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[bioontology-support] Issue

Rakesh Nagarajan rakesh at pieriandx.com
Wed Apr 8 06:17:45 PDT 2020


Thanks John. I agree it is intermittent but somewhat frequent. I got errors
for the following overnight:

Error in
http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_5503/children
Error in
http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_3185/children

When I get such an error I wait 60 seconds and then try again but then exit
when it fails 30 times. So these errors do occur for >30 minutes or so. I
also noticed that this specific ontology has long response times per call.
Any ideas how this can be more robust?

Thanks,
Rakesh



On Tue, Apr 7, 2020 at 6:56 PM John Graybeal <jgraybeal at stanford.edu> wrote:

> Rakesh,
>
> I'm sorry, I'm unable to duplicate this problem.
>
> When I click on the first URL I get the actual content I'd expect from the
> API. [1]
>
> When I click on the second URL I get a simple response that suggests there
> are no children, which matches what BioPortal and OntoBee say.
>
> My only thought is that perhaps there was a brief outage and your browser
> or application cached the results. Perhaps you can try another browser to
> see if it has the same behavior?
>
> If you are still having this problem in another browser, please let us
> know with any additional details you can provide, and we can brainstorm
> ideas about what might be happening.
>
> John
>
>
>
> [1] Content from API for
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>
> {
> • "prefLabel": "Warburg micro syndrome 3",
> • -"synonym": [
> • "Micro Syndrome 3",
> • "WARBM3"
> ],
> • -"definition": [
> • "A Warburg micro syndrome that has_material_basis_in autosomal recessive
> inheritance of homozygous or compound heterozygous mutation in the RAB18
> gene on chromosome 10p12."
> ],
> • "cui": [ ],
> • "semanticType": [ ],
> • "obsolete": false,
> • "@id": "http://purl.obolibrary.org/obo/DOID_0110718",
> • "@type": "http://www.w3.org/2002/07/owl#Class",
> • -"links": {
> • "self": "
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
> ",
> • "ontology": "http://data.bioontology.org/ontologies/DOID",
> • "children": "
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
> ",
>
> On Apr 7, 2020, at 1:26 PM, Rakesh Nagarajan <rakesh at pieriandx.com> wrote:
>
> Hello,
>      For the following URLs:
>
>
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718
> <http://data.bioontology.org/ontologies/DOID/classes/http://purl.obolibrary.org/obo/DOID_0110718>
>
>
> http://data.bioontology.org/ontologies/DOID/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_0110718/children
>
> I get the following error:
>
> {
> -"errors": [
> "Resource 'http://purl.obolibrary.org/obo/DOID_0110718' not found in
> ontology DOID submission 598"
> ],
> "status": 404
> }
>
>
> Can you please fix this?
>
> Thanks,
> Rakesh
> --
>
> *Rakesh Nagarajan*
>
> Founder and Executive Chairman
>
> m: 314-504-5620
> e: rakesh at pieriandx.com
>
> [image: pierian-logo-trans-light-background] <http://www.pieriandx.com/>
>  [image: linkedin_circle-512]
> <https://www.linkedin.com/in/rakeshnagarajan/> [image: twitter_circle-512]
> <https://twitter.com/pieriandx>
>
> Wisdom in Every Report™
>
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> the use of the intended recipient and may contain privileged, confidential
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>
>
>
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> ========================
> 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
>
>
>
>

-- 

*Rakesh Nagarajan*

Founder and Executive Chairman

m: 314-504-5620
e: rakesh at pieriandx.com

[image: pierian-logo-trans-light-background]
<http://www.pieriandx.com/>   [image:
linkedin_circle-512] <https://www.linkedin.com/in/rakeshnagarajan/> [image:
twitter_circle-512] <https://twitter.com/pieriandx>

Wisdom in Every Report™

CONFIDENTIALITY NOTICE: This message and any attachments are solely for the
use of the intended recipient and may contain privileged, confidential or
other legally protected information. If you are not the intended recipient,
please destroy all copies without reading or disclosing their contents and
notify the sender of the error by reply email.
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