Issue 18381

Oligochaeta (animal) linked to Oligochaeta (plant genus)

18381
Reporter: rdmpage
Assignee: jlegind
Type: Feedback
Summary: Oligochaeta (animal) linked to Oligochaeta (plant genus)
Description: Most of the records for the plant genus _Oligochaeta_ (A.P. de Candolle) K.H.E. Koch, 1843  http://www.gbif.org/species/5401803 are for worms (oligochaetes). Looks like these occurrences simply have scientificName as "Oligochaeta" with no other information (e.g., no information on whether it's an animal or a plant).
Priority: Unassessed
Status: InProgress
Created: 2016-04-07 14:13:48.685
Updated: 2016-10-28 16:08:04.402


Author: mdoering@gbif.org
Created: 2016-04-07 17:45:03.187
Updated: 2016-04-07 17:45:03.187
        
Unfortunately the class is not in Catalogue of Life:
http://www.catalogueoflife.org/col/search/all/key/Oligochaeta/fossil/0/match/1
https://en.wikipedia.org/wiki/Oligochaeta

There are quite a few cases like this causing problems for GBIF occurrences. Vertebrata, Heteropoda - all being a genus but also an entirely different, usually higher taxon. Usually in a different kingdom.

Often these higher taxa are not included in the backbone, so even for occurrences with a higher classification we interpret them wrongly.
And often the reason why we do not include them in the backbone is that the are non Linnean ranks like subclass or superfamily, see POR-2781
    


Author: mdoering@gbif.org
Created: 2016-04-07 17:54:11.315
Updated: 2016-04-07 17:54:11.315
        
I will add the class Oligochaeta as a synonym of the annelids class Clitellata in our patch list.
CoL uses Clitellata as the only other phylum in Annelida next to Polychaeta. It also includes the orders Haplotaxida, Lumbriculida & Moniligastrida which are orders of Oligochaeta:

https://en.wikipedia.org/wiki/Clitellata
https://en.wikipedia.org/wiki/Oligochaeta
    


Author: mdoering@gbif.org
Comment: https://github.com/gbif/backbone-patch/commit/f9c1e0b5cbd713d2d1f7a6b31e4a2589b1421b93
Created: 2016-04-07 18:14:41.038
Updated: 2016-04-07 18:14:41.038


Author: mdoering@gbif.org
Created: 2016-04-14 15:04:20.865
Updated: 2016-04-14 15:05:53.432
        
Oligochaeta without ranks gets you the plant genus:
http://api.gbif-uat.org/v1/species/match?verbose=true&name=Oligochaeta

With rank given you can get to the worm class now:
http://api.gbif-uat.org/v1/species/match?verbose=true&name=Oligochaeta&rank=CLASS

Also close ranks like SUBCLASS or PHYLUM work:
http://api.gbif-uat.org/v1/species/match?verbose=true&name=Oligochaeta&rank=SUBCLASS
    


Author: mdoering@gbif.org
Comment: [~jlegind@gbif.org], [~kbraak@gbif.org] is this something for the content team to follow up on? It would be great if the publishers of these doubtful records would be contacted and they would add a kingdom or other higher classification if they could.
Created: 2016-10-24 16:26:02.516
Updated: 2016-10-24 16:26:02.516


Author: kbraak@gbif.org
Created: 2016-10-24 17:32:35.745
Updated: 2016-10-24 17:32:35.745
        
Thanks Markus.

How about [~jlegind@gbif.org] and I write to the publishers of the invertebrates datasets below that contain doubtful records and ask them to add a kingdom or other higher classification?

Scottish Environment Protection Agency - River macroinvertebrate data ... (6,194 doubtful records)
dataset_key=98af357b-541e-4f16-b35c-8ca68767be99
Published by: UK National Biodiversity Network: http://www.gbif.org/publisher/07f617d0-c688-11d8-bf62-b8a03c50a862

Macroinvertebrate abunda… (299 doubtful records)
dataset_key=ece4ea69-9ec5-4773-a5dc-7a99b245e415
Published by PANGAEA: http://www.gbif.org/publisher/d5778510-eb28-11da-8629-b8a03c50a862

Invertebrates Collection… (166 doubtful records)
dataset_key=56aa0680-0c60-11dd-84cd-b8a03c50a862
Published by GBIF-Sweden: http://www.gbif.org/publisher/4c415e40-1e21-11de-9e40-a0d6ecebb8bf

Clitellata - SMF (102 doubtful records)
dataset_key=7f4020e2-1387-11e2-bb2e-00145eb45e9a
Published by Senckenberg: http://www.gbif.org/publisher/c76cf030-2a95-11da-9cc1-b8a03c50a862
    


Author: mdoering@gbif.org
Comment: Thanks Kyle, that would be good!
Created: 2016-10-24 22:41:05.712
Updated: 2016-10-24 22:41:05.712


Author: mdoering@gbif.org
Created: 2016-10-24 22:49:44.974
Updated: 2016-10-24 22:49:44.974
        
Maybe you could also get in touch with these which seem to have worms only and missing classifications:

EPA'S EMAP Database (1732 records)
http://www.gbif.org/dataset/838bb5ee-f762-11e1-a439-00145eb45e9a

Artdata (1359 records)
http://www.gbif.org/dataset/38b4c89f-584c-41bb-bd8f-cd1def33e92f

Norwegian Biodiversity Information Centre - Other datasets (1036 records)
http://www.gbif.org/dataset/492d63a8-4978-4bc7-acd8-7d0e3ac0e744

Here are all occurrence datasets: http://www.gbif.org/species/5401803/datasets?type=OCCURRENCE


When I see that long list of datasets I think we should flag all records that do not provide any classification at all.
[~cgendreau], how about we add missing classification to the new (occurrence) validator?
    


Author: jlegind@gbif.org
Comment: Publishers contacted
Created: 2016-10-28 16:08:04.402
Updated: 2016-10-28 16:08:04.402