https://github.com/sckott/gbif-backbone-sql
GBIF Darwin Core taxonomic backbone to SQLite
https://github.com/sckott/gbif-backbone-sql
Last synced: about 1 year ago
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GBIF Darwin Core taxonomic backbone to SQLite
- Host: GitHub
- URL: https://github.com/sckott/gbif-backbone-sql
- Owner: sckott
- License: mit
- Created: 2016-08-16T16:11:02.000Z (almost 10 years ago)
- Default Branch: main
- Last Pushed: 2024-04-10T20:26:36.000Z (over 2 years ago)
- Last Synced: 2025-06-28T10:14:46.056Z (about 1 year ago)
- Language: Ruby
- Homepage:
- Size: 41 KB
- Stars: 4
- Watchers: 4
- Forks: 2
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
GBIF taxonomy as SQLite
=======================
GBIF backbone taxonomy as SQLite DB
__Note:__ The backbone as sqlite is up at -
You can continue reading if you want to know the details of how it got there, and/or if you want to
run this darwin-core to sql conversion yourself.
## how we do
* download GBIF backbone taxonomy from as Darwin Core Archive
* unzip
* create sqlite DB `gbif.sqlite`
* import `taxon.txt` into sqlite DB
* zip up sqlite file
* upload `gbif.zip` to Amazon S3
All above is run once per day on [Github Actions](https://github.com/ropenscilabs/gbif-backbone-sql/actions?query=workflow%3Abuild-sqlite)
## Usage
download
```
git clone https://github.com/ropensci/gbif-backbone-sql.git
cd gbif-backbone-sql
```
bundle it
```
bundle install
```
```
rake --tasks
```
```
rake clean # clean files
rake fetch # get and unzip backbone
rake hello # say hello
rake s3 # upload database to s3
rake spine # get backbone, convert to sql, upload to amazon s3
rake sql # create sql database
rake zip # create zip file
```
`rake spine` does all the things
Or, you can do each separately with `rake fetch` then `rake sql`, then `rake zip`, then `rake s3`
### 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`
## Backbone as sqlite
## info
* GBIF backbone taxonomy citation:
> GBIF Secretariat: GBIF Backbone Taxonomy. doi:10.15468/39omei
Accessed via http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c on 2016-08-16
* GBIF backbone taxonomy license: `CC BY 3.0`