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[bioontology-support] Feedback from yuki

Michael Dorf mdorf at stanford.edu
Wed Apr 10 15:23:53 PDT 2019


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.

https://bioportal.bioontology.org/ontologies/TXPO?p=classes

Thanks!

Michael


On Apr 9, 2019, at 7:13 PM, y-yamagata <y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>> 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:
https://bioportal.bioontology.org<https://bioportal.bioontology.org/> /ontologies/TXPO/?p=classes&conceptid=http://bioportal.bioontology.org/ontologies/txpo/TXPO_0001731
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?

Sincerely,
Yuki Yamagata, Ph.D.
y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>
Laboratory of Toxicogenomics Informatics
National Institutes of Biomedical Innovation, Health and Nutrition
7-6-8 Asagi, Saito, Ibaraki,
567-0085, Osaka, Japan

2019/03/22 8:18、Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> のメール:

Hi Yuki,

Thank you for your patience with this issue. It took me some digging into our code to figure out the cause of the problem. Unfortunately, at this point there is only one solution you can implement on your end:

For each entity in your ontology, you would need to define a property called "http://www.w3.org/2004/02/skos/core#prefLabel”. Here is an example of ontology that defines this property:

http://data.bioontology.org/ontologies/HRDO/classes/http%3A%2F%2Fwww.limics.org%2Fhrdo%2Frdfns%23pat_id_10463?display=all&display_context=false&display_links=false
http://bioportal.bioontology.org/ontologies/HRDO/?p=classes&conceptid=http%3A%2F%2Fwww.limics.org%2Fhrdo%2Frdfns%23pat_id_10463&jump_to_nav=true

<skos:prefLabel xml:lang="en">Eales disease</skos:prefLabel>
<skos:prefLabel xml:lang="es">Enfermedad de Eales</skos:prefLabel>
<skos:prefLabel xml:lang="fr">Maladie d'Eales</skos:prefLabel>
<skos:prefLabel xml:lang="it">Malattia di Eales</skos:prefLabel>

Unfortunately, even this isn’t a 100% solution, as our the search indexing algorithm still doesn’t pick the correct label, even with the SKOS prefLabel property in place. I’ve created an issue in our Github tracking system that provides additional details and possible action items on our end to address this:

https://github.com/ncbo/ontologies_linked_data/issues/91

Thanks again and sorry I could not offer a better solution at this point.

Michael


On Mar 13, 2019, at 7:13 PM, y-yamagata <y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>> wrote:

Dear Michel,

Thank you for your quick response.
I tried to clear my browser cache, login again, and see my page.
I can see the latest version of TXPO.

However, I have a problem.
Why is the Japanese label of occurrent displayed?  I want to display all terms as English labels.
I did not use annotation property preferred label about the term “occurrent.”
However, the Preferred Label has been automatically given derived from the Japanese label, and it seems to be reflected in the tree.
Many TXPO terms also have given "preferred label" automatically in the BioPortal site, while I did not annotate the preferred label.
For instance,
http://bioportal.bioontology.org/ontologies/txpo/TXPO_0000271

If TXPO has Japanese English (or sometimes string in Protege) labels, I want to display all terms as English (or string) labels.

Another problem is that, in the mapping tab, it still seems that the mapping is not the latest version.
For example, I reuse GO terms:  http://purl.obolibrary.org/obo/GO_0006915
However, GO are no listed in the mapping table in the mapping tab.
I also use UBERON etc. But these are also not listed.

Best regards,
Yuki
y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>


2019/03/14 3:19???Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> ???????????????

Hi Yuki,

Thank you for contacting us. I am now able to see your ontology classes (see screenshot below). Try clearing your browser cache and refreshing your page. You should be able to see it as well.

Thanks,

Michael


<PastedGraphic-1.png>

On Mar 12, 2019, at 8:22 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: yuki

Email: y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>

Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FTXPO

Feedback:

Dear BioPortal staffs,
I have developed TXPO.
I uploaded TXPO last week in private, and I confirmed that I could download the ontology.
However, when I click the Classes tab, nothing is displayed except for the message "Problem retrieving classes."
Also, in the mapping tab, it seems that the mapping is not the latest version. It only displays the mapping data of the old version of our ontology that was already deleted,
All the other tabs also don't seem to work well.

How can I solve this?
Kind regards,
Yuki

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<TXPO_bioportal.pdf>



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