not existing parent name usage ids in the latest dwca

18165
Reporter: mdoering
Type: Bug
Summary: not existing parent name usage ids in the latest dwca
Priority: Major
Status: ToDo
Created: 2016-01-20 22:58:27.78
Updated: 2016-01-21 12:02:07.957
        
Description: not existing parent name usage ids in the latest dwca:
http://www.gbif.org/species/search?dataset_key=7ddf754f-d193-4cc9-b351-99906754a03b&issue=PARENT_NAME_USAGE_ID_INVALID

I have tried to grep the id mentioned in this record:
http://www.gbif.org/species/116192967/verbatim

And indeed there is no entry.
Just 2 records using it as a parentid (btw, is it correct to have 2 records for the same name?)

[crap@bla6 7ddf754f-d193-4cc9-b351-99906754a03b]$ grep -n "25576691" taxa.txt
3182441:25579865	urn:lsid:catalogueoflife.org:taxon:82b886e0-6ae5-11e5-9d43-bc764e092680:col20160114	106	WoRMS Echinoidea in Species 2000 & ITIS Catalogue of Life: 15th January 2016		25576691	accepted name	infraspecies		Agassizia cyrenaica pseudoinflala Desio, 1929	Animalia	Echinodermata	Echinoidea	Spatangoida		Prenasteridae	Agassizia	Agassizia		cyrenaica	pseudoinflala	Desio, 1929		Kroh, Andreas	11-Mar-2014			W-Ech-757599	http://www.catalogueoflife.org/annual-checklist/details/species/id/ae994262fca554fdbf19d249fc1be051	false

3182443:25579866	urn:lsid:catalogueoflife.org:taxon:82b7eb46-6ae5-11e5-9d43-bc764e092680:col20160114	106	WoRMS Echinoidea in Species 2000 & ITIS Catalogue of Life: 15th January 2016		25576691	accepted name	infraspecies		Agassizia cyrenaica pseudoclevei Desio, 1929	Animalia	Echinodermata	Echinoidea	Spatangoida		Prenasteridae	Agassizia	Agassizia		cyrenaica	pseudoclevei	Desio, 1929		Kroh, Andreas	11-Mar-2014			W-Ech-757598	http://www.catalogueoflife.org/annual-checklist/details/species/id/39115010b31dc63fe16330ef9ac7a377	false
]]>
    

Author: mdoering@gbif.org
Created: 2016-01-21 12:02:07.957
Updated: 2016-01-21 12:02:07.957
        
The problem consists of subspecies labelled extant, but with an extinct species as a parent. As currently extinct taxa are excluded from the export, this results in orphaned taxa in the download.

This issue for the download can be fixed quite easily by allowing extinct taxa in the download. Is there a good reason not to include extinct taxa?

The problem however also permeates to the CoL itself:

http://www.catalogueoflife.org/col/details/species/id/1ba6fa9b7197091f724e34cd59ce8606

If the "Include extinct taxa" is off, clicking the species or genus name in the classification leads to a tree opened up only to the family. As the genus and species are extinct, they will not appear.

Apparently this is an extra check we need to add somewhere in the conversion chain. The most logical step would be to "demote" taxa to extinct when their parent is extinct.

So two questions:

1. Do you we allow extinct taxa in the DCA archives
2. Do we post-process extant taxa with extinct parents?