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[bioontology-support] NCBI TAXON issues with API

Sai Lakshmi Subramanian sailakshmi.subramanian at bcm.edu
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.

Thanks,
Sai

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 lists.stanford.edu] On Behalf Of Sai
> Lakshmi Subramanian
> Sent: Tuesday, March 24, 2015 1:23 PM
> To: support at bioontology.org
> 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":
>
> http://data.bioontology.org/search?q=Homo%20sapiens&ontology=NCBITAXON&api
> key={APIKEY}&subtree_root=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FN
> CBITAXON%2F7742
>
> 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)
> http://data.bioontology.org/search?q=Homo%20sapiens&ontology=NCBITAXON&api
> key={APIKEY}&subtree_root=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FN
> CBITAXON%2F32524
>
> but fails with Internal Server Error for anything above Amniota - say
> Tetrapoda which is the immediate root of Amniota -
> http://data.bioontology.org/search?q=Homo%20sapiens&ontology=NCBITAXON&api
> key={APIKEY}&subtree_root=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FN
> CBITAXON%2F32523
>
> Can you please look into this?
>
> Thanks,
> Sai
>
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