TaxRef Collector - Documentation

Why ?

This tool allow to get species ids from the frebch Taxonomic Referential (TAXREF) from species information.

How ?

Only 3 informations are necessary :

1. Select a layer with species information

2. Select research mode

3. Enter fields with species information

4. Resolve conflicts when there is multiple match

User interface

1. Select a layer with species information

With the help of the combo box you can select a layer already placed in your QGIS project. This layer must be a vector layer. You can launch the request on selected features only if you check the dedicated checkbox.

For now there is no limit for the entry data number. The operation can take a long time if there is a lot of data.

2. Select research mode

For now there is only 3 research mode :

• Using the MNHN API (not working since the hack) by looking for species name. You can also add rank information for more precision.

• Using MikiData’s API by looking for corresponding id between GBIF’s id or iNaturalist’s id and TaxRef’s id.

• Using the GBIF API by looking for the scientific name of a species to find corresponding TaxRef’s id.

3. Enter fields with species information

API WikiData

Only one field is necessary and mandatory, he must contain GBIF’s id or iNaturalist’s id for every feature depending on the selected method. Every id will be tested on WikiData’s API. If a result is found, we will look for a corresponding id with the TaxRef.

API GBIF

Only one field is necessary and mandatory, he must contain scientific name of the specie. Every feature will be tested on GBIF API. If a result is found, we will look for a corresponding id with the TaxRef.

API MNHN

A field containing the specie’s name is mandatory, it is preferred to use the scientific name without the author’s name and the date. A field containing the rank can also be specified under one of this format :

english	Abreviation	French
domain	Dumm	Domaine
superkingdom	SPRG	Super-Règne
kingdom	KD	Règne
subkingdom	SSRG	Sous-Règne
infrakingdom	IFRG	Infra-Règne
phylum	PH	Phylum
subphylum	SBPH	Sous-Phylum
infraphylum	IFPH	Infra-Phylum
division	DIV	Division
subdivision	SDIV	Sous-Division
superclass	SPCL	Super-Classe
cladus	CLAD	Clade
class	CL	Classe
subclass	SBCL	Sous-Classe
infraclass	IFCL	Infra-Classe
parvclass	PVCL	Parv-Classe
legio	LEG	Legio
superorder	SPOR	Super-Ordre
cohort	COH	Cohorte
order	OR	Ordre
suborder	SBOR	Sous-Ordre
infraorder	IFOR	Infra-Ordre
parvorder	PVOR	Parv-Ordre
section	SC	Section
?	SCO	?
subsection	SBSC	Sous-Section
subsection	SSCO	Sous-Section
superfamily	SPFM	Super-Famille
family	FM	Famille
subfamily	SBFM	Sous-Famille
supertribe	SPTR	Super-Tribu
tribe	TR	Tribu
subtribe	SSTR	Sous-Tribu
genus	GN	Genre
subgenus	SSGN	Sous-Genre
section	SC	Section
subsection	SBSC	Sous-Section
series	SER	Série
subseries	SSER	Sous-Série
agregate	AGES	Agrégat
species	ES	Espèce
semispecies	SMES	Semi-Espèce
microspecies	MES	Micro-Espèce
subspecies	SSES	Sous-Espèce
natio	NAT	Natio
variety	VAR	Variété
subvariety	SVAR	Sous-Variété
form	FO	Forme
subform	SSFO	Sous-Forme
formaspecies	FOES	Forma species
linea	LIN	Linea
clone	CLO	Clône
race	RACE	Race
cultivar	CAR	Cultivar
morpha	MO	Morpha
abberation	AB	Abberatio

4. Resolve conflicts when there is multiple match

Multiples occurences can be a match between TaxRef and GBIF, iNaturalist or WikiData database. If it’s the case, a dialog will opened to allow the user to manually select the right match between the occurences.