taxizedb

Tools for Working with Taxonomic SQL Databases

https://github.com/ropensci/taxizedb

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
✓
DOI references
Found 2 DOI reference(s) in README
✓
Academic publication links
Links to: ncbi.nlm.nih.gov, zenodo.org
✓
Committers with academic emails
1 of 10 committers (10.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.5%) to scientific vocabulary

Keywords

itis r r-package rstats taxize taxonomic-databases taxonomy

Keywords from Contributors

genome biodiversity caching mock nomenclature darwincore biology geocode conservation http-mock

Last synced: 6 months ago · JSON representation

Repository

Tools for Working with Taxonomic SQL Databases

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage:
Size: 453 KB

Statistics

Stars: 33
Watchers: 5
Forks: 9
Open Issues: 14
Releases: 7

Topics

itis r r-package rstats taxize taxonomic-databases taxonomy

Created almost 10 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

---
output: github_document
editor_options: 
  chunk_output_type: console
---


taxizedb
========

```{r echo=FALSE}
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  collapse = TRUE,
  comment = "#>"
)
```

[![status](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![cran checks](https://badges.cranchecks.info/worst/taxizedb.svg)](https://badges.cranchecks.info/worst/taxizedb.svg)
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`taxizedb` - Tools for Working with Taxonomic Databases

Docs: 

`taxizedb` is an R package for interacting with taxonomic databases. Its functionality can be divided in two parts: 1. You can download the databases to your platform 2. You can query the downloaded databases to retrieve taxonomic information.

This two step approach is different from tools which interact with web services for each query, and has a number of advantages:

* Once you download a database you can work with it offline
* Once you download a database querying it is super fast
* As long as you store your database files all the queries in your analysis will be fully reproducible

## Data sources

When you download a database with `taxizedb` it will automatically convert it to SQLite and then all query functions will interact with this SQLite database. However, not all taxonomic databases are publicly available, or can be converted to SQLite. The following databases are supported:

- [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy)
- [ITIS](https://itis.gov/)
- [World Flora Online (WFO)](https://www.worldfloraonline.org/)
- [Catalogue of Life (COL)](https://www.catalogueoflife.org/)
- [Global Biodiversity Information Facility (GBIF)](https://www.gbif.org/)
- [Wikidata](https://zenodo.org/records/1213477)

Get in touch [in the issues](https://github.com/ropensci/taxizedb/issues) with
any ideas on new data sources.

## Data sources - legacy support

[The Plant List (TPL)](https://en.wikipedia.org/wiki/The_Plant_List) has been replaced by World Flora Online. The website seems to be down so `taxizedb` can no longer facilitate new downloads. However, already downloaded database files can still be queried using `taxizedb` functions, for reproducibility.

## Package API

This package for each data sources performs the following tasks:

* Downloaded taxonomic databases `db_download_*`
* Create `dplyr` SQL backend via `dbplyr::src_dbi` - `src_*` 
* Query and get data back into a data.frame - `sql_collect`
* Manage cached database files - `tdb_cache`
* Retrieve immediate descendents of a taxon - `children`
* Retrieve the taxonomic hierarchies from local database - `classification`
* Retrieve all taxa descending from a vector of taxa - `downstream`
* Convert species names to taxon IDs - `name2taxid`
* Convert taxon IDs to species names - `taxid2name`
* Convert taxon IDs to ranks - `taxid2rank`

You can use the `src` connections with `dplyr`, etc. to do operations downstream. Or use the database connection to do raw SQL queries.

## Installation

CRAN version

```{r eval=FALSE}
install.packages("taxizedb")
```

dev version

```{r eval=FALSE}
remotes::install_github("ropensci/taxizedb")
```

## Citation

To cite taxizedb in publications use:

* Chamberlain S, Arendsee Z, Stirling T (2023). taxizedb: Tools for Working with 'Taxonomic' Databases. R package version 0.3.1. 

## Meta

* Please [report any issues, bugs or feature requests](https://github.com/ropensci/taxizedb/issues).
* License: MIT
* Get citation information for `taxizedb` in R with `citation(package = 'taxizedb')`
* Please note that this package is released with a [Contributor Code of Conduct](https://ropensci.org/code-of-conduct). By contributing to this project, you agree to abide by its terms.

[![ropensci](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)

Owner

Name: rOpenSci
Login: ropensci
Kind: organization
Email: info@ropensci.org
Location: Berkeley, CA

Website: https://ropensci.org/
Twitter: rOpenSci
Repositories: 307
Profile: https://github.com/ropensci

CodeMeta (codemeta.json)

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GitHub Events

Total

Issues event: 2
Watch event: 3
Issue comment event: 4
Push event: 7
Pull request event: 10
Fork event: 2

Last Year

Issues event: 2
Watch event: 3
Issue comment event: 4
Push event: 7
Pull request event: 10
Fork event: 2

Committers

Last synced: about 2 years ago

All Time

Total Commits: 232
Total Committers: 10
Avg Commits per committer: 23.2
Development Distribution Score (DDS): 0.444

Past Year

Commits: 25
Committers: 3
Avg Commits per committer: 8.333
Development Distribution Score (DDS): 0.16

Top Committers

Name	Email	Commits
Scott Chamberlain	m**s@g**m	129
Zebulun Arendsee	a**e@i**u	46
Tamas Stirling	s**s@g**m	21
Carl Boettiger	c**g@g**m	16
Scott Chamberlain	s**t@f**m	10
T D James	t**1@u**m	4
Maëlle Salmon	m**n@y**e	3
Gaopeng Li	l**c@g**m	1
Rekyt	m**e@e**r	1
rOpenSci Bot	m**t@g**m	1

Committer Domains (Top 20 + Academic)

ens-lyon.fr: 1 fastmail.com: 1 iastate.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 65
Total pull requests: 39
Average time to close issues: 11 months
Average time to close pull requests: 12 days
Total issue authors: 25
Total pull request authors: 9
Average comments per issue: 3.52
Average comments per pull request: 2.23
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 2
Pull requests: 16
Average time to close issues: N/A
Average time to close pull requests: about 10 hours
Issue authors: 1
Pull request authors: 1
Average comments per issue: 0.0
Average comments per pull request: 0.31
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sckott (28)
stitam (9)
KaiAragaki (4)
arendsee (3)
cboettig (2)
kwymangrothem (1)
sagesteppe (1)
dlebauer (1)
pederengelstad (1)
GossypiumH (1)
gpli (1)
andzandz11 (1)
brunobrr (1)
mkhemmani (1)
NgAMB (1)

Pull Request Authors

stitam (24)
arendsee (7)
sckott (3)
KaiAragaki (2)
cboettig (2)
gpli (1)
tdjames1 (1)
kylebuscaglia (1)
Rekyt (1)

Top Labels

Issue Labels

bug (3) data-source (2) feature (1)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- cran 359 last-month
Total docker downloads: 88,618

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 10
(may contain duplicates)
Total versions: 9
Total maintainers: 1

cran.r-project.org: taxizedb

Offline Access to Taxonomic Databases

Homepage: https://docs.ropensci.org/taxizedb/
Documentation: http://cran.r-project.org/web/packages/taxizedb/taxizedb.pdf
License: MIT + file LICENSE
Latest release: 0.3.2
published 9 months ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 10
Downloads: 359 Last month
Docker Downloads: 88,618

Rankings

Docker downloads count: 0.0%

Dependent repos count: 9.2%

Forks count: 9.6%

Stargazers count: 9.7%

Average: 14.9%

Dependent packages count: 28.7%

Downloads: 32.3%

Maintainers (1)

stirling.tamas@gmail.com

Last synced: 6 months ago

conda-forge.org: r-taxizedb

Homepage: https://ropensci.github.io/taxizedb/, https://github.com/ropensci/taxizedb
License: MIT
Latest release: 0.3.0
published about 5 years ago

Versions: 2
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 34.0%

Stargazers count: 43.4%

Average: 44.1%

Forks count: 47.7%

Dependent packages count: 51.2%

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

DBI >= 0.6 imports
RSQLite >= 1.1.2 imports
curl >= 2.4 imports
dbplyr >= 1.0.0 imports
dplyr >= 0.7.0 imports
hoardr >= 0.1.0 imports
magrittr >= 1.5 imports
readr >= 1.1.1 imports
rlang * imports
tibble * imports
taxize * suggests
testthat * suggests

.github/workflows/R-check.yaml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact v2 composite
r-lib/actions/setup-pandoc v1 composite
r-lib/actions/setup-r v1 composite

.github/workflows/build-docs.yml actions

actions/cache v1 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite

.circleci/Dockerfile docker

rocker/tidyverse latest build

docker-compose.yml docker

mariadb latest
postgres latest