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

Rakesh Nagarajan rakesh at pieriandx.com
Wed Apr 24 19:56:51 PDT 2019


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%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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