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[bioontology-support] NCBI TAXON issues with API

Sai Lakshmi Subramanian sailakshmi.subramanian at
Wed Mar 25 07:07:04 PDT 2015

Hi Ray,

Yes, I figured the size of the ontology would be the reason.
I am planning to use one of the lower nodes in the tree for now.


On 3/24/15 6:45 PM, Ray Fergerson wrote:
> Sai,
> We know what is going on here. The current implementation of "search in
> subtree" is just too slow for large ontologies. NCBITAXON, at 900,000
> terms definitely is in the large ontology group. The call is timing out.
> We have today discussed how to make this operation perform better. We have
> a plan but it will take a while before it gets scheduled. It is not a huge
> amount of work but it isn't trivial either. My guess would be that we
> would have it done in a month or two.
> Until then, what can you do? Obviously if you can choose lower nodes in
> the tree (where, as you have found, the call is quick enough to not time
> out) as the roots of your tree, then this would help. You can also leave
> off the "subtree" part of the call and then do the pruning yourself. This
> will be time consuming but it would work, at least until we have a better
> implementation in place.
> Sorry that we don't have a better short term solution.
> Ray
> -----Original Message-----
> From: bioontology-support
> [mailto:bioontology-support-bounces at] On Behalf Of Sai
> Lakshmi Subramanian
> Sent: Tuesday, March 24, 2015 1:23 PM
> To: support at
> Subject: [bioontology-support] NCBI TAXON issues with API
> Hi,
> I have been having issues with using the API search endpoint with NCBI
> TAXON ontology.
> The following search for the term "Homo sapiens" fails with "Internal
> Server Error":
> key={APIKEY}&
> The subtree root is "Vertebrata" in this case.
> I found that the search works for all sub-tree roots below "Amniota"
> (which is a subtree under Vertebrata)
> key={APIKEY}&
> CBITAXON%2F32524
> but fails with Internal Server Error for anything above Amniota - say
> Tetrapoda which is the immediate root of Amniota -
> key={APIKEY}&
> CBITAXON%2F32523
> Can you please look into this?
> Thanks,
> Sai
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> bioontology-support at

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