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[bioontology-support] Issue

Rakesh Nagarajan rakesh at pieriandx.com
Mon Apr 13 14:03:31 PDT 2020


John,
     Let's discuss offline if you can, say by phone. I am simply trying to
get information about a node and then recursing through children to leaf to
get their information. To determine children for a part (one root node
only- e.g. "Drug, Food, Chemical, or Biomedical Material") of an ontology
like NCIT using the API is now taking more than 5 days when it used to
complete in about 1 day. Did something materially change to reduce the
performance of the API?

Thanks,
Rakesh

On Fri, Apr 10, 2020 at 6:17 PM John Graybeal <jgraybeal at stanford.edu>
wrote:

> Rakesh,
>
> Belatedly, we've thought about these behaviors and none of us could put
> our finger on what is causing your problem.
>
> It is the case that there is a timeout on API requests, I believe it is 60
> seconds. So if a request is making a complex query, it might be taking too
> long during period of heavy use.  The longer response times for this
> ontology suggest complexity that might be slowing things down.
>
> Sometimes when BioPortal gets a bad response from the backend store, it
> can get cached for an extended period. If you're able to check in real time
> when an error occurs, you could see if the browser gets the same error; and
> if other calls are getting the same error. Unfortunately our browser caches
> for as long as 2 hours, so that is not totally satisfying to know that.
> (Perhaps you could try making a different query that asks for more than
> just children, so that any cached results wouldn't affect the variant
> query.)
>
> We would be happy to take this offline if it remains a significant issue
> for you.
>
> John
>
> On Apr 8, 2020, at 6:17 AM, Rakesh Nagarajan <rakesh at pieriandx.com> wrote:
>
> 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™
>>
>> 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.
>>
>>
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> 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.
>
>
>
>
> ========================
> 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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