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[bioontology-support] NCBI TAXON issues with API

Sai Lakshmi Subramanian sailakshmi.subramanian at bcm.edu
Tue Mar 24 13:22:40 PDT 2015


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&apikey={APIKEY}&subtree_root=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%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&apikey={APIKEY}&subtree_root=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%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&apikey={APIKEY}&subtree_root=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%2F32523

Can you please look into this?

Thanks,
Sai



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