--- title: "Validating passport data" author: "Matija Obreza" date: "`r Sys.Date()`" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Validating passport data} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- Validating passport data ======================== [Genesys PGR](https://www.genesys-pgr.org) 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](https://validator.genesys-pgr.org). 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](https://npgsweb.ars-grin.gov/gringlobal/taxon/abouttaxonomy.aspx). 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.|Presl.| |5|Avena|sativa|||| |6|Dactylis|glomerata|L.|subsp juncinella|| |7|Linum|usitatissimum|L.|var intermedium|Vav. et Ell.| |8|Prunus|domestica|L.|subsp||domestica|| |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.