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[bioontology-support] Ontology Mappings Issue

Michael Dorf mdorf at stanford.edu
Sat Dec 7 09:37:37 PST 2019


Hi Juliusz,

Thanks again for you patience with this issue. It took some additional investigating and re-processing on our end, but DRON search index is now fully functional. If you now search for the term “prednisolone”, the expected plain result appears as the first hit. Again, appreciate your valuable report. Feel free to let us know if anything is still amiss.

Thanks,

Michael


On Dec 4, 2019, at 4:24 PM, Michael Dorf <mdorf at stanford.edu<mailto:mdorf at stanford.edu>> wrote:

Hi Juliusz,

Thank you for providing additional detail on your issue. I was able to reproduce this behavior on my end. The term “prednisolone” does exist in the ontology, but it has not been picked up by our search index.

https://bioportal.bioontology.org/ontologies/DRON/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_8378&jump_to_nav=true<https://bioportal.bioontology.org/ontologies/DRON/?p=classes&conceptid=http://purl.obolibrary.org/obo/CHEBI_8378&jump_to_nav=true>

I am going to re-process DRON to allow the indexing job to complete fully. Unfortunately, this is a sizable ontology with over 1/2 a million terms, so the indexing may take some time. I’ll keep you posted on the results.

Appreciate your patience with this!

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at stanford.edu<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Dec 4, 2019, at 12:02 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

forwarding to the list so the team can respond.

I'll just briefly offer that we can't control how REDCap uses BioPortal, though we (or you) can raise questions with them. But this tip will help us appreciate possible avenues of investigation.

John

Begin forwarded message:

From:
Subject: Re: [bioontology-support] Ontology Mappings Issue
Date: December 4, 2019 at 1:23:45 AM PST
To: "John Graybeal" <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>>

Hi John,

Thank you for your email.
When I go to: https://bioportal.bioontology.org/ontologies/DRON/
click on the Classes and start looking for: prednisolone
I will see list of results, see attached but none of them is plain prednisolone.

We are using REDCap with BioPortal as a source for ontology and pulling the same results as from the above URL.
That wasn't the case before, we had plain prednisolone as a result.
I've checked DRON and mapped CHEBI ontologies and there was no change to prednisolone
so my guess is that BioPortal must've changed something internally?

Best Regardcs,
Juliusz


December 4, 2019 4:24 AM, "John Graybeal" <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu?to=%22John%20Graybeal%22%20%3Cjgraybeal at stanford.edu%3E>> wrote:
Hello,
Thank you for your inquiry. Can you tell us, how exactly are you (were you) performing the search?
When I perform the search from the Search page and restrict it to the DRON ontology (see image), I see one primary match, and 51 other matches that have prednisolone in the name; they appear to be from the DRON ontology. This is what I would expect to see, but I may not fully understand your use case.
We would need to see an example of your previous search and search results to have the best chance to diagnose the change in behavior. It may be that previous versions of the ontology contained an exact match (the 'plain result' to which you refer), but no long have it in the ontology.
John
<Screen Shot 2019-12-03 at 8.14.42 PM.png>


On Dec 3, 2019, at 8:14 AM, filipowj at tchpc.tcd.ie<mailto:filipowj at tchpc.tcd.ie> wrote:
Hi,

We seem to have an issue with cross referenced ontologies, it appears that something has changed internally in Bioportal.
When we search for: prednisolone in DRON ontology
a plain result should appear (prednisolone), I believe that result was coming from mapped ontology called: Chemical Entities of Biological Interest Ontology (CHEBI)

Bioportal used to bring back a plain result, that is: prednisolone, now this behaviour has changed, we can see other options like (e.g. enema, injectable solution etc.)
.
Could you please investigate that for us?

Best regards,
J.

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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632 | ORCID 0000-0001-6875-5360


<Screenshot 2019-12-04 at 09.16.15.png>

========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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