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[bioontology-support] [BioPortal] Feedback from Philip van Damme

John Graybeal jgraybeal at
Fri Apr 10 16:10:35 PDT 2020


Thanks for your understanding, and your detailed query! I know we will not be able to dig into it this week, as it is not a trivial situation. We should have a chance to revisit this next week—please ping me if you haven't heard anything by late in the week.


On Apr 9, 2020, at 2:35 AM, Damme, P. van (Philip) <p.vandamme at<mailto:p.vandamme at>> wrote:

Dear Michael, others,

Thank you for your quick response back on the 12th of March, I appreciate it. First and foremost I hope you’re all doing well under the current circumstances.

I stumbled upon something what seems like a discrepancy between the mappings returned by the API calling "/ontologies/:ontology/classes/:cls/mappings” and "/mappings?ontologies=ONT1,ONT2”. When I try to get mappings between a pair of ontologies involving SNOMED CT, I get different results.

For example, I want to check if this mappings exists in BioPortal: = I can use the API calling<>
or,SNOMEDCT and check if the mapping exists. However, when I compare the returned set from the API calls above with<> I noticed the following:

  *   The mapping exists according to the class mappings on the webpage, referring to URI and SNOMEDCT.
  *   The mapping exists according to<>, however, using different URI ( and referring to ontology SNO_COPY which is not accessible.
  *   The mappings doesn’t exist according to,SNOMEDCT.

I decided to only use mappings from,SNOMEDCT, but that still makes me wonder why the webpage shows SNOMED CT mappings that are not returned by the API in the same way (point 1 vs. point 2). Am I missing something? I checked,SNO_COPY, which is returning an empty set.

I was hoping that you could help me to clarify this. Thank you in advance! Please know that you have my full understanding if it’s not possible to answer my email due to the coronavirus.

Best, Philip

On 12 Mar 2020, at 20:17, Michael Vladimir Dorf <mdorf at<mailto:mdorf at>> wrote:

Hi Philip,

Thank you for alerting us to this issue. We’ve had an operational outage yesterday that triggered a full rebuild of our Annotator/Recommender database. The services have now been fully restored. Please try your API calls again and let us know if you run into any further issues.

Thank you so much for your patience.


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

On Mar 11, 2020, at 9:24 AM, support at<mailto:support at> wrote:

Name: Philip van Damme

Email: p.vandamme at<mailto:p.vandamme at>



Both the annotator and the recommender don't return any results. A few hours ago the website had some brief downtime and did not accept API-calls.

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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

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