[bioontology-support] [BioPortal] Feedback from Fabio Saccona

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[bioontology-support] [BioPortal] Feedback from Fabio Saccona

support

Name: Fabio Saccona

Email: [hidden email]

Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA


Feedback:

Please, verify MedDRA classes page, because is notifying problem retrieving SOC (see: http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root).

Many thanks in advance, regards
Fabio Saccona


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Re: [bioontology-support] [BioPortal] Feedback from Fabio Saccona

Michael Dorf
Thank you for your report, Fabio. We’ve recently updated our UMLS distribution to its latest version, 2020AB, which included a new version of MEDDRA ontology. Unfortunately, it appears that we’re no longer able to retrieve the ontology roots, which is why the classes page is failing. I’ll keep you posted as soon as this issue is resolved.

Thank you for your patience.

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jan 19, 2021, at 9:03 AM, [hidden email] wrote:

Name: Fabio Saccona

[hidden email]

Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA


Feedback:

Please, verify MedDRA classes page, because is notifying problem retrieving SOC (see: http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root).

Many thanks in advance, regards
Fabio Saccona


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Re: [bioontology-support] [BioPortal] Feedback from Fabio Saccona

Michael Dorf
Hi Fabio,

Just wanted to give you an update on our MEDDRA investigation. We’ve discovered a number of significant differences between the latest (UMLS 2020AB) and the previous versions (UMLS 2020AA) of MEDDRA ontology.  Most notably, some of the subclass declarations that appear in the older version are missing from the latest one. If you’re interested in the nitty gritty details, they are all documented in this Github issue:


We don’t have a concrete solution at this point other than switching the ontology to a “flat” hierarchical mode, which allows browsing via the “Jump to” box. 


At the moment browsing the class tree no longer results in a “Page not found” error, but a more permanent fix that would allow browsing the tree structure is yet to be implemented.

As before, I’ll keep you posted once we fully resolve this issue.

Thank you again for your patience.

Michael




On Jan 20, 2021, at 8:44 PM, Michael Dorf <[hidden email]> wrote:

Thank you for your report, Fabio. We’ve recently updated our UMLS distribution to its latest version, 2020AB, which included a new version of MEDDRA ontology. Unfortunately, it appears that we’re no longer able to retrieve the ontology roots, which is why the classes page is failing. I’ll keep you posted as soon as this issue is resolved.

Thank you for your patience.

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jan 19, 2021, at 9:03 AM, [hidden email] wrote:

Name: Fabio Saccona

[hidden email]

Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA


Feedback:

Please, verify MedDRA classes page, because is notifying problem retrieving SOC (see: http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root).

Many thanks in advance, regards
Fabio Saccona


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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support


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Re: [bioontology-support] [BioPortal] Feedback from Fabio Saccona

Fabio Saccona
Many thanks for your explanation, Micheal! For my development team, a complete solution is not urgent, because we use your "Form autocomplete" widget in one of our applications (great job!).
Thanks for keeping me updated anyway, I need to report to an organization that usually uses your site and is very interested in solving the problem.

Best regards,
Fabio


Il giorno sab 23 gen 2021 alle ore 23:57 Michael Dorf <[hidden email]> ha scritto:
Hi Fabio,

Just wanted to give you an update on our MEDDRA investigation. We’ve discovered a number of significant differences between the latest (UMLS 2020AB) and the previous versions (UMLS 2020AA) of MEDDRA ontology.  Most notably, some of the subclass declarations that appear in the older version are missing from the latest one. If you’re interested in the nitty gritty details, they are all documented in this Github issue:


We don’t have a concrete solution at this point other than switching the ontology to a “flat” hierarchical mode, which allows browsing via the “Jump to” box. 


At the moment browsing the class tree no longer results in a “Page not found” error, but a more permanent fix that would allow browsing the tree structure is yet to be implemented.

As before, I’ll keep you posted once we fully resolve this issue.

Thank you again for your patience.

Michael




On Jan 20, 2021, at 8:44 PM, Michael Dorf <[hidden email]> wrote:

Thank you for your report, Fabio. We’ve recently updated our UMLS distribution to its latest version, 2020AB, which included a new version of MEDDRA ontology. Unfortunately, it appears that we’re no longer able to retrieve the ontology roots, which is why the classes page is failing. I’ll keep you posted as soon as this issue is resolved.

Thank you for your patience.

Michael


----------------------------------------------------
Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
[hidden email]
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Jan 19, 2021, at 9:03 AM, [hidden email] wrote:

Name: Fabio Saccona

[hidden email]

Location: http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FMEDDRA


Feedback:

Please, verify MedDRA classes page, because is notifying problem retrieving SOC (see: http://bioportal.bioontology.org/ontologies/MEDDRA/?p=classes&conceptid=root).

Many thanks in advance, regards
Fabio Saccona


_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support

_______________________________________________
bioontology-support mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/bioontology-support



--
Fabio SACCONA
SSD Epidemiologia Clinica e Valutativa - CRPT
SC Epidemiologia dei Tumori - CRPT U
AOU Città della Salute e della Scienza di Torino
Via Santena 7, 10126 Torino TO
Tel.: +39 0116336854, Fax: +39 0116334571

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