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[bioontology-support] NCBI TAXON issues with API

Ray Fergerson ray.fergerson at stanford.edu
Tue Mar 24 16:45:39 PDT 2015


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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