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[bioontology-support] [BioPortal] Feedback from yuki
mdorf at stanford.edu
Thu Mar 21 16:18:43 PDT 2019
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:
<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:
Thanks again and sorry I could not offer a better solution at this point.
On Mar 13, 2019, at 7:13 PM, y-yamagata <y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>> wrote:
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.
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.
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>> ???????????????
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.
On Mar 12, 2019, at 8:22 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:
Email: y-yamagata at nibiohn.go.jp<mailto:y-yamagata at nibiohn.go.jp>
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?
bioontology-support mailing list
bioontology-support at lists.stanford.edu<mailto:bioontology-support at lists.stanford.edu>
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