Validating passport data

Matija Obreza

2022-12-04

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.

ORICTY 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.