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[bioontology-support] metadata treeview error message

Pan, Huaqin (Helen) hpan at rti.org
Thu Mar 21 15:12:05 PDT 2019


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

[cid:image003.jpg at 01D4E011.96575A40]


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

[cid:image004.jpg at 01D4E011.96575A40]

From: Jennifer Leigh Vendetti <vendetti at stanford.edu>
Sent: Thursday, March 21, 2019 6:08 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: support at bioontology.org
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) <hpan at rti.org<mailto:hpan at rti.org>> 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?

  *   lungmap-m-partof<https://bioportal.bioontology.org/ontologies/M-PARTOF>
  *   LungMAP-Mouse_partof<https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P>

Thank you!
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Monday, March 18, 2019 8:24 AM
To: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 6:31 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
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

[1] https://protege.stanford.edu/products.php#desktop-protege
[2] http://protegeproject.github.io/protege/views/class-hierarchy/#display-relationships




On Mar 15, 2019, at 12:06 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> 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 <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Sent: Friday, March 15, 2019 2:56 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
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) <hpan at rti.org<mailto:hpan at rti.org>> 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”.

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

Thank you!
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 12:59 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Thanks, John! I will send questions to protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu> moving forward.

Best regards,
Helen

From: John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, March 14, 2019 2:10 AM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
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, protege-user at lists.stanford.edu<mailto:protege-user at lists.stanford.edu>. The people on that list should be able to help you.

John

________________________________
From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Wednesday, March 13, 2019 20:40
To: John Graybeal
Cc: support at bioontology.org<mailto:support at bioontology.org>; 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 <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Saturday, March 24, 2018 5:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
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 support at bioontology.org<mailto:support at bioontology.org>

On Mar 24, 2018, at 7:38 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> 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>_______________________________________________
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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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