Genesys PGR is the global database on plant genetic resources maintained ex situ in national, regional and international genebanks around the world.
genesysr uses the Genesys API to query Genesys data. The API is accessible at https://api.genesys-pgr.org.
Accessing data with genesysr is similar to downloading data in CSV or Excel format and loading it into R.
Accession passport data is retrieved with the
get_accessions function.
Accessing Genesys requires authentication so the first thing to do is to login:
## Setup: use Genesys Sandbox environment
# genesysr::setup_sandbox() # Use this to connect to our test environment https://sandbox.genesys-pgr.org
# genesysr::setup_production() # This is initialized by default when loading genesysr
# Open a browser: login to Genesys and authorize access
genesysr::user_login()The database is queried by providing a filter (see
Filters below) and the list of passport data fields that you wish to
download from Genesys. A basic list of MCPD descriptors (“INSTCODE”,
“ACCENUMB”, “DOI”, “HISTORIC”, “GENUS”, “SPECIES”, “SUBTAXA”,
“SAMPSTAT”) is used if you don’t specify your own list.
# Retrieve accessions for genus *Musa*
musa <- get_accessions(filters = list(taxonomy = list(genus = list('Musa'))))
# Retrieve all accession data for the Musa International Transit Center, Bioversity International
itc <- get_accessions(list(institute = list(code = list('BEL084'))))
# Retrieve all accession data for the Musa International Transit Center, Bioversity International (BEL084) and the International Center for Tropical Agriculture (COL003)
some <- get_accessions(list(institute = list(code = list('BEL084','COL003'))))genesysr provides utility functions to create
filter objects using Multi-Crop
Passport Descriptors (MCPD) definitions:
# Retrieve data by country of origin (MCPD)
get_accessions(mcpd_filter(ORIGCTY = list("DEU", "SVN")))Passport data follows MCPD standard and where multiple values are
possible, they will be separated by a semicolon ;.
Example: Column “STORAGE” may include 11;12 or a single
11.
The filter object is a named list() where
names match a Genesys filter and the value specifies the criteria to
match.
The records returned by Genesys match all filters provided (AND operation), while individual filters allow for specifying multiple criteria (OR operation):
# (GENUS == Musa) AND ((ORIGCTY == NGA) OR (ORIGCTY == CIV))
filter <- list(taxonomy = list(genus = c('Musa'), species = c('aa')), countryOfOrigin = list(iso3 = c('NGA', 'CIV')))
# OR
filter <- list();
filter$taxonomy$genus = list('Musa')
filter$taxonomy$species = list('aa')
filter$countryOfOrigin$iso3 = list('NGA', 'CIV')
# See filter object as JSON
jsonlite::toJSON(filters)There are a number of filtering options to retrieve data from Genesys. Best explore how filtering works on the actual website https://www.genesys-pgr.org/a/overview by inspecting the HTTP requests sent by your browser to the API server and then replicating them here.
taxonomy$genus filters by a list of genera.
taxonomy$species filters by a list of
species.
countryOfOrigin$iso3 filters by ISO3 code of country of
origin of PGR material.
# Material originating from Germany (DEU) and France (FRA)
filters <- list(countryOfOrigin = list(iso3 = list('DEU', 'FRA')))geo.latitude and geo.longitude filters by
latitude/longitude (in decimal format) of the collecting site.
institute$code filters by a list of FAO WIEWS
institute codes of the holding institutes.
institute$country$iso3 filters by a list of
ISO3 country codes of country of the holding institute.
Let’s take a look of all the process of fetching accession passport data from Genesys.
# Fetch only accession number, storage and taxonomic data for *Musa* accessions
musa <- genesysr::get_accessions(list(taxonomy = list(genus = list('Musa'))), fields = list("ACCENUMB", "STORAGE", "GENUS", "SPECIES", "SUBTAXA"))The following column names are available:
| Column | Description |
|---|---|
| INSTCODE | FAO WIEWS code of the genebank managing the material |
| ACCENUMB | Accession number |
| DOI | DOI of the accession |
| HISTORIC | Flag indicating if the accession record is historical
(true) or active (false) |
| CURATION | Type of curation applied to this accession |
| GENUS | Genus |
| SPECIES | Specific epithet |
| SPAUTHOR | Species authority |
| SUBTAXA | Subtaxon information at the most detailed taxonomic level |
| SUBTAUTHOR | Subtaxon authority |
| GRIN_TAXON_ID | GRIN Taxonomy ID of the taxon |
| GRIN_NAME | Taxon name according to GRIN Taxonomy |
| GRIN_AUTHOR | Taxon authority |
| CROPNAME | Crop name(s) as provided by the genebank |
| CROPCODE | Crop code used by Genesys |
| SAMPSTAT | Biological status of the accession |
| ACQDATE | Acquisition date |
| ACCENAME | Accession name |
| ORIGCTY | Country of provenance of the material |
| COLLSITE | Site of collecting |
| DECLATITUDE | Latitude of the collecting site |
| DECLONGITUDE | Longitude of the collecting site |
| COORDUNCERT | Coordinate uncertainty in meters |
| COORDDATUM | Coordinate datum |
| GEOREFMETH | Georeferencing method |
| ELEVATION | Elevation of the collecting site |
| COLLDATE | Collecting date |
| COLLSRC | Collecting source |
| COLLNUMB | Collecting number |
| COLLCODE | FAO WIEWS code of the institute that originally collected the material |
| COLLNAME | Name of the institute that collected the material |
| COLLINSTADDRESS | Address of the institute that collected the material |
| COLLMISSID | Collecting mission name/identifier |
| DONORCODE | FAO WIEWS code of the institute from which this accession was acquired |
| DONORNAME | Name of the institute from which this accession was acquired |
| DONORNUMB | Accession number at the donor institute |
| OTHERNUMB | Other numbers/identifiers associated with this accession |
| BREDCODE | FAO WIES code of the institute that developed/bred this material |
| BREDNAME | Name of the institute that developed this material |
| ANCEST | Ancestral data or pedigree information |
| DUPLSITE | FAO WIEWS codes of institutes where this accession is safety duplicated by the genebank |
| STORAGE | Types of germplasm storage |
| MLSSTAT | Status of the accession in the Multilateral System of the ITPGRFA |
| ACCEURL | Accession URL |
| REMARKS | Notes and remarks |
| DATAPROVIDERID | Database ID of this record in genebank’s own database |
| PDCI | Passport Data Completeness Index for this accession |
| UUID | UUID assigned to this record by Genesys |
| LASTMODIFIED | Date when this record was last updated in Genesys |
Please use sparingly!
accessions <- get_accessions(filters = c(historic = list('false')))