bold

Interface to the Bold Systems barcode webservice

https://github.com/ropensci/bold

Science Score: 36.0%

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
○
Academic publication links
✓
Committers with academic emails
3 of 8 committers (37.5%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.0%) to scientific vocabulary

Keywords

api-wrapper barcodes r r-package rstats sequences taxize

Keywords from Contributors

bicycle-hire bicycle-hire-systems bike-data bike-hire

Last synced: 4 months ago · JSON representation

Repository

Interface to the Bold Systems barcode webservice

Basic Info

Host: GitHub
Owner: ropensci
License: other
Language: R
Default Branch: master
Homepage: https://docs.ropensci.org/bold
Size: 12.3 MB

Statistics

Stars: 18
Watchers: 5
Forks: 11
Open Issues: 6
Releases: 14

Topics

api-wrapper barcodes r r-package rstats sequences taxize

Created over 14 years ago · Last pushed 12 months ago

Metadata Files

Readme Changelog Contributing License Codemeta

README.Rmd

bold
====

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

[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![cran version](https://www.r-pkg.org/badges/version/bold)](https://cran.r-project.org/package=bold)
[![cran checks](https://cranchecks.info/badges/worst/bold)](https://cranchecks.info/pkgs/bold)
[![R-check](https://github.com/ropensci/bold/workflows/R-check/badge.svg)](https://github.com/ropensci/bold/actions/)
[![codecov.io](https://codecov.io/github/ropensci/bold/coverage.svg?branch=master)](https://codecov.io/github/ropensci/bold?branch=master)
[![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/bold)](https://github.com/r-hub/cranlogs.app)

`bold` accesses BOLD barcode data.

The Barcode of Life Data Systems (BOLD) is designed to support the generation and application of DNA barcode data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench.

This package retrieves data from the BOLD database of barcode clusters, and allows for searching of over 1.7M public records using multiple search criteria including sequence data, specimen data, specimen *plus* sequence data, as well as trace files.

Documentation for the BOLD API: http://v4.boldsystems.org/index.php/api_home

See also the taxize book for more options for taxonomic workflows with BOLD: https://taxize.dev/

## Installation

__Installation instructions__

__Stable Version__

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

__Development Version__

Install `sangerseqR` first (used in function `bold::bold_trace()` only)

For R < 3.5

```{r eval=FALSE}
source("http://bioconductor.org/biocLite.R")
biocLite("sangerseqR")
```

For R >= 3.5

```{r eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("sangerseqR")
```

Then install `bold`

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


## Usage
```{r}
library("bold")
```


### Search for sequence data only

By default you download `fasta` file, which is given back to you as a `data.frame`

```{r}
res <- bold_seq(taxon='Coelioxys')
head(res)
```

You can optionally get back the `crul` response object

```{r}
res <- bold_seq(taxon='Coelioxys', response=TRUE)
res$response_headers
```

### Search for specimen data only

By default you download `tsv` format data, which is given back to you as a `data.frame`

```{r}
res <- bold_specimens(taxon='Osmia')
head(res[,1:8])
```

### Search for specimen plus sequence data

By default you download `tsv` format data, which is given back to you as a `data.frame`

```{r}
res <- bold_seqspec(taxon='Osmia', sepfasta=TRUE)
res$fasta[1:2]
```

Or you can index to a specific sequence like

```{r}
res$fasta['GBAH0293-06']
```

### Get trace files

This function downloads files to your machine - it does not load them into your R session - but prints out where the files are for your information.

```{r}
x <- bold_trace(ids = 'ACRJP618-11', progress = FALSE)
read_trace(x$ab1)
```

### Large data

Sometimes with `bold_seq()` you request a lot of data, which can cause problems due 
to BOLD's servers. 

An example is the taxonomic name _Arthropoda_. When you send a request like 
`bold_seq(taxon = "Arthropoda")` BOLD attempts to give you back sequences
for all records under _Arthropoda_. This, as you can imagine, is a lot of 
sequences. 


```{r}
library("taxize")
```

Using `taxize::downstream` get children of _Arthropoda_

```{r}
x <- downstream("Arthropoda", db = "ncbi", downto = "class")
nms <- x$Arthropoda$childtaxa_name
```

Optionally, check that the name exists in BOLD's data. Any that are not in 
BOLD will give back a row of NAs

```{r}
checks <- bold_tax_name(nms)
# all is good
checks[,1:5]
```

Then pass those names to `bold_seq()`. You could pass all names in at once,
but we're trying to avoid the large data request problem here, so run each 
one separately with `lapply` or a for loop like request. 

```{r eval = FALSE}
out <- lapply(nms, bold_seq)
```

## Citation

Get citation information for `bold` in R by running: `citation(package = 'bold')`

## Meta

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

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: 4
Issue comment event: 12
Push event: 6
Pull request event: 4
Create event: 1

Last Year

Issues event: 2
Watch event: 4
Issue comment event: 12
Push event: 6
Pull request event: 4
Create event: 1

Committers

Last synced: almost 2 years ago

All Time

Total Commits: 431
Total Committers: 8
Avg Commits per committer: 53.875
Development Distribution Score (DDS): 0.364

Past Year

Commits: 117
Committers: 1
Avg Commits per committer: 117.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Scott Chamberlain	m**s@g**m	274
Salix	3****d	146
Grace Li	g**8@b**u	4
Francois Michonneau	f**u@g**m	2
katieroserice	k**e@b**u	2
Chris Fields	c**s@i**u	1
Diana Ly	d**6@g**m	1
ropenscibot	m**t@g**m	1

Committer Domains (Top 20 + Academic)

berkeley.edu: 2 illinois.edu: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 84
Total pull requests: 16
Average time to close issues: 4 months
Average time to close pull requests: about 21 hours
Total issue authors: 25
Total pull request authors: 7
Average comments per issue: 2.58
Average comments per pull request: 1.25
Merged pull requests: 15
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 1
Average time to close issues: N/A
Average time to close pull requests: 1 minute
Issue authors: 0
Pull request authors: 1
Average comments per issue: 0
Average comments per pull request: 0.0
Merged pull requests: 1
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

sckott (44)
salix-d (6)
devonorourke (5)
dougwyu (5)
tadeu95 (3)
jphill01 (2)
griffinp (2)
boopsboops (2)
mdogniez (1)
LunaSare (1)
VascoElbrecht (1)
pieterprovoost (1)
vanessamata (1)
bastianegeter (1)
cjfields (1)

Pull Request Authors

salix-d (13)
diana-ly (1)
graceli8 (1)
sckott (1)
katieroserice (1)
fmichonneau (1)
cjfields (1)

Top Labels

Issue Labels

bug (14) API-related (5) enhancement (4) question (1) later (1) Beginner (1) asking for feedback (1)

Pull Request Labels

Packages

Total packages: 1
Total downloads: unknown

Total dependent packages: 1
Total dependent repositories: 0
Total versions: 7

conda-forge.org: r-bold

Homepage: https://github.com/ropensci/bold
License: MIT
Latest release: 1.2.0
published over 4 years ago

Versions: 7
Dependent Packages: 1
Dependent Repositories: 0

Rankings

Dependent packages count: 28.8%

Dependent repos count: 34.0%

Average: 37.7%

Forks count: 40.0%

Stargazers count: 47.8%

Last synced: 5 months ago

Dependencies

DESCRIPTION cran

crul >= 0.3.8 imports
data.table * imports
jsonlite * imports
plyr * imports
reshape * imports
stringr * imports
tibble * imports
xml2 * imports
sangerseqR * suggests
testthat * suggests
vcr >= 0.5.4 suggests

.github/workflows/R-check.yaml actions

actions/checkout v3 composite
actions/upload-artifact master composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

bold

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

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Topics

Metadata Files

README.Rmd

Owner

CodeMeta (codemeta.json)

GitHub Events

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All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

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Packages

conda-forge.org: r-bold

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