col-sql's Introduction

Catalogue of Life taxonomy as SQLite

COL taxonomy as SQLite DB

TLDR: The backbone as sqlite is up at https://s3-us-west-2.amazonaws.com/taxize-dbs/col.zip

how we do

download COL taxonomy from http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c as Darwin Core Archive
unzip
create sqlite DB col.sqlite
import data files into sqlite DB
zip up sqlite file
upload col.zip to Amazon S3

All above is run once per day on Github Actions

Usage

download

git clone https://github.com/ropensci/col-sql.git
cd col-sql

bundle it

bundle install

rake --tasks

rake all    # get data, convert to sql, upload to amazon s3
rake clean  # delete files not needed
rake fetch  # get and unzip data
rake s3     # upload database to s3
rake sql    # create sql database
rake zip    # create zip file

rake all does all the things

Or, you can do each separately with rake fetch then rake sql, then rake zip, then rake s3, then rake clean

Env vars

rake s3 requires AWS keys. If you want to upload to AWS, make sure you have env vars with the names AWS_S3_WRITE_ACCESS_KEY and AWS_S3_WRITE_SECRET_KEY

COL sqlite file

https://taxize-dbs.s3-us-west-2.amazonaws.com/col.zip

COL taxonomy citation:

Roskov Y.; Ower G.; Orrell T.; Nicolson D.; Bailly N.; Kirk P.M.; Bourgoin T.; DeWalt R.E.; Decock W.; Nieukerken E. van; Penev L.; eds. (2020). Species 2000 & ITIS Catalogue of Life, 2020-06-04 Beta. Digital resource at www.catalogueoflife.org/col. Species 2000: Naturalis, Leiden, the Netherlands. ISSN 2405-8858.

See also http://www.catalogueoflife.org/col/info/cite for how to cite COL individual databases, and more.

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