Issue 10744
Issue organizing occurrences of Thlapsi
10744
Reporter: trobertson
Assignee: mdoering
Type: Bug
Summary: Issue organizing occurrences of Thlapsi
Priority: Minor
Resolution: WontFix
Status: Closed
Created: 2012-02-02 15:27:02.902
Updated: 2016-05-11 16:00:55.266
Resolved: 2016-05-11 16:00:55.154
Description: By email from Herbario SANT :
a visitor to our herbarium just discovered something odd in our
data when making this search:
http://data.gbif.org/occurrences/searchWithTable.htm?c[0].s=20&c[0].p=0&c[0].o=3052635&c[1].s=25&c[1].p=0&c[1].o=66&c[2].s=13&c[2].p=0&c[2].o=SANT
That search only returns 8 records of "Thlaspi arvense", but it should
be returning 38 of many other specimens belonging to genus "Thlaspi".
For example, this one:
http://data.gbif.org/occurrences/60043457/
Actually, our tapirlink interface returns 38 records. I have checked
the original table and all of them have identical values in higher
taxonomic concepts (genus, family, ...)
This happens when searching by "Classification includes Genus: Thlaspi".
It also happens when searching by "Scientific name is Thlaspi" (only
the 8 records of "Thlaspi arvense" being returned)
If I search for the non-returned records using a different filter,
like "Catalogue number is 1602", there is no problem. They are
returned:
http://data.gbif.org/occurrences/searchWithTable.htm?c[0].s=25&c[0].p=0&c[0].o=66&c[1].s=13&c[1].p=0&c[1].o=SANT&c[2].s=14&c[2].p=0&c[2].o=1602
If I order our table by catalognumber, the first matched record
belongs to "Thlaspi arvense" (the only scientificname which is being
returned by data.gbif.org)
The oddest thing is that I cannot reproduce the same behaviour when I
query for some other genus (only in Thlaspi by now).
Why is this happening? Am I missing something? Could be something
related to a cache somewhere?
Thanks,
David
PS - I just tried to add more collectioncodes to the same search and,
add one more species of Thlaspi, to see what happens:
http://data.gbif.org/occurrences/searchWithTable.htm?c[0].s=0&c[0].p=0&c[0].o=Thlaspi&c[1].s=0&c[1].p=0&c[1].o=Thlaspi
perfoliatum&c[2].s=13&c[2].p=0&c[2].o=Herbarium
Berolinense&c[3].s=13&c[3].p=0&c[3].o=LEB-Cormo&c[4].s=13&c[4].p=0&c[4].o=SALA&c[5].s=13&c[5].p=0&c[5].o=SANT
I can understand what's going on:
- SALA seems to work well (returns all species of Thlaspi when
searching for "Scientific name is Thlaspi")
- SANT and LEB-Cormo do the same odd thing (just return Thlaspi
arvense, and I need to add other species like Thlaspi perfoliatum, in
order to get them in dataset)
- Herbarium Berolinense is returning all kind of stuff: both Thlaspi
(correctly, all species), but also other non requested genus which
belong to the same family (like Aethionema). A mistery
--
Herbario SANT
Facultade de Farmacia - Laboratorio de Botánica
Universidade de Santiago de Compostela
15782 - Galicia (Spain)
http://www.usc.es/herbario
Tel. +34 881815022
Fax +34 981594912]]>
Author: mdoering@gbif.org
Created: 2012-02-02 16:00:52.623
Updated: 2012-02-02 16:00:52.623
Trying to investigate into the problem. The nub only has a single concept for both the genus Thlaspi and the species T. arvense:
http://data.gbif.org/species/browse/taxon/3052635
http://data.gbif.org/species/3052635
http://data.gbif.org/species/3052680
Doing a new search starting with the GBIF concept of Thlaspi and adding 4 datasets (SANT,SALA,LEB-Como&Berolinense) I get
http://data.gbif.org/occurrences/search.htm?c%5B0%5D.s=20&c%5B0%5D.p=0&c%5B0%5D.o=3052635&dr=8003&dr=239&dr=1095&dr=222
It appears the "missing" specimen like the following are not tight to the GBIF taxonomy for some reason:
http://data.gbif.org/occurrences/60043457/
It says "GBIF classification", but in fact the species id given and linked leads to the native taxonomy of the occurrence dataset:
http://data.gbif.org/species/browse/taxon/50522050
When trying to link this record manually to our "nub" taxonomy it is correct when using the name without classification:
nubId=3050634, confidence=44
http://mogo.gbif.org:8080/ws-nub/nub/?name=Thlaspi%20perfoliatum%20L.
With the genus & family brassicaceae (the one used in the nub) it is:
nubId=3050634, confidence=95
http://mogo.gbif.org:8080/ws-nub/nub/?family=Brassicaceae&genus=Thlaspi&name=Thlaspi%20perfoliatum%20L.
When using the exact same occurrence classification with family=Cruciferae it is still the same:
nubId: 3050634, confidence: 95,
http://mogo.gbif.org:8080/ws-nub/nub/?family=Cruciferae&genus=Thlaspi&name=Thlaspi%20perfoliatum%20L.
A bit clueless why this has happened...