Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/datacite/bolognese

Ruby gem and command-line utility for conversion of DOI metadata
https://github.com/datacite/bolognese

Last synced: 3 months ago
JSON representation

Ruby gem and command-line utility for conversion of DOI metadata

Host: GitHub
URL: https://github.com/datacite/bolognese
Owner: datacite
License: mit
Created: 2017-02-13T13:58:12.000Z (over 7 years ago)
Default Branch: master
Last Pushed: 2024-02-28T07:33:12.000Z (8 months ago)
Last Synced: 2024-07-19T04:03:37.575Z (4 months ago)
Language: Ruby
Homepage:
Size: 9.75 MB
Stars: 40
Watchers: 15
Forks: 14
Open Issues: 14
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE.md
- Citation: CITATION

Awesome Lists containing this project

data-science-with-ruby - bolognese

README

[![Identifier](https://img.shields.io/badge/doi-10.5438%2Fn138--z3mk-fca709.svg)](https://doi.org/10.5438/n138-z3mk)
[![Gem Version](https://badge.fury.io/rb/bolognese.svg)](https://badge.fury.io/rb/bolognese)
![Build Ruby Gem](https://github.com/datacite/bolognese/workflows/Build%20Ruby%20Gem/badge.svg)
[![Code Climate](https://codeclimate.com/github/datacite/bolognese/badges/gpa.svg)](https://codeclimate.com/github/datacite/bolognese)
[![Test Coverage](https://codeclimate.com/github/datacite/bolognese/badges/coverage.svg)](https://codeclimate.com/github/datacite/bolognese/coverage)

# Bolognese: a Ruby library for conversion of DOI Metadata

Ruby gem and command-line utility for conversion of DOI metadata from and to different metadata formats, including [schema.org](https://schema.org).

## Features

Bolognese reads and/or writes these metadata formats:

Format
Name
Content Type
Read
Write

CrossRef Unixref XML
crossref
application/vnd.crossref.unixref+xml
Yes
No

DataCite XML
datacite
application/vnd.datacite.datacite+xml
Yes
Yes

DataCite JSON
datacite_json
application/vnd.datacite.datacite+json
Yes
Yes

Schema.org in JSON-LD
schema_org
application/vnd.schemaorg.ld+json
Yes
Yes

RDF XML
rdf_xml
application/rdf+xml
No
Yes

RDF Turtle
turtle
text/turtle
No
Yes

Citeproc JSON
citeproc
application/vnd.citationstyles.csl+json
Yes
Yes

Formatted text citation
citation
text/x-bibliography
No
Yes

Codemeta
codemeta
application/vnd.codemeta.ld+json
Yes
Yes

JATS
jats
application/vnd.jats+xml
No
Yes

CSV
csv
text/csv
No
Yes

BibTeX
bibtex
application/x-bibtex
Yes
Yes

RIS
ris
application/x-research-info-systems
Yes
Yes

Crosscite
crosscite
application/vnd.crosscite.crosscite+json
Yes
Yes

**Crosscite** is the format used internally by bolognese.

## Installation

Requires Ruby 2.2 or later. Then add the following to your `Gemfile` to install the
latest version:

```ruby
gem 'bolognese'
```

Then run `bundle install` to install into your environment.

You can also install the gem system-wide in the usual way:

```bash
gem install bolognese
```

## Commands

Run the `bolognese` command with either an identifier (DOI or URL) or filename:

```
bolognese https://doi.org/10.7554/elife.01567
```

```
bolognese example.xml
```

Bolognese can read BibTeX files (file extension `.bib`), RIS files (file extension `.ris`), Crossref or DataCite XML files (file extension `.xml`), DataCite JSON files (file extension `Citeproc JSON files ().

The input format (e.g. Crossref XML or BibteX) is automatically detected, but
you can also provide the format with the `--from` or `-f` flag. The supported
input formats are listed in the table above.

The output format is determined by the `--to` or `-t` flag, and defaults to `schema_org`.

Show all commands with `bolognese help`:

```
Commands:
bolognese # convert metadata
bolognese --version, -v # print the version
bolognese help [COMMAND] # Describe available commands or one specific command
```
## Errors

Errors are returned to STDOUT.

All DataCite XML input is validated against the corresponding schema version (kernel 2.1, 2.2, 3, or 4).

## Examples

Read Crossref XML:

```
bolognese https://doi.org/10.7554/elife.01567 -t crossref

eLife
2050-084X

02
11
2014

3

Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth

Martial
Sankar

Kaisa
Nieminen

Laura
Ragni

Ioannis
Xenarios

Christian S
Hardtke

02
11
2014

10.7554/eLife.01567

1
eLifesciences

www.elifesciences.org

false

2013-09-20
2013-12-24
2014-02-11

SystemsX

EMBO
http://dx.doi.org/10.13039/501100003043

Swiss National Science Foundation
http://dx.doi.org/10.13039/501100001711

University of Lausanne
http://dx.doi.org/10.13039/501100006390

http://creativecommons.org/licenses/by/3.0/
http://creativecommons.org/licenses/by/3.0/
http://creativecommons.org/licenses/by/3.0/

10.7554/eLife.01567
http://elifesciences.org/lookup/doi/10.7554/eLife.01567

...

Sankar
2014
10.5061/dryad.b835k

...

...

```

Convert Crossref XML to schema.org/JSON-LD:
```
bolognese https://doi.org/10.7554/elife.01567

{
"@context": "http://schema.org",
"@type": "ScholarlyArticle",
"@id": "https://doi.org/10.7554/elife.01567",
"url": "http://elifesciences.org/lookup/doi/10.7554/eLife.01567",
"additionalType": "JournalArticle",
"name": "Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth",
"author": [{
"@type": "Person",
"givenName": "Martial",
"familyName": "Sankar"
}, {
"@type": "Person",
"givenName": "Kaisa",
"familyName": "Nieminen"
}, {
"@type": "Person",
"givenName": "Laura",
"familyName": "Ragni"
}, {
"@type": "Person",
"givenName": "Ioannis",
"familyName": "Xenarios"
}, {
"@type": "Person",
"givenName": "Christian S",
"familyName": "Hardtke"
}],
"license": "http://creativecommons.org/licenses/by/3.0/",
"datePublished": "2014-02-11",
"dateModified": "2015-08-11T05:35:02Z",
"isPartOf": {
"@type": "Periodical",
"name": "eLife",
"issn": "2050-084X"
},
"citation": [{
"@type": "CreativeWork",
"@id": "https://doi.org/10.1038/nature02100",
"position": "1",
"datePublished": "2003"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1534/genetics.109.104976",
"position": "2",
"datePublished": "2009"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1034/j.1399-3054.2002.1140413.x",
"position": "3",
"datePublished": "2002"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1162/089976601750399335",
"position": "4",
"datePublished": "2001"
}, {
"@type": "CreativeWork",
"position": "5",
"datePublished": "1995"
}, {
"@type": "CreativeWork",
"position": "6",
"datePublished": "1993"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1016/j.semcdb.2009.09.009",
"position": "7",
"datePublished": "2009"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1242/dev.091314",
"position": "8",
"datePublished": "2013"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1371/journal.pgen.1002997",
"position": "9",
"datePublished": "2012"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1038/msb.2010.25",
"position": "10",
"datePublished": "2010"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1016/j.biosystems.2012.07.004",
"position": "11",
"datePublished": "2012"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1016/j.pbi.2005.11.013",
"position": "12",
"datePublished": "2006"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1105/tpc.110.076083",
"position": "13",
"datePublished": "2010"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1073/pnas.0808444105",
"position": "14",
"datePublished": "2008"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1016/0092-8674(89)90900-8",
"position": "15",
"datePublished": "1989"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1126/science.1066609",
"position": "16",
"datePublished": "2002"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1104/pp.104.040212",
"position": "17",
"datePublished": "2004"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1038/nbt1206-1565",
"position": "18",
"datePublished": "2006"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1073/pnas.77.3.1516",
"position": "19",
"datePublished": "1980"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1093/bioinformatics/btq046",
"position": "20",
"datePublished": "2010"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1105/tpc.111.084020",
"position": "21",
"datePublished": "2011"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.5061/dryad.b835k",
"position": "22",
"datePublished": "2014"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1016/j.cub.2008.02.070",
"position": "23",
"datePublished": "2008"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1111/j.1469-8137.2010.03236.x",
"position": "24",
"datePublished": "2010"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1007/s00138-011-0345-9",
"position": "25",
"datePublished": "2012"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1016/j.cell.2012.02.048",
"position": "26",
"datePublished": "2012"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.1038/ncb2764",
"position": "27",
"datePublished": "2013"
}],
"funder": [{
"@type": "Organization",
"name": "SystemsX"
}, {
"@type": "Organization",
"@id": "https://doi.org/10.13039/501100003043",
"name": "EMBO"
}, {
"@type": "Organization",
"@id": "https://doi.org/10.13039/501100001711",
"name": "Swiss National Science Foundation"
}, {
"@type": "Organization",
"@id": "https://doi.org/10.13039/501100006390",
"name": "University of Lausanne"
}],
"provider": {
"@type": "Organization",
"name": "Crossref"
}
}
```

Convert Crossref XML to DataCite XML:
```
bolognese https://doi.org/10.7554/elife.01567 -t datacite

10.7554/eLife.01567

Sankar, Martial
Martial
Sankar

Nieminen, Kaisa
Kaisa
Nieminen

Ragni, Laura
Laura
Ragni

Xenarios, Ioannis
Ioannis
Xenarios

Hardtke, Christian S
Christian S
Hardtke

Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth

eLife
2014
JournalArticle

SystemsX

EMBO
https://doi.org/10.13039/501100003043

Swiss National Science Foundation
https://doi.org/10.13039/501100001711

University of Lausanne
https://doi.org/10.13039/501100006390

2014-02-11
2015-08-11T05:35:02Z

https://doi.org/10.1038/nature02100
https://doi.org/10.1534/genetics.109.104976
https://doi.org/10.1034/j.1399-3054.2002.1140413.x
https://doi.org/10.1162/089976601750399335
https://doi.org/10.1016/j.semcdb.2009.09.009
https://doi.org/10.1242/dev.091314
https://doi.org/10.1371/journal.pgen.1002997
https://doi.org/10.1038/msb.2010.25
https://doi.org/10.1016/j.biosystems.2012.07.004
https://doi.org/10.1016/j.pbi.2005.11.013
https://doi.org/10.1105/tpc.110.076083
https://doi.org/10.1073/pnas.0808444105
https://doi.org/10.1016/0092-8674(89)90900-8
https://doi.org/10.1126/science.1066609
https://doi.org/10.1104/pp.104.040212
https://doi.org/10.1038/nbt1206-1565
https://doi.org/10.1073/pnas.77.3.1516
https://doi.org/10.1093/bioinformatics/btq046
https://doi.org/10.1105/tpc.111.084020
https://doi.org/10.5061/dryad.b835k
https://doi.org/10.1016/j.cub.2008.02.070
https://doi.org/10.1111/j.1469-8137.2010.03236.x
https://doi.org/10.1007/s00138-011-0345-9
https://doi.org/10.1016/j.cell.2012.02.048
https://doi.org/10.1038/ncb2764

Creative Commons Attribution 3.0 (CC-BY 3.0)

```
Convert Crossref XML to BibTeX:

```
bolognese https://doi.org/10.7554/elife.01567 -t bibtex

@article{https://doi.org/10.7554/elife.01567,
doi = {10.7554/eLife.01567},
url = {http://elifesciences.org/lookup/doi/10.7554/eLife.01567},
author = {Sankar, Martial and Nieminen, Kaisa and Ragni, Laura and Xenarios, Ioannis and Hardtke, Christian S},
title = {Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth},
journal = {eLife},
year = {2014}
}
```

Read DataCite XML:
```
bolognese 10.5061/DRYAD.8515 -t datacite

10.5061/DRYAD.8515
1

Ollomo, Benjamin

Durand, Patrick

Prugnolle, Franck

Douzery, Emmanuel J. P.

Arnathau, Céline

Nkoghe, Dieudonné

Leroy, Eric

Renaud, François

Data from: A new malaria agent in African hominids.

Dryad Digital Repository
2011

Phylogeny
Malaria
Parasites
Taxonomy
Mitochondrial genome
Africa
Plasmodium

DataPackage

Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.

10.5061/DRYAD.8515/1
10.5061/DRYAD.8515/2
10.1371/JOURNAL.PPAT.1000446
19478877

```

Convert DataCite XML to schema.org/JSON-LD:
```sh
bolognese 10.5061/DRYAD.8515

{
"@context": "http://schema.org",
"@type": "Dataset",
"@id": "https://doi.org/10.5061/dryad.8515",
"additionalType": "DataPackage",
"name": "Data from: A new malaria agent in African hominids.",
"alternateName": "Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.",
"author": [{
"@type": "Person",
"givenName": "Benjamin",
"familyName": "Ollomo"
}, {
"@type": "Person",
"givenName": "Patrick",
"familyName": "Durand"
}, {
"@type": "Person",
"givenName": "Franck",
"familyName": "Prugnolle"
}, {
"@type": "Person",
"givenName": "Emmanuel J. P.",
"familyName": "Douzery"
}, {
"@type": "Person",
"givenName": "Céline",
"familyName": "Arnathau"
}, {
"@type": "Person",
"givenName": "Dieudonné",
"familyName": "Nkoghe"
}, {
"@type": "Person",
"givenName": "Eric",
"familyName": "Leroy"
}, {
"@type": "Person",
"givenName": "François",
"familyName": "Renaud"
}],
"license": "http://creativecommons.org/publicdomain/zero/1.0/",
"version": "1",
"keywords": "Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium",
"datePublished": "2011",
"hasPart": [{
"@type": "CreativeWork",
"@id": "https://doi.org/10.5061/dryad.8515/1"
}, {
"@type": "CreativeWork",
"@id": "https://doi.org/10.5061/dryad.8515/2"
}],
"citation": [{
"@type": "CreativeWork",
"@id": "https://doi.org/10.1371/journal.ppat.1000446"
}],
"schemaVersion": "http://datacite.org/schema/kernel-3",
"publisher": {
"@type": "Organization",
"name": "Dryad Digital Repository"
},
"provider": {
"@type": "Organization",
"name": "DataCite"
}
}
```

Convert DataCite XML to schema version 4.0:
```
bolognese 10.5061/DRYAD.8515 -t datacite --schema_version http://datacite.org/schema/kernel-4

10.5061/DRYAD.8515

Ollomo, Benjamin
Benjamin
Ollomo

Durand, Patrick
Patrick
Durand

Prugnolle, Franck
Franck
Prugnolle

Douzery, Emmanuel J. P.
Emmanuel J. P.
Douzery

Arnathau, Céline
Céline
Arnathau

Nkoghe, Dieudonné
Dieudonné
Nkoghe

Leroy, Eric
Eric
Leroy

Renaud, François
François
Renaud

Data from: A new malaria agent in African hominids.

Dryad Digital Repository
2011
DataPackage

Ollomo B, Durand P, Prugnolle F, Douzery EJP, Arnathau C, Nkoghe D, Leroy E, Renaud F (2009) A new malaria agent in African hominids. PLoS Pathogens 5(5): e1000446.

Phylogeny
Malaria
Parasites
Taxonomy
Mitochondrial genome
Africa
Plasmodium

2011

https://doi.org/10.5061/dryad.8515/1
https://doi.org/10.5061/dryad.8515/2
https://doi.org/10.1371/journal.ppat.1000446

1

Public Domain (CC0 1.0)

```

Convert DataCite XML to Codemeta:

```
bolognese https://doi.org/10.5063/f1m61h5x -t codemeta

{
"@context":"https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
"@type":"SoftwareSourceCode",
"@id":"https://doi.org/10.5063/f1m61h5x",
"identifier":"https://doi.org/10.5063/f1m61h5x",
"title":"dataone: R interface to the DataONE network of data repositories",
"agents":{
"@type":"Person",
"givenName":"Matthew B.",
"familyName":"Jones"
},
"datePublished":"2016",
"publisher":{
"@type":"Organization",
"name":"KNB Data Repository"
}
}
```

Convert DataCite XML to BibTeX:

```
bolognese 10.5061/DRYAD.8515 -t bibtex

@misc{https://doi.org/10.5061/dryad.8515,
doi = {10.5061/DRYAD.8515},
author = {Ollomo, Benjamin and Durand, Patrick and Prugnolle, Franck and Douzery, Emmanuel J. P. and Arnathau, Céline and Nkoghe, Dieudonné and Leroy, Eric and Renaud, François},
keywords = {Phylogeny, Malaria, Parasites, Taxonomy, Mitochondrial genome, Africa, Plasmodium},
title = {Data from: A new malaria agent in African hominids.},
publisher = {Dryad Digital Repository},
year = {2011}
}
```

Convert schema.org/JSON-LD to DataCite XML:

```
bolognese https://blog.datacite.org/eating-your-own-dog-food -t datacite

10.5438/4k3m-nyvg

Fenner, Martin
Martin
Fenner
http://orcid.org/0000-0003-1419-2405

Eating your own Dog Food

DataCite
2016
BlogPosting

MS-49-3632-5083

datacite
doi
metadata
featured

2016-12-20
2016-12-20
2016-12-20

https://doi.org/10.5438/0000-00ss
https://doi.org/10.5438/0012
https://doi.org/10.5438/55e5-t5c0

1.0

Eating your own dog food is a slang term to describe that an organization should itself use the products and services it provides. For DataCite this means that we should use DOIs with appropriate metadata and strategies for long-term preservation for...

```

Convert schema.org/JSON-LD to BibTeX:

```
bolognese https://blog.datacite.org/eating-your-own-dog-food -t bibtex

@article{https://doi.org/10.5438/4k3m-nyvg,
doi = {10.5438/4k3m-nyvg},
url = {https://blog.datacite.org/eating-your-own-dog-food},
author = {Fenner, Martin},
keywords = {datacite, doi, metadata, featured},
title = {Eating your own Dog Food},
publisher = {DataCite},
year = {2016}
}
```

Convert Codemeta to schema.org/JSON-LD:

```
bolognese https://github.com/datacite/maremma

{
"@context":"http://schema.org",
"@type":"SoftwareSourceCode",
"@id":"https://doi.org/10.5438/qeg0-3gm3",
"url":"https://github.com/datacite/maremma",
"name":"Maremma: a Ruby library for simplified network calls",
"author":{
"@type":"person",
"@id":"http://orcid.org/0000-0003-0077-4738",
"name":"Martin Fenner"
},
"description":"Simplifies network calls, including json/xml parsing and error handling. Based on Faraday.",
"keywords":"faraday, excon, net/http",
"dateCreated":"2015-11-28",
"datePublished":"2017-02-24",
"dateModified":"2017-02-24",
"publisher":{
"@type":"Organization",
"name":"DataCite"
}
}
```

Convert Codemeta to DataCite XML:

```
bolognese https://github.com/datacite/maremma -t datacite

10.5438/qeg0-3gm3

Martin Fenner
http://orcid.org/0000-0003-0077-4738

Maremma: a Ruby library for simplified network calls

DataCite
2017
SoftwareSourceCode

faraday
excon
net/http

2015-11-28
2017-02-24
2017-02-24

Simplifies network calls, including json/xml parsing and error handling. Based on Faraday.

```

## Development

We use rspec for unit testing:

```
bundle exec rspec
```

Follow along via [Github Issues](https://github.com/datacite/bolognese/issues).
Please open an issue if conversion fails or metadata are not properly supported.

### Note on Patches/Pull Requests

* Fork the project
* Write tests for your new feature or a test that reproduces a bug
* Implement your feature or make a bug fix
* Do not mess with Rakefile, version or history
* Commit, push and make a pull request. Bonus points for topical branches.

## License
**bolognese** is released under the [MIT License](https://github.com/datacite/bolognese/blob/master/LICENSE.md).