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[bioontology-support] [BioPortal] Feedback from Andrey Fedorov

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Feb 12 15:33:35 PST 2018


Hello Andrey,

It’s unclear to me from your initial post if you’re specifically referring just to the DCM ontology. I downloaded / examined this ontology and it’s worth noting that it’s an unusual one due to the almost complete lack of any hierarchical structure in the class tree. There are 3,866 classes with only one SubClassOf axiom. In other words, this ontology appears to be a flat list of classes, with only one class appearing as a subclass of another.

It’s not particularly surprising that the initial page load time for this ontology is somewhat slow. In order to construct a class tree, BioPortal has to retrieve class data for 3,865 root level classes. However, after the initial page load, the class data is cached and subsequent navigation to other classes in the tree is fast. I clicked on several other classes in the tree and the Chrome developer console shows load times less than a second.

I compared the load times of the underlying REST call for constructing the initial class tree between DCM and a much larger ontology - SNOMEDCT at 327K classes. Chrome developer console shows a load time for SNOMEDCT of 456ms compared to 7.5s for DCM. This is again due to the lack of any hierarchy / very large number of root level classes in DCM.

If on the other hand, you’re referring to programmatic access to class data, the more expedient method is via the REST API. Issuing a REST call for the class information you listed below:

http://data.bioontology.org/ontologies/DCM/classes/http%3A%2F%2Fdicom.nema.org%2Fresources%2Fontology%2FDCM%2F113206?apikey=32688b66-537e-45b7-badc-ce525bebca4d<http://data.bioontology.org/ontologies/DCM/classes/http://dicom.nema.org/resources/ontology/DCM/113206?apikey=32688b66-537e-45b7-badc-ce525bebca4d>

...completes in roughly 743ms on the first uncached attempt, then roughly 75ms on subsequent cached retrievals. You can also retrieve all classes for DCM with the classes endpoint, which implements paging:

http://data.bioontology.org/ontologies/DCM/classes

Kind regards,
Jennifer



On Feb 12, 2018, at 1:32 PM, Andrey Fedorov <andrey.fedorov at gmail.com<mailto:andrey.fedorov at gmail.com>> wrote:

John, thank you for the reply. I will see if I can do more
comprehensive profiling.

I also cc David Clunie, who has also always been mentioning how slow
BioPortal is. Perhaps he can chime in.

On Sun, Feb 11, 2018 at 5:53 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:
Andrey,

To answer this question in a useful way (not just "yes"), we'd need to hear
more details about your use case, including the exact queries you're trying
to answer, and when and for how long it has seemed slow.

Many of the queries can be expected to take seconds to tens of seconds,
because they have to perform a lot of computations and/or transmit a lot of
data. (When I look at the class list in DICOM, it seems to take a while, but
it's sending information about more than 3000 terms over my slow DSL...)

So if you can post some example queries (or indicate what web page you're
trying to access), and tell us your expectations in terms of response time,
we can tell whether we need to troubleshoot something, and if so, what.
Thanks!

John

On Feb 10, 2018, at 9:43 AM, support at bioontology.org<mailto:support at bioontology.org> wrote:

Name: Andrey Fedorov

Email: andrey.fedorov at gmail.com<mailto:andrey.fedorov at gmail.com>

Location:
http%3A%2F%2Fbioportal.bioontology.org%2Fontologies%2FDCM%3Fp%3Dclasses%26conceptid%3Dhttp%253A%252F%252Fdicom.nema.org%252Fresources%252Fontology%252FDCM%252F113206


Feedback:

Can anything be done to make BioPortal queries faster? It literally takes
seconds to get a response.


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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


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