Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

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

Michael Dorf mdorf at stanford.edu
Fri Apr 26 14:57:40 PDT 2019


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<mailto: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<mailto: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<mailto:mdorf at stanford.edu>
O: 650-723-0357
M: 650-995-4374
----------------------------------------------------

On Apr 23, 2019, at 6:46 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Rakesh Nagarajan

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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20190426/75d436d4/attachment-0001.html>


More information about the bioontology-support mailing list