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[bioontology-support] Error querying bioportal NCBITaxon

Ray Fergerson 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.



Ray



From: bioontology-support 
[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



Dear responsible(s),



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 
concrete pathogen.



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:



http://data.bioontology.org/ontologies/NCBITAXON/classes/28556?apikey=a865fdd8-dbe0-4516-a666-0b05dd5a372c 
<http://data.bioontology.org/ontologies/NCBITAXON/classes/28556?apikey=a865fdd8-dbe0-4516-a666-0b05dd5a372c&format=xml> 
&format=xml



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):



http://bioportal.bioontology.org/ontologies/NCBITAXON?p=classes 
<http://bioportal.bioontology.org/ontologies/NCBITAXON?p=classes&conceptid=28556> 
&conceptid=28556



This URL returns an error.



It shouldn't, because if you provide any other correct ID (for eg 5017), it 
works:



http://bioportal.bioontology.org/ontologies/NCBITAXON?p=classes 
<http://bioportal.bioontology.org/ontologies/NCBITAXON?p=classes&conceptid=5017> 
&conceptid=5017



The problem can be fixed changing in the concept parameter the ID to the 
complete URL of the concept:



http://bioportal.bioontology.org/ontologies/NCBITAXON/?p=classes 
<http://bioportal.bioontology.org/ontologies/NCBITAXON/?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%2F28556> 
&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FNCBITAXON%2F28556



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.



Cheers,



Alejandro






-- 

Dr. Alejandro Rodríguez González - PhD

Bioinformatics at Centre for Plant Biotechnology and Genomics UPM-INIA

Technical University of Madrid

http://www.alejandrorg.com <http://www.alejandrorg.com/>
Phone: +34 914524900 . Ext: 25550





Once the game is over, the king and the pawn go back in the same box. - 
Italian proverb

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