10903
Reporter: jcuadra
Assignee: mdoering
Type: Bug
Summary: Nub lookup for species "Gadus morhua" goes wrong
Priority: Major
Resolution: Fixed
Status: Closed
Created: 2012-02-20 17:08:45.509
Updated: 2013-12-09 13:40:34.649
Resolved: 2012-05-09 23:14:47.191
Description: Please see
http://data.gbif.org/species/2335052
and/or
http://data.gbif.org/species/6008172/
Effects on the data portal:
- Hundreds of "Gadus morhua" occurrences appear without a species_concept_id associated, and their nub_concept_id points to a genus.
An email sent by a user:
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When I search for "Gadus morhua" I only get 232 occurences of this very common species.
If I search for only "Gadus" I get many thousands of Gadhus morhua in the result that not show up in the "Gadus morhua" search.
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Author: mdoering@gbif.org
Created: 2012-02-21 15:07:17.365
Updated: 2012-02-21 15:07:17.365
Seems like a nub lookup issue. I can only find exactly one Gadus morhua in the nub and also in the CoL:
http://ecat-dev.gbif.org/usage/2415835
But the lookup without classification does not match anzthing:
http://boma.gbif.org:8080/ws-nub/nub/?name=Gadus%20morhua
With the family given it matches to the genus, not the species:
http://boma.gbif.org:8080/ws-nub/nub/?family=Gadidae&name=Gadus%20morhua
Author: mdoering@gbif.org
Created: 2012-05-08 16:30:37.402
Updated: 2012-05-08 16:30:37.402
The issue is that there are also 2 cultivars with the same species name and the canonical name for those 3 is identical.
Updating the nub lookup to prefer non cultivars and informal names
Author: mdoering@gbif.org
Comment: simple name lookup now returns correct results
Created: 2012-05-09 23:14:47.223
Updated: 2012-05-09 23:14:47.223
Author: mdoering@gbif.org
Created: 2012-05-10 14:11:11.685
Updated: 2012-05-10 14:11:11.685
The additional names actually came from NCBI and are of course not a cultivar as they are fishes.
The suffix 'NCC' refers to the isolate name instead:
http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=328277&lvl=3&keep=1&srchmode=1&unlock&mod=1#modif
We need to make sure cultivars only exist inside the planate kingdom in the nub.