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

Michael Dorf mdorf at
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.


On Apr 24, 2019, at 7:56 PM, Rakesh Nagarajan <rakesh at<mailto:rakesh at>> wrote:

Thanks a lot Michael. These alternate URLs meet my immediate need. I also noticed yesterday that (repeatedly) the URL: 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<mailto:mdorf at>> 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.

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:,synonym,definition,cui,semanticType,obsolete<,synonym,definition,cui,semanticType,obsolete><><>

Hope this helps!


Michael Dorf
Chief Software Architect
The National Center for Biomedical Ontology
Stanford Biomedical Informatics Research
mdorf at<mailto:mdorf at>
O: 650-723-0357
M: 650-995-4374

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

Name: Rakesh Nagarajan

Email: rakesh at<mailto:rakesh at>



When I try to access the following URL via the API: I get a 504 Gateway Time out:

Can you please fix?


bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>


Rakesh Nagarajan

Founder and Executive Chairman

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

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