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[bioontology-support] [BioPortal] Feedback from Rakesh Nagarajan

Rakesh Nagarajan rakesh at pieriandx.com
Sat Apr 27 10:21:06 PDT 2019


Thanks Michael. This is very helpful and I'll make the changes to my code.

On Fri, Apr 26, 2019 at 4:57 PM Michael Dorf <mdorf at stanford.edu> wrote:

> Hi Rakesh,
>
> The calls with “include=all” parameter in place are generally resource
> intensive, since they must pull many different data pieces for a term from
> a number of graphs in our triple store. For a hefty ontology like MESH,
> this results in a timeout for terms located deeper in the tree. At the
> moment, we use an older 4store backend that doesn’t scale well in the face
> of our ever growing ontology repository. There is currently a project in
> the works to replace the 4store with a newer and more scalable triple store
> server, but it’s still months away from going live.
>
> Until then, I’d replace the costly “include=all” calls with a combination
> of the more optimized calls below, depending on the info you need to
> retrieve.
>
> Michael
>
>
> On Apr 24, 2019, at 7:56 PM, Rakesh Nagarajan <rakesh at pieriandx.com>
> wrote:
>
> Thanks a lot Michael. These alternate URLs meet my immediate need. I also
> noticed yesterday that (repeatedly) the URL:
> http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD009381?include=all
> was giving an HTTP 404 error. However, today it worked. I have seen such
> intermittent errors making it hard to loop through a set of terms and
> access robustly. Would you happen to know why such errors occur.
>
>
>
> On Wed, Apr 24, 2019 at 7:59 PM Michael Dorf <mdorf at stanford.edu> wrote:
>
>> Hi Rakesh,
>>
>> Thank you for contacting us. The class that you’re referring to
>> (prefLabel: Family Characteristics) contains a fair number of overall
>> properties that, unfortunately, take longer to retrieve as a whole than our
>> server is willing to allow for an API service call.  I’ve logged this issue
>> into our Github system, where you can track our progress on resolving it,
>> which, due to our resource constraints, will not be immediate.
>>
>> https://github.com/ncbo/ontologies_linked_data/issues/92
>>
>> Meanwhile, is there a specific purpose that forces you to use the
>> "include=all" flag? The same info can be retrieved by breaking this call
>> down to these three (much more performant) requests:
>>
>>
>> http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD005191?include=prefLabel,synonym,definition,cui,semanticType,obsolete
>> <http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D005191?include=prefLabel,synonym,definition,cui,semanticType,obsolete>
>>
>> http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD005191/parents
>> <http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D005191/parents>
>>
>> http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD005191?include=unmapped
>> <http://data.bioontology.org/ontologies/MESH/classes/http://purl.bioontology.org/ontology/MESH/D005191?include=unmapped>
>>
>> Hope this helps!
>>
>> Michael
>>
>>
>>
>>
>> ----------------------------------------------------
>> Michael Dorf
>> Chief Software Architect
>> The National Center for Biomedical Ontology
>> Stanford Biomedical Informatics Research
>> mdorf at stanford.edu
>> O: 650-723-0357
>> M: 650-995-4374
>> ----------------------------------------------------
>>
>> On Apr 23, 2019, at 6:46 AM, support at bioontology.org wrote:
>>
>> Name: Rakesh Nagarajan
>>
>> Email: rakesh at pieriandx.com <rakesh at pieriandx.com>
>>
>> Location: https%3A%2F%2Fbioportal.bioontology.org
>> <http://2fbioportal.bioontology.org/>%2Flost_pass
>>
>>
>> *Feedback:*
>>
>> Hello,
>> When I try to access the following URL via the API: I get a 504 Gateway
>> Time out:
>>
>> http://data.bioontology.org/ontologies/MESH/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMESH%2FD005191?include=all
>>
>> Can you please fix?
>>
>> Thanks,
>> Rakesh
>>
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>
> --
>
> *Rakesh Nagarajan*
>
> Founder and Executive Chairman
>
> m: 314-504-5620
> e: rakesh at pieriandx.com
>
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>
> Wisdom in Every Report™
>
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-- 

*Rakesh Nagarajan*

Founder and Executive Chairman

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

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CONFIDENTIALITY NOTICE: This message and any attachments are solely for the
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please destroy all copies without reading or disclosing their contents and
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