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[bioontology-support] Feedback from yuki

Michael Dorf mdorf at
Thu Apr 11 11:50:09 PDT 2019

Hi Yuki,

I was able to reproduce the problem (“We’re sorry…”), and I know the exact cause. Unfortunately, this isn’t a trivial one, and deleting your ontology and simply re-creating it isn’t going to address it. All I can say at this point is we are looking for possible solutions. I’ll keep you posted. Thank you so much for your patience!


On Apr 11, 2019, at 2:06 AM, y-yamagata <y-yamagata at<mailto:y-yamagata at>> wrote:

Dear John and Michael,

Thank you for the correspondence.
The display always shows  ’Problem retrieving classes’ or ‘We’re sorry, but something has gone wrong...', regardless of how much the cache is cleared. I tried it on Chrome and Opera or FireFox.
It has not changed since several months ago.
If possible, can you delete the acronym TXPO and all data of TXPO from the BioPortal server and can I register the acronym TXPO again?

Best regards,

2019/04/11 13:45、John Graybeal <jgraybeal at<mailto:jgraybeal at>> のメール:


Sorry for your remaining problems, thank you for providing those details.

When I tried your first example (classes of TXPO), the first time I tried it I got a failure indicator. But when I refreshed the browser the problem went away. Perhaps there is a timeout before this succeeds; you may find clearing your cache helps.

Re the second question, I only see 5 ontologies, not including BAO, go-plus, Uber Anatomy. Since the log looks OK, this suggests an issue with one of the other ontologies may be interfering with the display, or possibly something else has happened. I'll have to let Misha dig into that for you. (@Misha, the API endpoint seems consistent with the following list; but did not let me view info for the TXPO ontology as a whole.)


Genotype Ontology<> 23
Influenza Ontology<> 60
Ontology of Drug Neuropathy Adverse Events<>       70
Ontology of Genes and Genomes<>      1,246
Ontology of Host-Microbe Interactions<>     33

On Apr 10, 2019, at 7:07 PM, y-yamagata <y-yamagata at<mailto:y-yamagata at>> wrote:

Hi Micahel,

Sorry, but there are still problems.

1. Class tab with the display.
I tried to clear my browser cache, log in again, and then I entered a URI However, my screen always shows ‘We ‘re sorry but something has gone wrong’
How is it displayed on your screen?
How can I display it correctly?
Curiously, it appears when I type in the URL of the term directly.<> /ontologies/TXPO/?p=classes&conceptid=

2. Mapping
I reuse the term 'anatomical entity' in the UBERON ontology.<> /ontologies/TXPO/?p=classes&conceptid=<>
The display shows:
Number of class mappings are 378.
Ontology mapping to Bio assay ontology, go-plus, Uber Anatomy Ontology etc.
However, in the mapping tab,  why is it not included UBERON, ?
Also, go-plus, Cell ontology, and so on, are not listed.

Best regards,

2019/04/11 7:23、Michael Dorf <mdorf at<mailto:mdorf at>> のメール:

Hi Yuki,

Thank you for contacting us again. This is no bother at all. Feel free to reach out to us anytime you have an issue or question related to BioPortal.  As far as TXPO, please accept our apologies, our ontology processing engine had been disabled for the last few days due to an issue, which is why your new version hasn’t gotten processed.  It has now been re-enabled, and your ontology has been re-processed. It is now correctly displayed in BioPortal. Hopefully, fixing this issue has addressed all of the problems below. If this is not the case, please let us know.



On Apr 9, 2019, at 7:13 PM, y-yamagata <y-yamagata at<mailto:y-yamagata at>> wrote:

Hi, Michel,

I apologize for bothering you over and over again.

I prepared an English version of the TXPO ontology, and my colleague uploaded it (2019/04/08).
However, there are problems.

1. Class tab
I tried to clear my browser (Chrome) cache, log in again, and see my page.
However, when I click the Classes tab, nothing is displayed except for the message "Problem retrieving classes.”

Next, to try out a class (TXPO_1171) that I could see before, I entered the following address into the chrome address bar:<> /ontologies/TXPO/?p=classes&conceptid=
As a result, the Japanese mixed version, which is the old version, is displayed.
How can I see the latest version?

2. Other tabs
Also, the displays of other tabs are not the latest version.

I uploaded TXPO many times before, but it seems that the cache on the BioPortal server side is not cleared every time.
In the mapping tab, there are too few mapped numbers. It reflects the numbers from the old Japanese version. Many terms should be mapped to Gene ontology.

3. Summary tab
 I cannot download 'beta1 with our Japanese version' that was uploaded in 04/08/2019 as CVS, RDF/XML, or Diff.

The contents of TXPO are updated frequently. Therefore, we try to upload many times.
But I feel uncomfortable to post to the mailing list "the display is not the latest version" many times.
Can you suggest solutions to these problems so that we can always view the latest trees and mappings for TXPO?

Yuki Yamagata, Ph.D.


John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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