taxizedb-package: taxizedb
In ropenscilabs/taxizedb: Tools for Working with 'Taxonomic' Databases

taxizedb-package

R Documentation

taxizedb

Description

Taxonomic databases interface

Supported data sources and database structure

All are using SQLite as the database

NCBI: text files are provided by NCBI, which we stitch into a sqlite db
ITIS: they provide a sqlite dump, which we use here
The PlantList: created from stitching together csv files. this source is no longer updated as far as we can tell. they say they've moved focus to the World Flora Online
Catalogue of Life: created from Darwin Core Archive dump. Using the latest monthly edition via http://www.catalogueoflife.org/DCA_Export/archive.php
GBIF: created from Darwin Core Archive dump. right now we only have the taxonomy table (called gbif), but will add the other tables in the darwin core archive later
Wikidata: aggregated taxonomy of Open Tree of Life, GLoBI and Wikidata. On Zenodo, created by Joritt Poelen of GLOBI.
World Flora Online: http://www.worldfloraonline.org/

Update schedule for databases

NCBI: since db_download_ncbi creates the database when the function is called, it's updated whenever you run the function
ITIS: since ITIS provides the sqlite database as a download, you can delete the old file and run db_download_itis to get a new dump; they I think update the dumps every month or so
The PlantList: no longer updated, so you shouldn't need to download this after the first download
Catalogue of Life: a GitHub Actions job runs once a day at 00:00 UTC, building the lastest COL data into a SQLite database thats hosted on Amazon S3
GBIF: a GitHub Actions job runs once a day at 00:00 UTC, building the lastest COL data into a SQLite database thats hosted on Amazon S3
Wikidata: last updated April 6, 2018. Scripts are available to update the data if you prefer to do it yourself.
World Flora Online: since db_download_wfo creates the database when the function is called, it's updated whenever you run the function

Examples

## Not run: 
library(dplyr)

# data source: NCBI
db_download_ncbi()
src <- src_ncbi()
df <- tbl(src, "names")
filter(df, name_class == "scientific name")

# data source: ITIS
## download ITIS database
db_download_itis()
## connect to the ITIS database
src <- src_itis()
## use SQL syntax
sql_collect(src, "select * from hierarchy limit 5")
### or pipe the src to sql_collect
src %>% sql_collect("select * from hierarchy limit 5")
## use dplyr verbs
src %>%
  tbl("hierarchy") %>%
  filter(ChildrenCount > 1000)
## or create tbl object for repeated use
hiers <- src %>% tbl("hierarchy")
hiers %>% select(TSN, level)

# data source: The PlantList
## download tpl datababase
db_download_tpl()
## connecto the tpl database
src <- src_tpl()
## do queries
tpl <- tbl(src, "tpl")
filter(tpl, Family == "Pinaceae")

# data source: Catalogue of Life
## download col datababase
db_download_col()
## connec to the col database
src <- src_col()
## do queries
names <- tbl(src, "taxa")
select(names, taxonID, scientificName)

# data source: GBIF
## download gbif datababase
db_download_gbif()
## connecto the gbif database
src <- src_gbif()
## do queries
df <- tbl(src, "gbif")
select(df, taxonID, scientificName)

# data source: Wikidata
db_download_wikidata()
src <- src_wikidata()
df <- tbl(src, "wikidata")
filter(df, rank_id == "Q7432")

# data source: World Flora Online
db_download_wfo()
src <- src_wfo()
df <- tbl(src, "wfo")
filter(df, taxonID == "wfo-0000000010")

## End(Not run)

ropenscilabs/taxizedb documentation built on May 4, 2023, 7:05 a.m.