
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy
 
Owl is attached.
 
Thanks!
Helen
 
 
<Human_bioportal.owl>_______________________________________________
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

 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)

Awesome! Thank you, Michael!

 

Helen

 

From: Michael Dorf <[hidden email]>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: Jennifer Leigh Vendetti <[hidden email]>; [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

Apologies, our ontology processing engine was disabled for a few days due to an issue. I’ve re-processed your ontology, and it’s now visible in BioPortal.

 

 

Let us know if you run into further issues.

 

Thanks!

 

Michael



On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I uploaded an ontology file a few days ago and it hasn’t been parsed yet. Usually it doesn’t take this long. Would you please take a look ?

 

Thanks a lot!

Helen

 

From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message

 

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)
In reply to this post by Michael Dorf

Hi Michael,

 

Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?

 

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

 

 

Thank you!

Helen

 

From: Michael Dorf <[hidden email]>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: Jennifer Leigh Vendetti <[hidden email]>; [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen,

 

Apologies, our ontology processing engine was disabled for a few days due to an issue. I’ve re-processed your ontology, and it’s now visible in BioPortal.

 

 

Let us know if you run into further issues.

 

Thanks!

 

Michael



On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I uploaded an ontology file a few days ago and it hasn’t been parsed yet. Usually it doesn’t take this long. Would you please take a look ?

 

Thanks a lot!

Helen

 

From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message

 

Hi Jennifer,

 

Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.

 

I appreciate your help!

 

Helen

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

OK - thank you for the clarification.

 

The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:

 

1). For OWL ontologies we use “subClassOf".

2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.

3). For SKOS ontologies we use “broader”.

 

There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.

 

As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].

 

Kind regards,

Jennifer

 

 

 

 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi Jennifer,

 

I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 

 

I am available for a phone call or web conference if that’s helpful.

 

I appreciate your help!

 

Helen

919-434-4665

 

 

From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message

 

Hi Helen, 

 

Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?

 

I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.

 

Kind regards,

Jennifer

 

 

 

 

<image001.png>

 

 




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hi John,

 

I think this question is for your team 😊

 

I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.

 

 

Thank you!

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

Just the ontologies ones. Everything about your BioPortal experience still comes to us!

 

Best wishes.

 

john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Thanks, John! I will send questions to [hidden email] moving forward.

 

Best regards,

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message

 

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

 

Hi Helen,

 

This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 

 

John

 


From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 

 

Hi John,

 

I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?

 

Thank you for your help!

 

Helen

 

From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!

 

Helen, 

 

I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.

 

Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.

 

I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.

 

When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.

 

Thanks,

 

John

 

[1]  Results of submission:

 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1

If you have any questions or problems, please email the BioPortal support team at [hidden email]

 

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

 

Hello,

 

Hello, I tried several times to submit an ontology:

 

initial submission always got 

<image002.jpg>

Another try always got 

<image004.jpg>

 

It repeats that when I tried different name/acronyms on different web browsers.

 

Would you please help me create the ontology? 

Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung

Acronym: LUNGMAP-HUMAN

Public

Anatomy

 

Owl is attached.

 

Thanks!

Helen

 

 

<Human_bioportal.owl>_______________________________________________
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

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 

 

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

 


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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|

Re: [bioontology-support] metadata treeview error message

Michael Dorf
Hi Helen,

Sorry, but I don’t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael

On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

Hi Michael,
 
Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?
 
 
 
Thank you!
Helen
 
From: Michael Dorf <[hidden email]> 
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: Jennifer Leigh Vendetti <[hidden email]>; [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Apologies, our ontology processing engine was disabled for a few days due to an issue. I’ve re-processed your ontology, and it’s now visible in BioPortal.
 
 
Let us know if you run into further issues.
 
Thanks!
 
Michael


On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi Jennifer,
 
I uploaded an ontology file a few days ago and it hasn’t been parsed yet. Usually it doesn’t take this long. Would you please take a look ?
 
Thanks a lot!
Helen
 
From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message
 
Hi Jennifer,
 
Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.
 
I appreciate your help!
 
Helen
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
OK - thank you for the clarification.
 
The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:
 
1). For OWL ontologies we use “subClassOf".
2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.
3). For SKOS ontologies we use “broader”.
 
There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.
 
As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].
 
Kind regards,
Jennifer
 
 
 
 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi Jennifer,
 
I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 
 
I am available for a phone call or web conference if that’s helpful.
 
I appreciate your help!
 
Helen
919-434-4665
 
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?
 
I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.
 
Kind regards,
Jennifer
 
 
 
 
<image001.png>
 
 




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi John,
 
I think this question is for your team 😊
 
I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.
 
 
Thank you!
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
Just the ontologies ones. Everything about your BioPortal experience still comes to us!
 
Best wishes.
 
john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Thanks, John! I will send questions to [hidden email] moving forward.
 
Best regards,
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.
 
Hi Helen,
 
This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 
 
John
 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 
 
Hi John,
 
I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?
 
Thank you for your help!
 
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!
 
Helen, 
 
I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.
 
Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.
 
I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.
 
When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.
 
Thanks,
 
John
 
[1]  Results of submission:
 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at [hidden email]
 
On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hello,
 
Hello, I tried several times to submit an ontology:
 
initial submission always got 
<image002.jpg>
Another try always got 
<image004.jpg>
 
It repeats that when I tried different name/acronyms on different web browsers.
 
Would you please help me create the ontology? 
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy
 
Owl is attached.
 
Thanks!
Helen
 
 
<Human_bioportal.owl>_______________________________________________
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

 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
 
 
_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support
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|

Re: [bioontology-support] metadata treeview error message

Pan, Huaqin (Helen)
Hi Michael,

It’s working now! Thank you!

Helen

 

From: Michael Dorf <[hidden email]>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen,

Sorry, but I don’t see the issue on my end. The link below works fine, and the ontology class tree loads for me as well. Is the problem still reproducible on your end?

Thanks!

Michael

On Apr 25, 2019, at 12:47 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:

Hi Michael,
 
Hope you are doing well. I am experiencing the same issue again, i.e. the ontology file is loaded and parsed, but I am getting error messages when access the file link. Would you please help taking a look?
 
 
 
Thank you!
Helen
 
From: Michael Dorf <[hidden email]> 
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: Jennifer Leigh Vendetti <[hidden email]>; [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Apologies, our ontology processing engine was disabled for a few days due to an issue. I’ve re-processed your ontology, and it’s now visible in BioPortal.
 
 
Let us know if you run into further issues.
 
Thanks!
 
Michael


On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi Jennifer,
 
I uploaded an ontology file a few days ago and it hasn’t been parsed yet. Usually it doesn’t take this long. Would you please take a look ?
 
Thanks a lot!
Helen
 
From: Pan, Huaqin (Helen) <[hidden email]> 
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: RE: [bioontology-support] metadata treeview error message
 
Hi Jennifer,
 
Thank you for the clarification! Very helpful! I will discuss with the team and hope to find a solution.
 
I appreciate your help!
 
Helen
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
OK - thank you for the clarification.
 
The way in which BioPortal constructs class trees for ontologies is dependent on the ontology language:
 
1). For OWL ontologies we use “subClassOf".
2). For OBO ontologies we use “part_of”, “contains”, and “develops from”.
3). For SKOS ontologies we use “broader”.
 
There is no standard property built into the OWL language for representing "part of” relationships, which is why we only use subClassOf when constructing class trees for OWL ontologies.
 
As an alternative, you could try version 5.5.0 of the Protege ontology editor (released today) [1]. They’ve added new functionality that allows the class tree to display other parent/child relationships besides subClassOf [2].
 
Kind regards,
Jennifer
 
 
 
 

 

On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi Jennifer,
 
I am looking for the tree view as displayed in https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=summary, which has an exclusive “subclass_of” property. Now I am trying to update it with a new version as listed inhttp://bioportal.bioontology.org/ontologies/M-PARTOF/?p=summary, to include the correct partition of “subclass_of” and “part_of”, but I am having trouble display the “part_of” relations in a tree view. 
 
I am available for a phone call or web conference if that’s helpful.
 
I appreciate your help!
 
Helen
919-434-4665
 
 
From: Jennifer Leigh Vendetti <[hidden email]> 
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] metadata treeview error message
 
Hi Helen, 
 
Could you please be more specific, e.g., give us a concrete example of a class that you feel is not being displayed where you would expect in the tree?
 
I compared the tree structure that BioPortal displays with the tree structure that the Protege ontology editor displays, and they look the same to me.
 
Kind regards,
Jennifer
 
 
 
 
<image001.png>
 
 




On Mar 15, 2019, at 6:44 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hi John,
 
I think this question is for your team 😊
 
I uploaded an ontology file with properties of “subclass”, “part_of”, and “treeview”. Currently only the “subclass” displays as tree view. How do I make the “part_of” relation also display in tree view at BioPortal? I added the “treeview” properties for both  “subclass” and “part_of”.
 
 
Thank you!
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
Just the ontologies ones. Everything about your BioPortal experience still comes to us!
 
Best wishes.
 
john





On Mar 14, 2019, at 5:16 AM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Thanks, John! I will send questions to [hidden email] moving forward.
 
Best regards,
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]; Pan, Huaqin (Helen) <[hidden email]>
Subject: Re: [bioontology-support] metadata treeview error message
 
EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.
 
Hi Helen,
 
This kind of question about ontologies should be sent to the Protege mail list, [hidden email]. The people on that list should be able to help you. 
 
John
 

From: Pan, Huaqin (Helen) <[hidden email]>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: [hidden email]; Pan, Huaqin (Helen)
Subject: [bioontology-support] metadata treeview error message 
 
Hi John,
 
I got an error message “The prefix "metadata" for element "metadata:treeView" is not bound” when I load the .xrdf file in Protege. I attached the code. Would you please help me figure out the issue?
 
Thank you for your help!
 
Helen
 
From: John Graybeal <[hidden email]> 
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <[hidden email]>
Cc: [hidden email]
Subject: Re: [bioontology-support] problem with ontology submission - please help!
 
Helen, 
 
I have submitted your OWL file under the LUNGMAP-HUMAN1 acronym, and got the results below [1]. I did not get any error messages.
 
Note that you probably will want to redo your submission under the same acronym but leaving off the '1'. Once that is successful, we can delete this ontology.
 
I am wondering when you attempted your submissions. If you submitted it before late Thursday, we were having problems with the system up until that point, and these were likely interfering with your efforts.
 
When you try to submit under LUNGMAP-HUMAN, please keep track of the Add Submission process as you go, and let us know if there are any issues.
 
Thanks,
 
John
 
[1]  Results of submission:
 

Thank you for submitting your ontology to BioPortal.

We will now put your ontology in the queue to be processed. Please keep in mind that it may take up to several hours before BioPortal users will be able to explore and search your ontology.

When your ontology is ready for viewing, it will be available here: 
http://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN1
If you have any questions or problems, please email the BioPortal support team at [hidden email]
 
On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <[hidden email]> wrote:
 
Hello,
 
Hello, I tried several times to submit an ontology:
 
initial submission always got 
<image002.jpg>
Another try always got 
<image004.jpg>
 
It repeats that when I tried different name/acronyms on different web browsers.
 
Would you please help me create the ontology? 
Name: Anatomic Ontology for Alveolar Development and Maturation in the Mouse Lung
Acronym: LUNGMAP-HUMAN
Public
Anatomy
 
Owl is attached.
 
Thanks!
Helen
 
 
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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

 
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