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.
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.
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.