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[bioontology-support] Feedback from yuki

y-yamagata y-yamagata at nibiohn.go.jp
Sat Apr 13 01:08:17 PDT 2019


Hi Michael,

Thank you very much for your detailed investigation.
I can browse my ontology!

With regard to the mapping problem, I only reuse the external ontology term UBERON_0001062, Anatomical entity. The term is also used for many other existing ontologies. I'm not sure why other ontologies do not generate errors.
Also, I guess errors may be more likely to occur as the upper-level entities since they are mapped to more ontologies.

I have annotated manually, so,there might be some other mappings to ontologies that does not exist due to typographical errors during construction. I would be grateful if you could tell me such errors if you have already found automatically.  

Sincerely, 
Yuki

-----Original message-----
From:Michael Dorf<mdorf at stanford.edu>
To:y-yamagata<y-yamagata at nibiohn.go.jp>
Cc:John Graybeal<jgraybeal at stanford.edu>,support at bioontology.org<support at bioontology.org>
Date: Sat, 13 Apr 2019 05:54:52
Subject: Re: [bioontology-support] Feedback from yuki
Hi Yuki, 

We’ve deployed a fix to our production servers this morning that addressed the issue with viewing classes of your ontology. You should now be able to browse your ontology without issues:

http://stage.bioontology.org/ontologies/TXPO/?p=classes
http://stage.bioontology.org/ontologies/TXPO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0001062&jump_to_nav=true
http://bioportal.bioontology.org/ontologies/TXPO/?p=classes&conceptid=http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2Ftxp%2FTXP_0001731

I did not want to include the nitty gritty of the problem, but if you are curious, the two Github issues below provide more detail:

https://github.com/ncbo/bioportal_web_ui/issues/86
https://github.com/ncbo/ontologies_api/issues/53 

Unfortunately, the problem with mappings still remains. The error is triggered by a mapping to a non-existent ontology (BILA) that is found in this class:

http://bioportal.bioontology.org/ontologies/TXPO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0001062

We are looking into ways of addressing this issue, but it may not happen immediately.

Again, sorry for all the troubles with your ontology.

Michael



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