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[bioontology-support] Issue

John Graybeal jgraybeal at stanford.edu
Fri Apr 10 16:17:20 PDT 2020


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<mailto: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<mailto: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<mailto: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<mailto:rakesh at pieriandx.com>

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

Wisdom in Every Report™

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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





--

Rakesh Nagarajan

Founder and Executive Chairman

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

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



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