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[bioontology-support] Error querying bioportal NCBITaxon

Alejandro Rodríguez González alejandro.rodriguezg at upm.es
Wed Apr 22 05:13:29 PDT 2015


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&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&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&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&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
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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