Validating passport data

Genesys PGR is the global database on plant genetic resources maintained ex situ in national, regional and international genebanks around the world.

genesysr provides functions to check accession passport data with the Genesys Validator. This service provides tools to check spelling of taxonomic names against the GRIN-Taxonomy database and coordinates of the collecting site against the country of origin.

Scientific names spell-check

The tool checks data against the GRIN-Global Taxonomy database maintained by USDA-ARS, distributed with the GRIN-Global installer. See GRIN Taxonomy for Plants.

Only the following MCPD columns will be checked for taxonomic data: GENUS, SPECIES, SPAUTHOR, SUBTAXA, SUBTAUTHOR.

id	GENUS	SPECIES	SPAUTHOR	SUBTAXA	SUBTAUTHOR
1	Onobrychis		viciifolia
2	Agrostis	tenuis	Sibth.
3	Arachis	hypogaea	L.
4	Arrhenatherum	elatius	(L.) J. et C.Presl.	var. elatius	(L.) J. et C.
5	Avena	sativa
6	Dactylis	glomerata	L.	subsp juncinella
7	Linum	usitatissimum	L.	var intermedium	Vav. et Ell.
8	Prunus	domestica	L.	subsp
9	Prunus		hybrid

taxaCheck <- genesysr::check_taxonomy(mcpd);

The validator returns all incoming columns, but annotates the taxonomic data with new *_check columns.

Checking coordinates

Geo tests require DECLATITUDE, DECLONGITUDE and ORIGCTY for country border check and suggested coordinate fixes.

…	ORIGCTY	DECLATITUDE	DECLONGITUDE
…	DEU	20	30
…	SVN	40	NA
…	NGA	NA	NA
…	GTM	-90	30

geoCheck <- genesysr::check_country(mcpd)

The validator returns all incoming columns, but annotates the taxonomic data with new *_check columns.