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

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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:

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:

gem 'bolognese'

Then run bundle install to install into your environment.

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

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"?>
<doi_records>
  <doi_record owner="10.7554" timestamp="2015-08-11 07:35:02">
    <crossref>
      <journal>
        <journal_metadata language="en">
          <full_title>eLife</full_title>
          <issn media_type="electronic">2050-084X</issn>
        </journal_metadata>
        <journal_issue>
          <publication_date media_type="online">
            <month>02</month>
            <day>11</day>
            <year>2014</year>
          </publication_date>
          <journal_volume>
            <volume>3</volume>
          </journal_volume>
        </journal_issue>
        <journal_article publication_type="full_text">
          <titles>
            <title>Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth</title>
          </titles>
          <contributors>
            <person_name contributor_role="author" sequence="first">
              <given_name>Martial</given_name>
              <surname>Sankar</surname>
            </person_name>
            <person_name contributor_role="author" sequence="additional">
              <given_name>Kaisa</given_name>
              <surname>Nieminen</surname>
            </person_name>
            <person_name contributor_role="author" sequence="additional">
              <given_name>Laura</given_name>
              <surname>Ragni</surname>
            </person_name>
            <person_name contributor_role="author" sequence="additional">
              <given_name>Ioannis</given_name>
              <surname>Xenarios</surname>
            </person_name>
            <person_name contributor_role="author" sequence="additional">
              <given_name>Christian S</given_name>
              <surname>Hardtke</surname>
            </person_name>
          </contributors>
          <publication_date media_type="online">
            <month>02</month>
            <day>11</day>
            <year>2014</year>
          </publication_date>
          <publisher_item>
            <identifier id_type="doi">10.7554/eLife.01567</identifier>
          </publisher_item>
          <crossmark>
            <crossmark_version>1</crossmark_version>
            <crossmark_policy>eLifesciences</crossmark_policy>
            <crossmark_domains>
              <crossmark_domain>
                <domain>www.elifesciences.org</domain>
              </crossmark_domain>
            </crossmark_domains>
            <crossmark_domain_exclusive>false</crossmark_domain_exclusive>
            <custom_metadata>
              <assertion name="received" label="Received" group_name="publication_history" group_label="Publication History" order="0">2013-09-20</assertion>
              <assertion name="accepted" label="Accepted" group_name="publication_history" group_label="Publication History" order="1">2013-12-24</assertion>
              <assertion name="published" label="Published" group_name="publication_history" group_label="Publication History" order="2">2014-02-11</assertion>
              <program name="fundref">
                <assertion name="fundgroup">
                  <assertion name="funder_name">SystemsX</assertion>
                </assertion>
                <assertion name="fundgroup">
                  <assertion name="funder_name">
                    EMBO
                    <assertion name="funder_identifier">http://dx.doi.org/10.13039/501100003043</assertion>
                  </assertion>
                </assertion>
                <assertion name="fundgroup">
                  <assertion name="funder_name">
                    Swiss National Science Foundation
                    <assertion name="funder_identifier">http://dx.doi.org/10.13039/501100001711</assertion>
                  </assertion>
                </assertion>
                <assertion name="fundgroup">
                  <assertion name="funder_name">
                    University of Lausanne
                    <assertion name="funder_identifier" provider="crossref">http://dx.doi.org/10.13039/501100006390</assertion>
                  </assertion>
                </assertion>
              </program>
              <program name="AccessIndicators">
                <license_ref applies_to="vor">http://creativecommons.org/licenses/by/3.0/</license_ref>
                <license_ref applies_to="am">http://creativecommons.org/licenses/by/3.0/</license_ref>
                <license_ref applies_to="tdm">http://creativecommons.org/licenses/by/3.0/</license_ref>
              </program>
            </custom_metadata>
          </crossmark>
          <doi_data>
            <doi>10.7554/eLife.01567</doi>
            <resource>http://elifesciences.org/lookup/doi/10.7554/eLife.01567</resource>
          </doi_data>
          <citation_list>
            ...
            <citation key="22">
              <author>Sankar</author>
              <cYear>2014</cYear>
              <doi>10.5061/dryad.b835k</doi>
            </citation>
            ...
          </citation_list>
          <component_list>
           ...
          </component_list>
        </journal_article>
      </journal>
    </crossref>
  </doi_record>
</doi_records>

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"?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
  <identifier identifierType="DOI">10.7554/eLife.01567</identifier>
  <creators>
    <creator>
      <creatorName>Sankar, Martial</creatorName>
      <givenName>Martial</givenName>
      <familyName>Sankar</familyName>
    </creator>
    <creator>
      <creatorName>Nieminen, Kaisa</creatorName>
      <givenName>Kaisa</givenName>
      <familyName>Nieminen</familyName>
    </creator>
    <creator>
      <creatorName>Ragni, Laura</creatorName>
      <givenName>Laura</givenName>
      <familyName>Ragni</familyName>
    </creator>
    <creator>
      <creatorName>Xenarios, Ioannis</creatorName>
      <givenName>Ioannis</givenName>
      <familyName>Xenarios</familyName>
    </creator>
    <creator>
      <creatorName>Hardtke, Christian S</creatorName>
      <givenName>Christian S</givenName>
      <familyName>Hardtke</familyName>
    </creator>
  </creators>
  <titles>
    <title>Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth</title>
  </titles>
  <publisher>eLife</publisher>
  <publicationYear>2014</publicationYear>
  <resourceType resourceTypeGeneral="Text">JournalArticle</resourceType>
  <fundingReferences>
    <fundingReference>
      <funderName>SystemsX</funderName>
    </fundingReference>
    <fundingReference>
      <funderName>EMBO</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">https://doi.org/10.13039/501100003043</funderIdentifier>
    </fundingReference>
    <fundingReference>
      <funderName>Swiss National Science Foundation</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">https://doi.org/10.13039/501100001711</funderIdentifier>
    </fundingReference>
    <fundingReference>
      <funderName>University of Lausanne</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">https://doi.org/10.13039/501100006390</funderIdentifier>
    </fundingReference>
  </fundingReferences>
  <dates>
    <date dateType="Issued">2014-02-11</date>
    <date dateType="Updated">2015-08-11T05:35:02Z</date>
  </dates>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1038/nature02100</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1534/genetics.109.104976</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1034/j.1399-3054.2002.1140413.x</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1162/089976601750399335</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1016/j.semcdb.2009.09.009</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1242/dev.091314</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1371/journal.pgen.1002997</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1038/msb.2010.25</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1016/j.biosystems.2012.07.004</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1016/j.pbi.2005.11.013</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1105/tpc.110.076083</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1073/pnas.0808444105</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1016/0092-8674(89)90900-8</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1126/science.1066609</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1104/pp.104.040212</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1038/nbt1206-1565</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1073/pnas.77.3.1516</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1093/bioinformatics/btq046</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1105/tpc.111.084020</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.5061/dryad.b835k</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1016/j.cub.2008.02.070</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1111/j.1469-8137.2010.03236.x</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1007/s00138-011-0345-9</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1016/j.cell.2012.02.048</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1038/ncb2764</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/3.0/">Creative Commons Attribution 3.0 (CC-BY 3.0)</rights>
  </rightsList>
</resource>

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"?>
<resource
    xmlns="http://datacite.org/schema/kernel-3"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:mets="http://www.loc.gov/METS/"
    xmlns:dspace="http://www.dspace.org/xmlns/dspace/dim"
    xmlns:dim="http://www.dspace.org/xmlns/dspace/dim"
    xmlns:dryad="http://purl.org/dryad/terms/"
    xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
    <identifier identifierType="DOI">10.5061/DRYAD.8515</identifier>
    <version>1</version>
    <creators>
        <creator>
            <creatorName>Ollomo, Benjamin</creatorName>
        </creator>
        <creator>
            <creatorName>Durand, Patrick</creatorName>
        </creator>
        <creator>
            <creatorName>Prugnolle, Franck</creatorName>
        </creator>
        <creator>
            <creatorName>Douzery, Emmanuel J. P.</creatorName>
        </creator>
        <creator>
            <creatorName>Arnathau, Céline</creatorName>
        </creator>
        <creator>
            <creatorName>Nkoghe, Dieudonné</creatorName>
        </creator>
        <creator>
            <creatorName>Leroy, Eric</creatorName>
        </creator>
        <creator>
            <creatorName>Renaud, François</creatorName>
        </creator>
    </creators>
    <titles>
        <title>Data from: A new malaria agent in African hominids.</title>
    </titles>
    <publisher>Dryad Digital Repository</publisher>
    <publicationYear>2011</publicationYear>
    <subjects>
        <subject>Phylogeny</subject>
        <subject>Malaria</subject>
        <subject>Parasites</subject>
        <subject>Taxonomy</subject>
        <subject>Mitochondrial genome</subject>
        <subject>Africa</subject>
        <subject>Plasmodium</subject>
    </subjects>
    <resourceType resourceTypeGeneral="Dataset">DataPackage</resourceType>
    <alternateIdentifiers>
        <alternateIdentifier alternateIdentifierType="citation">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.</alternateIdentifier>
    </alternateIdentifiers>
    <relatedIdentifiers>
        <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/1</relatedIdentifier>
        <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">10.5061/DRYAD.8515/2</relatedIdentifier>
        <relatedIdentifier relatedIdentifierType="DOI" relationType="IsReferencedBy">10.1371/JOURNAL.PPAT.1000446</relatedIdentifier>
        <relatedIdentifier relatedIdentifierType="PMID" relationType="IsReferencedBy">19478877</relatedIdentifier>
    </relatedIdentifiers>
    <rightsList>
        <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/"/>
    </rightsList>
</resource>

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

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"?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
  <identifier identifierType="DOI">10.5061/DRYAD.8515</identifier>
  <creators>
    <creator>
      <creatorName>Ollomo, Benjamin</creatorName>
      <givenName>Benjamin</givenName>
      <familyName>Ollomo</familyName>
    </creator>
    <creator>
      <creatorName>Durand, Patrick</creatorName>
      <givenName>Patrick</givenName>
      <familyName>Durand</familyName>
    </creator>
    <creator>
      <creatorName>Prugnolle, Franck</creatorName>
      <givenName>Franck</givenName>
      <familyName>Prugnolle</familyName>
    </creator>
    <creator>
      <creatorName>Douzery, Emmanuel J. P.</creatorName>
      <givenName>Emmanuel J. P.</givenName>
      <familyName>Douzery</familyName>
    </creator>
    <creator>
      <creatorName>Arnathau, Céline</creatorName>
      <givenName>Céline</givenName>
      <familyName>Arnathau</familyName>
    </creator>
    <creator>
      <creatorName>Nkoghe, Dieudonné</creatorName>
      <givenName>Dieudonné</givenName>
      <familyName>Nkoghe</familyName>
    </creator>
    <creator>
      <creatorName>Leroy, Eric</creatorName>
      <givenName>Eric</givenName>
      <familyName>Leroy</familyName>
    </creator>
    <creator>
      <creatorName>Renaud, François</creatorName>
      <givenName>François</givenName>
      <familyName>Renaud</familyName>
    </creator>
  </creators>
  <titles>
    <title>Data from: A new malaria agent in African hominids.</title>
  </titles>
  <publisher>Dryad Digital Repository</publisher>
  <publicationYear>2011</publicationYear>
  <resourceType resourceTypeGeneral="Dataset">DataPackage</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="Local accession number">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.</alternateIdentifier>
  </alternateIdentifiers>
  <subjects>
    <subject>Phylogeny</subject>
    <subject>Malaria</subject>
    <subject>Parasites</subject>
    <subject>Taxonomy</subject>
    <subject>Mitochondrial genome</subject>
    <subject>Africa</subject>
    <subject>Plasmodium</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2011</date>
  </dates>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">https://doi.org/10.5061/dryad.8515/1</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="HasPart">https://doi.org/10.5061/dryad.8515/2</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.1371/journal.ppat.1000446</relatedIdentifier>
  </relatedIdentifiers>
  <version>1</version>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/publicdomain/zero/1.0/">Public Domain (CC0 1.0)</rights>
  </rightsList>
</resource>

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"?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
  <identifier identifierType="DOI">10.5438/4k3m-nyvg</identifier>
  <creators>
    <creator>
      <creatorName>Fenner, Martin</creatorName>
      <givenName>Martin</givenName>
      <familyName>Fenner</familyName>
      <nameIdentifier schemeURI="http://orcid.org/" nameIdentifierScheme="ORCID">http://orcid.org/0000-0003-1419-2405</nameIdentifier>
    </creator>
  </creators>
  <titles>
    <title>Eating your own Dog Food</title>
  </titles>
  <publisher>DataCite</publisher>
  <publicationYear>2016</publicationYear>
  <resourceType resourceTypeGeneral="Text">BlogPosting</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="Local accession number">MS-49-3632-5083</alternateIdentifier>
  </alternateIdentifiers>
  <subjects>
    <subject>datacite</subject>
    <subject>doi</subject>
    <subject>metadata</subject>
    <subject>featured</subject>
  </subjects>
  <dates>
    <date dateType="Created">2016-12-20</date>
    <date dateType="Issued">2016-12-20</date>
    <date dateType="Updated">2016-12-20</date>
  </dates>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPartOf">https://doi.org/10.5438/0000-00ss</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.5438/0012</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="References">https://doi.org/10.5438/55e5-t5c0</relatedIdentifier>
  </relatedIdentifiers>
  <version>1.0</version>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/"/>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">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...</description>
  </descriptions>
</resource>

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"?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
  <identifier identifierType="DOI">10.5438/qeg0-3gm3</identifier>
  <creators>
    <creator>
      <creatorName>Martin Fenner</creatorName>
      <nameIdentifier schemeURI="http://orcid.org/" nameIdentifierScheme="ORCID">http://orcid.org/0000-0003-0077-4738</nameIdentifier>
    </creator>
  </creators>
  <titles>
    <title>Maremma: a Ruby library for simplified network calls</title>
  </titles>
  <publisher>DataCite</publisher>
  <publicationYear>2017</publicationYear>
  <resourceType resourceTypeGeneral="Software">SoftwareSourceCode</resourceType>
  <subjects>
    <subject>faraday</subject>
    <subject>excon</subject>
    <subject>net/http</subject>
  </subjects>
  <dates>
    <date dateType="Created">2015-11-28</date>
    <date dateType="Issued">2017-02-24</date>
    <date dateType="Updated">2017-02-24</date>
  </dates>
  <descriptions>
    <description descriptionType="Abstract">Simplifies network calls, including json/xml parsing and error handling. Based on Faraday.</description>
  </descriptions>
</resource>

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.

About

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

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Nov 14, 2024
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