Data citations (DEPRECATED)

Status: Published
Version: 1.0
This recommendation document is licensed under CC BY-ND 2.0 UK

Context

<ref>, <mixed-citation>, <element-citation>, <person-group>, <data-title>, <source>, <year>, <pub-id>, <ext-link>, <version>

@publication-type, @person-group-type, @pub-id-type, @assigning-authority, @designator, @xlink:href

Description

This recommendation contains best practices for tagging citations to datasets in a reference list.

1. This recommendation only applies to JATS 1.1d2 and forward, because the tags needed to make data citations machine-readable are only available from 1.1d2 onwards.
2. The following recommendation is specifically about citations related to data and datasets. See JATS4R’s recommendations for Citations (general).

Additional reading

• Adapting JATS to support data citation
• Force 11 Joint Declaration on Data Citation Principles

Recommendation

1. @publication-type=”data” on <mixed-citation> or <element-citation>. Use “data” as the value of @publication-type to indicate that the citation is to a dataset, even if that dataset is the entire data repository.
   
   [[Validator tool result:  Error if @ not “data” and <data-title> is present]]
2. @person-group-type on <person-group>. As of version 1.1d2, the list of values for this attribute includes ‘curator’, specifically to support data citations. Use “curator” whenever appropriate.
   
   [[Validator tool result:  Info]]
3. <data-title> / <source>. At least one of <data-title> or <source> must be present. <data-title> should hold the title of the dataset. <source> Should contain the name of the holding repository. Both should be present if applicable.
   
   [[Validator tool result: Error if one not present ]]
4. <year>. This should contain the 4-digit year the data was deposited. (Or in the case of datasets updated regularly, the year the data was used in the work in which it is being cited.)
   
   [[Validator tool result: Error if year is not 4 digit]]
5. <pub-id>. This element should be used to hold both the repository ID for the data, in the element content, and, if applicable, the full URI to the data, in the @xlink:href attribute. The URI should be a DOI or similar persistent identifier. The @pub-id-type attribute must be used — see the next recommendation for details.
   
   [[Validator tool result: Info]]
6. @pub-id-type on <pub-id>. In contrast to what is stated in the Tag Library (“Type of publication identifier or the organization or system that defined the identifier”) this attribute should only be used to state the type of identifier, and not to specify the organisation or system that defined the identifier. To specify the latter, use @assigning-authority (see the next recommendation). For example, a DOI that is assigned by CrossRef should have “doi” as the @pub-id-type, and “crossref” as the @assigning-authority. For many types of identifiers, there is only one assigning authority. For example, PubMed IDs are always assigned by the National Library of Medicine. In these cases, use @pub-id-type and not @assigning-authority.
   
   [[Validator tool result:  Defer result pending the discussion of the attribute value registry]]
7. @assigning-authority on <pub-id> and <ext-link>. When the given type of identifier can be assigned by more than one organisation, and the organisation registering the identifier is known, include the @assigning-authority attribute on the <pub-id> element. Values might be, for example, “crossref” or “figshare”. Values should be in lowercase.
   
   [[Validator tool result: Info for now; may change pending attribute value registry implementation]]
8. @designator on <version>. (1.1d2+) Use this attribute to contain the machine-readable version number of the dataset. The element contents can be a more human-readable note (see the example).
   
   [[Validator tool result: error if not present]]

Examples

Example 1

<ref id="d1">
   <element-citation publication-type="data">
      <person-group person-group-type="author">
         <collab>The Concerto Consortium</collab>
         <name>
            <surname>van Beethoven</surname>
            <given-names>Ludwig</given-names>
         </name>
         <name>
            <surname>Liszt</surname>
            <given-names>F</given-names>
       </name>
    </person-group>
    <person-group person-group-type="curator">
       <name>
          <surname>Bach</surname>
          <given-names>JS</given-names>
      </name>
   </person-group>
   <data-title>Title of data set</data-title>
   <year iso-8601-date="2014">2014</year>
   <source>Repository Name</source>
   <pub-id pub-id-type="doi" assigning-authority="figshare" xlink:href="http://dx.doi.org/10.1234/1234321">10.1234/1234321</pub-id>
   <version designator="16.2">16th version, second release</version>
   </element-citation>
</ref>

Example 2: some additional examples from eLife

<?xml version="1.0" encoding="UTF-8"?>
 <!--Data reference: Dryad dataset -->
            <ref id="bib8">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Kok</surname>
                            <given-names>K</given-names>
                        </name>
                        <name>
                            <surname>Ay</surname>
                            <given-names>A</given-names>
                        </name>
                        <name>
                            <surname>Li</surname>
                            <given-names>L</given-names>
                        </name>
                        <name>
                            <surname>Arnosti</surname>
                            <given-names>DN</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2015">2015</year>
                    <data-title>Data from: Genome-wide errant targeting by Hairy</data-title>
                    <source>Dryad Digital Repository</source>
                    <pub-id pub-id-type="doi" assigning-authority="Dryad Digital Repository"
                        xlink:href="http://datadryad.org/resource/doi:10.5061/dryad.cv323"
                        >10.5061/dryad.cv323</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: RCSB Protein Data Bank -->
            <ref id="bib9">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Du</surname>
                            <given-names>J</given-names>
                        </name>
                        <name>
                            <surname>Johnson</surname>
                            <given-names>LM</given-names>
                        </name>
                        <name>
                            <surname>Groth</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Feng</surname>
                            <given-names>S</given-names>
                        </name>
                        <name>
                            <surname>Hale</surname>
                            <given-names>CJ</given-names>
                        </name>
                        <name>
                            <surname>Li</surname>
                            <given-names>S</given-names>
                        </name>
                        <name>
                            <surname>Vashisht</surname>
                            <given-names>AA</given-names>
                        </name>
                        <name>
                            <surname>Gallego-Bartolome</surname>
                            <given-names>J</given-names>
                        </name>
                        <name>
                            <surname>Wohlschlegel</surname>
                            <given-names>JA</given-names>
                        </name>
                        <name>
                            <surname>Patel</surname>
                            <given-names>DJ</given-names>
                        </name>
                        <name>
                            <surname>Jacobsen</surname>
                            <given-names>SE</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2014">2014</year>
                    <data-title>Crystal structure of KRYPTONITE in complex with mCHH DNA and
                        SAH</data-title>
                    <source>RCSB Protein Data Bank</source>
                    <pub-id pub-id-type="doi" assigning-authority="RCSB Protein Data Bank"
                        >10.2210/pdb4qen/pdb</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: ProteomeXchange: pub-id-type="archive" - not clear what this number is, so default option -->
            <ref id="bib10">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Radoshevich</surname>
                            <given-names>L</given-names>
                        </name>
                        <name>
                            <surname>Impens</surname>
                            <given-names>F</given-names>
                        </name>
                        <name>
                            <surname>Ribet</surname>
                            <given-names>D</given-names>
                        </name>
                        <name>
                            <surname>Quereda</surname>
                            <given-names>JJ</given-names>
                        </name>
                        <name>
                            <surname>Nam Tham</surname>
                            <given-names>T</given-names>
                        </name>
                        <name>
                            <surname>Nahori</surname>
                            <given-names>MA</given-names>
                        </name>
                        <name>
                            <surname>Bierne</surname>
                            <given-names>H</given-names>
                        </name>
                        <name>
                            <surname>Dussurget</surname>
                            <given-names>O</given-names>
                        </name>
                        <name>
                            <surname>Pizarro-Cerdá</surname>
                            <given-names>J</given-names>
                        </name>
                        <name>
                            <surname>Knobeloch</surname>
                            <given-names>KP</given-names>
                        </name>
                        <name>
                            <surname>Cossart</surname>
                            <given-names>P</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2015">2015a</year>
                    <data-title>ISG15 counteracts <italic>Listeria monocytogenes</italic>
                        infection</data-title>
                    <source>ProteomeXchange</source>
                    <pub-id pub-id-type="archive"
                        xlink:href="http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD001805"
                        >PXD001805</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: ArrayExpress: pub-id-type="accession"-->
            <ref id="bib11">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Radoshevich</surname>
                            <given-names>L</given-names>
                        </name>
                        <name>
                            <surname>Impens</surname>
                            <given-names>F</given-names>
                        </name>
                        <name>
                            <surname>Ribet</surname>
                            <given-names>D</given-names>
                        </name>
                        <name>
                            <surname>Quereda</surname>
                            <given-names>JJ</given-names>
                        </name>
                        <name>
                            <surname>Nam Tham</surname>
                            <given-names>T</given-names>
                        </name>
                        <name>
                            <surname>Nahori</surname>
                            <given-names>MA</given-names>
                        </name>
                        <name>
                            <surname>Bierne</surname>
                            <given-names>H</given-names>
                        </name>
                        <name>
                            <surname>Dussurget</surname>
                            <given-names>O</given-names>
                        </name>
                        <name>
                            <surname>Pizarro-Cerdá</surname>
                            <given-names>J</given-names>
                        </name>
                        <name>
                            <surname>Knobeloch</surname>
                            <given-names>KP</given-names>
                        </name>
                        <name>
                            <surname>Cossart</surname>
                            <given-names>P</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2015">2015b</year>
                    <article-title>Transcription profiling by high throughput sequencing of LoVo
                        cells infected with Listeria for 24 hr compared to uninfected
                        cells</article-title>
                    <source>ArrayExpress</source>
                    <pub-id pub-id-type="accession"
                        xlink:href="https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3649/"
                        >E-MTAB-3649</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: NCBI Gene Expression Omnibus: pub-id-type="accession" assigning-authority="NCBI"-->
            <ref id="bib12">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Bouveret</surname>
                            <given-names>R</given-names>
                        </name>
                        <name>
                            <surname>Waardenberg</surname>
                            <given-names>AJ</given-names>
                        </name>
                        <name>
                            <surname>Schonrock</surname>
                            <given-names>N</given-names>
                        </name>
                        <name>
                            <surname>Ramialison</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Doan</surname>
                            <given-names>T</given-names>
                        </name>
                        <name>
                            <surname>de Jong</surname>
                            <given-names>D</given-names>
                        </name>
                        <name>
                            <surname>Bondue</surname>
                            <given-names>A</given-names>
                        </name>
                        <name>
                            <surname>Kaur</surname>
                            <given-names>G</given-names>
                        </name>
                        <name>
                            <surname>Mohamed</surname>
                            <given-names>S</given-names>
                        </name>
                        <name>
                            <surname>Fonoudi</surname>
                            <given-names>H</given-names>
                        </name>
                        <name>
                            <surname>Chen</surname>
                            <given-names>C</given-names>
                        </name>
                        <name>
                            <surname>Wouters</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Bhattacharya</surname>
                            <given-names>S</given-names>
                        </name>
                        <name>
                            <surname> Plachta</surname>
                            <given-names>N</given-names>
                        </name>
                        <name>
                            <surname>Dunwoodie</surname>
                            <given-names>SL</given-names>
                        </name>
                        <name>
                            <surname>Chapman</surname>
                            <given-names>G</given-names>
                        </name>
                        <name>
                            <surname>Blanpain</surname>
                            <given-names>C</given-names>
                        </name>
                        <name>
                            <surname>Harvey</surname>
                            <given-names>RP</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2015">2015</year>
                    <data-title>NKX2-5 mutations causative for congenital heart disease retain
                        functionality and are directed to hundreds of targets</data-title>
                    <source>NCBI Gene Expression Omnibus</source>
                    <pub-id pub-id-type="accession" assigning-authority="NCBI"
                        xlink:href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE44902"
                        >GSE44902</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: NCBI Nucleotide: pub-id-type="accession" assigning-authority="NCBI" contains version details-->
            <ref id="bib13">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Gavrilov</surname>
                            <given-names>S</given-names>
                        </name>
                        <name>
                            <surname>Harvey</surname>
                            <given-names>RP</given-names>
                        </name>
                        <name>
                            <surname>Papaioannou</surname>
                            <given-names>VE</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2014">2014</year>
                    <data-title>Mus musculus T-box 2 (Tbx2), mRNA</data-title>
                    <source>NCBI Nucleotide</source>
                    <pub-id pub-id-type="accession" assigning-authority="NCBI"
                        xlink:href="http://www.ncbi.nlm.nih.gov/nuccore/120407038"
                        >NM_009324</pub-id>
                    <version designator="NM_009324.2">NM_009324.2</version>
                </element-citation>
            </ref>
            <!--Data reference: NCBI Gene Expression Omnibus (GEO): pub-id-type="accession" assigning-authority="NCBI"-->
            <ref id="bib14">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Hoang</surname>
                            <given-names>C</given-names>
                        </name>
                        <name>
                            <surname>Swift</surname>
                            <given-names>GH</given-names>
                        </name>
                        <name>
                            <surname>Azevedo-Pouly</surname>
                            <given-names>A</given-names>
                        </name>
                        <name>
                            <surname>MacDonald</surname>
                            <given-names>RJ</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2015">2015</year>
                    <data-title>Effects on the transcriptome of adult mouse pancreas (principally
                        acinar cells) by the inactivation of the Ptf1a gene in vivo</data-title>
                    <source>NCBI Gene Expression Omnibus</source>
                    <pub-id pub-id-type="accession" assigning-authority="NCBI"
                        xlink:href="http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70542"
                        >GSE70542</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: NCBI BioProject: author is a collab pub-id-type="accession" assigning-authority="NCBI" example of 3 references with same author/year-->
            <ref id="bib15">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <collab>The <italic>Shigella</italic> Genome Sequencing Consortium</collab>
                    </person-group>
                    <year iso-8601-date="2015">2015a</year>
                    <data-title>Global Diversity of Shigella Species</data-title>
                    <source>NCBI BioProject</source>
                    <pub-id pub-id-type="accession" assigning-authority="NCBI"
                        xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB2846"
                        >PRJEB2846</pub-id>
                </element-citation>
            </ref>
            <ref id="bib16">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <collab>The <italic>Shigella</italic> Genome Sequencing Consortium</collab>
                    </person-group>
                    <year iso-8601-date="2015">2015b</year>
                    <data-title>Shigella sonnei and flexneri from around the world</data-title>
                    <source>NCBI BioProject</source>
                    <pub-id pub-id-type="accession" assigning-authority="NCBI"
                        xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/204320"
                        >PRJEB2460</pub-id>
                </element-citation>
            </ref>
            <ref id="bib17">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <collab>The <italic>Shigella</italic> Genome Sequencing Consortium</collab>
                    </person-group>
                    <year iso-8601-date="2015">2015c</year>
                    <data-title>Shigella flexneri from around the world</data-title>
                    <source>NCBI BioProject </source>
                    <pub-id pub-id-type="accession" assigning-authority="NCBI"
                        xlink:href="http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJEB2542"
                        >PRJEB2542</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: JASPAR-->
            <ref id="bib18">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Staab</surname>
                            <given-names>TA</given-names>
                        </name>
                        <name>
                            <surname>Griffen</surname>
                            <given-names>TC</given-names>
                        </name>
                        <name>
                            <surname>Corcoran</surname>
                            <given-names>C</given-names>
                        </name>
                        <name>
                            <surname>Evgrafov</surname>
                            <given-names>O</given-names>
                        </name>
                        <name>
                            <surname>Knowles</surname>
                            <given-names>JA</given-names>
                        </name>
                        <name>
                            <surname>Sieburth</surname>
                            <given-names>D</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2013">2013</year>
                    <data-title>SKN-1 from the JASPAR CORE database</data-title>
                    <source>JASPAR</source>
                    <pub-id pub-id-type="art-access-id"
                        xlink:href="http://jaspar.genereg.net/cgi-bin/jaspar_db.pl"
                        >MA0547.1</pub-id>
                </element-citation>
            </ref>
            <!--Data reference: modMine pub-id-type="archive"-->
            <ref id="bib19">
                <element-citation publication-type="data">
                    <person-group person-group-type="author">
                        <name>
                            <surname>Zhong</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Snyder</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Slightam</surname>
                            <given-names>C</given-names>
                        </name>
                        <name>
                            <surname>Kim</surname>
                            <given-names>S</given-names>
                        </name>
                        <name>
                            <surname>Murray</surname>
                            <given-names>J</given-names>
                        </name>
                        <name>
                            <surname>Waterston</surname>
                            <given-names>R</given-names>
                        </name>
                        <name>
                            <surname>Gerstein</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Niu</surname>
                            <given-names>W</given-names>
                        </name>
                        <name>
                            <surname>Janette</surname>
                            <given-names>J</given-names>
                        </name>
                        <name>
                            <surname>Raha</surname>
                            <given-names>D</given-names>
                        </name>
                        <name>
                            <surname>Agarwal</surname>
                            <given-names>A</given-names>
                        </name>
                        <name>
                            <surname>Reinke</surname>
                            <given-names>V</given-names>
                        </name>
                        <name>
                            <surname>Sarov</surname>
                            <given-names>M</given-names>
                        </name>
                        <name>
                            <surname>Hyman</surname>
                            <given-names>A</given-names>
                        </name>
                    </person-group>
                    <year iso-8601-date="2013">2013</year>
                    <data-title>ChIP-Seq Identification of C. elegans TF Binding Sites</data-title>
                    <source>modMine</source>
                    <pub-id pub-id-type="archive" xlink:href="http://intermine.modencode.org/release-33/report.do?id=77000379">modENCODE_3369</pub-id>
                </element-citation>
            </ref>