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.

Features

Bolognese reads and/or writes these metadata formats:

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

<?xml version="1.0" encoding="UTF-8"?> eLife 2050-084X 02 11 2014 3 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

<?xml version="1.0" encoding="UTF-8"?> 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 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

<?xml version="1.0" encoding="UTF-8"?> 10.5061/DRYAD.8515 1 Ollomo, Benjamin Durand, Patrick Prugnolle, Franck Douzery, Emmanuel J. P. Arnathau, Céline Nkoghe, Dieudonné Leroy, Eric Renaud, François 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

<?xml version="1.0" encoding="UTF-8"?> 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 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

<?xml version="1.0" encoding="UTF-8"?> 10.5438/4k3m-nyvg Fenner, Martin Martin Fenner http://orcid.org/0000-0003-1419-2405 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

<?xml version="1.0" encoding="UTF-8"?> 10.5438/qeg0-3gm3 Martin Fenner http://orcid.org/0000-0003-0077-4738 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. 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.