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[bioontology-support] metadata treeview error message

Pan, Huaqin (Helen) hpan at rti.org
Sat Jul 13 09:32:21 PDT 2019


Thank you, Michael! I appreciate you logging this issue in your bug list.

Best regards,
Helen

From: Michael Dorf <mdorf at stanford.edu>
Sent: Friday, July 12, 2019 7:27 PM
To: Pan, Huaqin (Helen) <hpan at rti.org>
Cc: John Graybeal <jgraybeal at stanford.edu>; support at bioontology.org
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Thank you for reporting this. I’ve checked both ontologies, and there does appear to be a multitude of mappings that aren’t reported on the mappings page for these ontologies. They are visible under the individual terms, such as:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FLMMA_00185#mappings<https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=classes&conceptid=http://purl.obolibrary.org/obo/LMMA_00185#mappings>

Unfortunately, this isn’t a trivial problem to address. I’ve created an issue in our tracker to record our actions on this bug:

https://github.com/ncbo/ontologies_linked_data/issues/94

Meanwhile, as a workaround, our REST mappings services below do accurately represent mappings for these ontologies:

http://data.bioontology.org/ontologies/LUNGMAP-HUMAN/mappings
http://data.bioontology.org/ontologies/LUNGMAP-MOUSE/mappings

Thanks again, and sorry I couldn’t offer an immediate solution.

Michael



On Jul 12, 2019, at 12:41 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi John and Michael,

I submitted 2 ontologies with xref links to 78 UBERON and 45 CL classes. However, the mapping for these 2 ontologies I submitted have limited mapping to some ontologies other than UBERON and CL. I would greatly appreciate it if you can take a look and figure out why the UBERSON and CL mappings are not found by the mapping tools.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE/?p=mappings
https://bioportal.bioontology.org/ontologies/LUNGMAP-HUMAN/?p=mappings

Best regards,
Helen


From: Pan, Huaqin (Helen)
Sent: Saturday, May 11, 2019 8:47 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>; Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Subject: RE: [bioontology-support] metadata treeview error message

Hi John and Michael,

I just did another upload of mouse obo file, and indeed it was able to reload successfully. I will try clear cache if I run into any errors.

Yes, the single root class is what I wanted. Thanks again for your help!

Best regards,
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, May 10, 2019 8:20 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: support at bioontology.org<mailto:support at bioontology.org>; John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

Both ontologies appear properly on my end as well. The LungMap ontology now has a single root class, “respiratory system”, hope that’s as intended.  As John said, it does take a bit of time for the results of the processing to propagate through our various architecture layers. Feel free to contact us if the issue still persists.

Thanks,

Michael


On May 10, 2019, at 4:53 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Helen,

I just looked at this link, and at the link http://data.bioontology.org/ontologies/M-PARTOF/classes/roots, and both look fine to me. Can you be more explicit about what issue you are seeing?

It shouldn't be necessary for us to take any action if the processing proceeds normally in BioPortal, though sometimes it may take a little while for the internal caches to update (perhaps as long as 2 hours?).

However, it is sometimes necessary to clear caches in your browser to see the updated display, as your browser's cached view for the URL simply re-displays the previous error. In Chrome I do this using Developer Tools and then click on the reload button, which offers options to clear the cache.

John



On May 10, 2019, at 2:59 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Same error for mouse file, https://bioportal.bioontology.org/ontologies/M-PARTOF?p=classes

Thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Friday, May 10, 2019 4:42 PM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; 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 Michael,

Is the reprocessing has something to do with the obo format or something I can do at my end? Since Protégé doesn’t display the hierarchical structure for the “part_of”, I have to reply on BioPortal reloading to verify the hierarchical structure and clean up the loners outside the hierarchical structure. I just uploaded another version of the human obo file and ran into the same error. Can you help me do another (hopefully the last) reprocessing?

I am getting real close for cleaning up the human file, but just started on the mouse file. Is there anything I can do on my end to avoid the reprocessing at your end, so I don’t have to bug you for each upload?

Thank you for your help!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, May 10, 2019 2:51 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

I’ve reprocessed your ontology once again and cleared caches on our end to make sure the cached data isn’t causing any conflicts. The ontology displays correctly on my end now. Let me know if this isn’t the case for you.

Thanks,

Michael

On May 10, 2019, at 4:25 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

The owl format doesn’t display the hierarchical structure for “part-of”. So I uploaded a obo file and got the error message again. Would you please take another look?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Thursday, May 9, 2019 7:52 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Helen,

The latest version (1.0.2) failed in our UI because the ontology roots endpoint was returning empty results:

http://data.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/classes/roots

The ontology had failed to process correctly due to the fact that the ontology format was set to OBO, but the latest uploaded version resolved to an OWL file. The previous version (1.0.1) is set to OBO on both the format as well as the file extension. I’ve changed the ontology format to OWL to be consistent with the file format and re-processed the ontology. This has fixed the issue. Your ontology is now browsable at:

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2?p=classes

Thanks,

Michael





On May 9, 2019, at 2:29 PM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> wrote:

Hi Michael,

I got error message again for accessing https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2. Would you please help me take a look?

Interestingly, I got no error message for accessing 3 other files that uploaded after this one, so the system is working fine.

Many thanks,
Helen

From: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Sent: Saturday, April 27, 2019 1:59 AM
To: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] metadata treeview error message

Hi Michael,

It’s working now! Thank you!

Helen

Get Outlook for iOS<https://aka.ms/o0ukef>

________________________________
From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Friday, April 26, 2019 11:00 PM
To: Pan, Huaqin (Helen)
Cc: Jennifer Leigh Vendetti; support at bioontology.org<mailto:support at bioontology.org>
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) <hpan at rti.org<mailto:hpan at rti.org>> 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?

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


Thank you!
Helen

From: Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>>
Sent: Wednesday, April 10, 2019 6:14 PM
To: Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>>
Cc: Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>; support at bioontology.org<mailto:support at bioontology.org>
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.

https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2/?p=classes

Let us know if you run into further issues.

Thanks!

Michael

On Apr 10, 2019, at 10:20 AM, Pan, Huaqin (Helen) <hpan at rti.org<mailto:hpan at rti.org>> 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 ?
https://bioportal.bioontology.org/ontologies/LUNGMAP-MOUSE_P2

Thanks a lot!
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>_______________________________________________
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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

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https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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https://mailman.stanford.edu/mailman/listinfo/bioontology-support


_______________________________________________
bioontology-support mailing list
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https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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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

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