The PR2 database is provided as a data frame.
This is a join between the following tables:
pr2_main
pr2_taxonomy
pr2_sequence
pr2_metadata
pr2_traits
pr2_silva
euribo
The metadata contains different types of fields
gb_ : originating from the GenBank entry
eukref_ : annotated by the Eukref project
pr2_ : annotated by pr2 such latitude and longitude
eukribo_: information from the EukRibo database
Description of fields: https://pr2-database.org/documentation/pr2-fields
Examples
# Read the whole database
my_pr2 <- pr2_database()
# Select a specific genus
pr2_ostreo <- pr2_database()
pr2_ostreo <- dplyr::filter(pr2_ostreo , genus == "Ostreococcus")
pr2_ostreo <- dplyr::select(pr2_ostreo, pr2_accession, species)
head(pr2_ostreo)
#> # A tibble: 6 × 2
#> pr2_accession species
#> <chr> <chr>
#> 1 AF525872.1.1766_U Ostreococcus_lucimarinus
#> 2 EU562149.1.836_U Ostreococcus_lucimarinus
#> 3 AY425309.1.1728_U Ostreococcus_lucimarinus
#> 4 GQ426346.1.1652_U Ostreococcus_tauri
#> 5 KC583118.1.1764_U Ostreococcus_clade_B
#> 6 JN862906.1.1568_U Ostreococcus_mediterraneus