Search Mailing List Archives
[bioontology-support] Error querying bioportal NCBITaxon
ray.fergerson at stanford.edu
Fri May 15 15:45:40 PDT 2015
This seems to be working now at least for the examples given. I suspect
that it was timing out before because of the size of the NCBITaxon ontology.
We made some performance improvements in the last few weeks that may have
addressed this problem.
Please let me know if you continue to have problems.
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Alejandro Rodríguez González
Sent: Wednesday, April 22, 2015 5:13 AM
To: support at bioontology.org; info at ncbi.nlm.nih.gov
Subject: [bioontology-support] Error querying bioportal NCBITaxon
My name is Alejandro Rodríguez, a post-doc fellowship at Centre for Plant
Biotechnology and Genomics (CBGP) in Spain.
I'm working on a project which consumes NCBITaxon ontology from bioportal
and I've found a problem/error, but I'm not sure who should be notified
(bioportal or ncbi). For this reason I'm sending this email to both.
This is the problem: I'm trying to obtain trhough REST API the hierarchy of
a set of pathogens but I found, at least (for the moment), problems with a
If I try to get hierarchy of pathogen with NCBI Taxonomy ID 5017 (Bipolaris
zeicola), it returns as "father" Bipolaris (NCBI Taxonomy ID 33194). The
next father should be the one with ID 28556 (which according to the
visualization of the 5017 species tree (see figure 1) is Pleosporaceae).
The problem is that the query to the REST API of this given ID returns a
400. The query is the following:
This happens also if you try to go directly to the URL of this ID using the
browser (or the link provided to Pleosporaceae as indicated figure 2):
This URL returns an error.
It shouldn't, because if you provide any other correct ID (for eg 5017), it
The problem can be fixed changing in the concept parameter the ID to the
complete URL of the concept:
But I guess that it should be working with both ways, right?
I can of course modify my code to enter to the conceptid providing the
entire URL, but I suppose that this is some kind of bug (I don't know if in
bioportal or in the ontology).
Please let me know any fix or comment.
Dr. Alejandro Rodríguez González - PhD
Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA
Technical University of Madrid
Phone: +34 914524900 . Ext: 25550
Once the game is over, the king and the pawn go back in the same box. -
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the bioontology-support