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Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2015.

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Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015 [Internet].

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Adapting JATS to support data citation

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Data referred to in articles is usually not cited in a consistent or structured fashion. To address this, Force 11 have developed the Joint Declaration of Data Citation Principles.[1] JATS 1.1d1 has provisions for citing articles and other sources, but does not offer straightforward ways of expressing some of the concepts needed for data citation. In order to facilitate the citation of data in JATS-tagged documents in a way that is compliant with the Joint Declaration of Data Citation Principles, the Force11 Data Citation Implementation Group[2] held a meeting in June of last year, at which several new elements, attributes and values for attributes were suggested to be added to JATS. These have since been submitted to the JATS Standing Committee, which largely accepted them, so they are now included in the latest JATS draft standard, 1.1d2. This talk will explain the decision criteria behind the elements that were proposed, and how they were selected for JATS 1.1d2. It will in addition provide suggested examples for use of the new tags.

Introduction

Since the late 1980s, the deposition of data in separate repositories, and the corresponding citation of those data in articles, has been common practice in the life sciences in particular[3][4]. Beginning with crystallographic data and nucleotide sequences, the practice of linking between databases and articles has since been adopted by many research communities, journals and data resources as a collaborative effort. More recently, since journals became predominantly accessible online, supplemental data files are now also linked from within the article.

However, data in articles are usually cited by either (a) mentioning the corresponding persistent identifier (PID) from a public database in the narrative flow of the text; (b) referring to one or more files attached to the article; or (c) citing an article that reports about the corresponding database. Citing data in a more formal manner, similar to the way articles are cited, is a relatively recent phenomenon in the scholarly literature and has been pioneered by a few leading journals to date[5]. The drive to improve the way data are cited in articles comes from several aspects of how digital infrastructures are changing the way research is done and will be done in the future (“open science”[6]); more specifically, a more formal, human and machine-readable mode of data citation recognises that:

  • data are a key component of research outputs;
  • data citations are a key element of making data discoverable;
  • the amount of data that is publicly available for others to reuse is growing quickly;
  • the use of data and data sets cannot always be adequately represented by citations to formal publications;
  • the publication of data for others to reuse is something that should be rewarded within scientific credit systems;
  • clear and explicit citations of supporting data in research articles builds trust in the research being reported.

Guidelines and best practices around data citations have been put forward and further developed by a number of groups; for example, the CODATA-ICSTI Task Group on Data Citation Standards and Practices[3], the Research Data Alliance (RDA) Data Citation Working Group[4], and Force11. All of these efforts have engaged key stakeholder groups and each other to build consensus. As mentioned above, Force11 have also condensed their views into the Joint Declaration of Data Citation Principles, which “recognize the dual necessity of creating citation practices that are both human understandable and machine-actionable.”[1]

In this paper, we focus on machine readability of data citations, specifically within the context of NISO Z39.96-2012 JATS (henceforth simply JATS), which is an XML standard for encoding research articles from any discipline.

JATS – like its precursors – has had provisions for handling citations from the start. The current standard NISO JATS 1.0 (henceforth JATS 1.0) as well as the draft standard JATS 1.1d1, however, are limited in how they can handle data citations.

In order to address the issue of supporting data citation in JATS according to the Force11 Data Citation Principles, the Force 11 JATS Data Citation Working Group was formed. The core group consisted of about 18 journal editors, production staff and JATS experts. The group met in London, June 2014, to examine elements, attributes and values that exist in JATS 1.0, collect evidence on how they are being used and suggest how this tagging infrastructure could be adapted to accommodate the needs of data citation. Importantly, we agreed that the modifications discussed should be capable of fully supporting the Data Citation Principles, but should also allow current practices to be accommodated, as machine-readable descriptions of simple data references represents an improvement over no structure at all.

Two main approaches to achieve this were considered:

  • modifying the JATS standard itself
  • creating an extension of the JATS standard.

The former fits with the normal workflows for evolving the JATS standard, while the latter approach was piloted with the TaxPub extension for handling biodiversity-related information, which has been the subject of JATS-Con contributions in 2010[8] and 2012[9].

The two options were discussed at the June 2014 meeting, and it was quickly agreed that the existing JATS infrastructure for citations was comprehensive enough that a small set of changes to it would accommodate the data citation needs identified by the group. The benefit of this approach is that no repetition of elements would be required within an extension (elements such as publication date are required by both article and data citations), and furthermore, including the additional support for data citation in the main JATS standard should encourage uptake.

As a result, the group made several suggestions to the JATS Standing Committee, issued as public comments against the 1.1d1 draft standard[10].

Changes to JATS

The following sections summarize the suggestions that the JATS Data Citation Working Group made to the JATS Standing Committee in reference to JATS 1.1d1, along with the Standing Committee’s responses, and the changes that were made to JATS as of 1.1d2. For verbatim copies of the Standing Committee responses, see the appendix.

Box 1

Note on versioning

These additions have been built into the latest draft version of JATS 1.1 (which is 1.1d2). We fully expect that these changes will be incorporated into the official version 1.1 when that is released. However, while the JATS Standing Committee has made these decisions for JATS 1.1d2, they are not yet part of the official NISO Z39.96 standard.

Add two new elements: <version> and <data-title>[11]

Traditionally, bibliographic objects are not versioned in the same way that data objects are, so there was no <version> element available in the citation models in JATS 1.1d1. We proposed this new element to accommodate the precise version number of the data used. This was similar to, but not the same as, the existing JATS <edition> element and the @version attribute for the <tex-math> element. The group decided that the differences between <edition> and <version> are great enough that to use <edition> as a proxy for version would be confusing for both implementors and those reusing open content.

Also, there was no data-specific title available in JATS. We proposed the new element <data-title> for the formal title of a dataset. This is similar both to JATS <article-title> and <source> elements but is specific to data sources.

We suggested that these elements should be added to at least ‘mixed-citation', 'element-citation', and ‘related-object’ models.

Changes to JATS

The <version> element was added to the list of citation elements, for inclusion in citations. This should take, as its value, the precise version or revision number of the data set. This element is similar to, but not the same as, the current JATS <edition> element.

The <data-title> element was also added to the list of citation elements, to be used to give the name of the data piece being referenced, which might include applicable dates. <data-title> is intended to be analogous to the <article-title> in a normal citation. Note that <source> could also be given, which would identify the data repository in which the data set resides.

The following example was added to the Tag Library page for <data-title>:

<mixed-citation publication-type="data">Xu, J. <etal/>
  <data-title>Cross-platform ultradeep transcriptomic profiling of human 
    reference RNA samples by RNA-Seq</data-title>. 
  <source>Sci. Data</source>
  <volume>1</volume>:<elocation-id>140020</elocation-id> 
  doi: <pub-id pub-id-type="doi" 
    xlink:href='http://dx.doi.org/10.1038/sdata.2014.20'>10.1038/sdata.2014.20</pub-id> 
  (<year iso-8601-date="2014">2014</year>).</mixed-citation>

Add new attribute @assigning-authority for elements <ext-link> and <pub-id>[12]

The attribute @pub-id-type is documented to handle two different types of information. From its entry in the 1.1d1 Tag Library:

The type of identifier should be named for established types (DOIs, SICIs, and Codens). If the identifier is not of an established type, name the assigning agency (PMC, OCLC) or type of assigning agency (aggregator, archive, indexing service, publisher) which assigned the identifier.[13]

This conflation can be problematic if there is a need to specify both the type of identifier and the assigning agency. We proposed a new attribute to <pub-id> and <ext-link>, @assigning-authority, to name the organization that assigned the identifier (for example, 'pdb', 'uniprot', 'genbank').

This frees up @pub-id-type to hold the identifier type information only (see below for a description of how the identifier type values have been extended.

Changes to JATS

A new attribute @assigning-authority was added to the elements <ext-link> and <pub-id>.

The @pub-id-type should now only be used to state how the element content is to be interpreted as an identifier. For example, a “DOI” would have the @pub-id-type value of “doi”, and the @assigning-authority value might be ‘crossref” or “figshare”. (Note that values should be in lowercase for both attributes). Another example typical for the life sciences would be: @pub-id-type value of “accession”, @assigning-authority “uniprot”.

The @assigning-authority attribute is also allowed on the <ext-link> element. That covers the case where <ext-link> is used to mark up an identifier; but best practice is to always use <pub-id> for that purpose.

Here is an example of how @assigning-authority might be used:

<mixed-citation>
  <name><surname>Mulvany</surname><given-names>Ian</given-names></name>,
  <data-title>citing-dataset-elements</data-title>.
  <source>FigShare</source>, 
  <date-in-citation content-type=”pub-date” 
    iso-8601-date='2014-06-30'><day>30</day><month>06</month>
    <year>2014</year></date-in-citation>,
  <pub-id pub-id-type='doi' xlink:href='http://dx.doi.org/10.6084/m9.figshare.1088363'
    assigning-authority='figshare'>10.6084/m9.figshare.1088363</pub-id>.
</mixed-citation>

Add “data” as a suggested value for attribute @publication-type[14]

The attribute @publication-type on the citation elements is a string-type (CDATA) attribute. The values “book”, “letter”, “review”, “journal”, “patent”, “report”, “standard”, and “working-paper” are suggested in the Tag Library. We requested that the value “data” be added to this list so that anyone writing data citations could use the same value.

Changes to JATS

In the Tag Library, the description of the @publication-type attribute was updated to include the suggested value “data” for “dataset, database, spreadsheet, et al.”. Also, a couple of examples were added to that page.

For an example of how this attribute value would be used, see the citation example under Add two new elements: <version> and <data-title>, above.

Note that this example differs from what was added to the tag library. Here, we use <pub-id> for the DOI, but in the tag library page, it is <ext-link>. We think that <pub-id> is to be prefered, for the reasons outlined above.

Add a new value for attribute @person-group-type, for the data curator[15]

The attribute @person-group-type is an optional attribute that takes CDATA content in the Archiving and Interchange tag set and has a restricted set of values in the Journal Publishing tag set. We suggested adding the value "data-curator" to the suggested and restricted lists of values for the attribute @person-group-type.

Changes to JATS

The value “curator” was added to the list of suggested values for the @person-group-type attribute.

Here is an example of how the "curator" value might be used for @person-group-type.[16]

<mixed-citation>
  <person-group person-group-type='curator'>
    <name><surname>Frankis</surname><given-names>Michael</given-names></name>
  </person-group>, curator.
  "<data-title>Mountain bluebird</data-title>."
  <source>Encyclopedia of Life</source>, available from 
  <ext-link ext-link-type='uri' 
    xlink:href='http://eol.org/pages/1177542'>http://eol.org/pages/1177542</ext-link>.
  Accessed 30 Mar 2015.
</mixed-citation>

The Standing Committee has indicated that they will revisit this issue in light of the CRediT- Contributor Role Taxonomy, which has just been published.[17]

Add additional identifier values for the @pub-id-type attribute[18]

The @pub-id-type attribute on <pub-id> is used to identify the type of identifier or the organization or system that defines the identifier. It is a string-type (CDATA) attribute in the Archiving and Interchange tag set and had a restricted set of values in the Journal Publishing tag set. We suggested adding 'accession', 'ark', and 'handle' to the suggested and restricted lists for @pub-id-type.

Changes to JATS

The suggested values were adopted, both for the suggested and restricted lists. The following descriptions were added to the Tag Libraries:

  • accession - (bioinformatics) a unique identifier given to a DNA or protein sequence record for tracking the sequence record and the associated sequence over time in a data repository.
  • ark - Archival Resource Key — a Uniform Resource Locator (URL) containing the word "ark" that is a multi-purpose identifier for information objects of any type
  • handle - Handle identifier, part of the Handle System for assigning, managing, and resolving persistent identifiers for digital objects and other resources on the Internet

Here is an example of how the “accession” identifier-type value might be used. Note that it is accompanied by an @assigning-authority, to make clear the provenance of the identifier.

<mixed-citation publication-type='data'>
  <name><surname>Heinz</surname><given-names>D.W.</given-names></name>,
  <name><surname>Baase</surname><given-names>W.A.</given-names></name>,
  <etal>et. al.</etal>
  <data-title>How amino-acid insertions are allowed in an alpha-helix of T4 
    lysozyme</data-title>.
  <source>RCSB Protein Data Bank</source>,
  accession <pub-id pub-id-type='accession' assigning-authority='pdb'
    xlink:href='http://www.rcsb.org/pdb/explore/explore.do?structureId=102l'>102l</pub-id>.
  <pub-id pub-id-type='doi'
    xlink:href='http://dx.doi.org/10.2210/pdb102l/pdb'>10.2210/pdb102l/pdb</pub-id>
</mixed-citation>
                    

Add linking attributes for element <pub-id>[19]

This suggestion is not specific to data citations but came out of the discussion of this group.

The <pub-id> element is defined as an “Identifier of a publication in a bibliographic reference or product description.” However, it is often used to build a link to the object that is being identified. We proposed that the linking attributes (specifically the parameter entity %might-link-atts;) be added to <pub-id>.

Changes to JATS

The “might-link” attributes were added to <pub-id>, so that a <pub-id> that is a DOI (for example) can carry the linking attributes and be made into a live link.

For an example of how this attribute value would be used, see the citation example under Add two new elements: <version> and <data-title>, above.

Practical Examples

The following are examples of how data citations should be tagged in JATS. The examples given above are duplicated here, with some added discussion. In addition, a variety of other examples are given, so as to provide a reference for best practices for these kinds of citations.

The Force11 DCIG “mantra” applies here: “We recognize any recommendations we make, ever, will be incomplete, and will not cover all possible cases.”[20]

Data set described by a publication

The following citation references a data source that is described by Scientific Data, a “publication for descriptions of scientifically valuable datasets”. Note that this example was used above, in Add two new elements: <version> and <data-title>. Note the use of:

  • the new <data-title> element,
  • the <pub-id> element (as opposed to <ext-link>) for the DOI, and
  • the @xlink:href attribute on the <pub-id> element, which facilitates turning the DOI into a hyperlink

<mixed-citation publication-type="data">Xu, J. <etal/>
  <data-title>Cross-platform ultradeep transcriptomic profiling of human reference RNA 
    samples by RNA-Seq</data-title>. <source>Sci. Data</source>
  <volume>1</volume>:<elocation-id>140020</elocation-id> 
  doi: <pub-id pub-id-type="doi" 
    xlink:href='http://dx.doi.org/10.1038/sdata.2014.20'>10.1038/sdata.2014.20</pub-id> 
  (<year iso-8601-date="2014">2014</year>).
</mixed-citation>
                

Database on CD-ROM, DVD, or disk

This example was derived from examples given in the Tag Library, database citations and the PMC Tagging Guidelines, Database on CD-ROM, DVD, or disk with an individual(s) as author.

A mashup of those two examples is as follows:

<mixed-citation publication-type="database" publication-format="disk">
  <name><surname>Walker</surname><given-names>MM</given-names></name>, 
  <name><surname>Keith</surname><given-names>LH</given-names></name>. 
  <source>EPA's Clean Air Act air toxics database [disk]</source>. 
  <publisher-loc>Boca Raton (FL)</publisher-loc>: 
  <publisher-name>Lewis Publishers</publisher-name>; 
  <date-in-citation content-type="copyright-year"
    iso-8601-date="1992">1992-1993</date-in-citation>.
  4 computer disks: 3 1/2 in.
</mixed-citation>
                

With the new data citations recommendations, this citation would change, such that it:

  • Uses “data” in the @publication-type
  • Uses the new <data-title> element, instead of <source>

<mixed-citation publication-type="data" publication-format="disk">
  <name><surname>Walker</surname><given-names>MM</given-names></name>, 
  <name><surname>Keith</surname><given-names>LH</given-names></name>. 
  <data-title>EPA's Clean Air Act air toxics database</data-title> [disk]. 
  <publisher-loc>Boca Raton (FL)</publisher-loc>: 
  <publisher-name>Lewis Publishers</publisher-name>; 
  <date-in-citation content-type="copyright-year"
    iso-8601-date="1992">1992-1993</date-in-citation>.
  4 computer disks: 3 1/2 in.
</mixed-citation>

Record from a web data repository

The following example is from the Crystallography Open Database[21], record 1517518, revision (version) 130981:

<mixed-citation publication-type='data'>
  <name><surname>Benz</surname><given-names>Michael</given-names></name>;
  <name><surname>Braband</surname><given-names>Henrik</given-names></name>;
  <name><surname>Schmutz</surname><given-names>Paul</given-names></name>;
  <name><surname>Halter</surname><given-names>Jonathan</given-names></name>; 
  <name><surname>Alberto</surname><given-names>Roger</given-names></name>.
  <data-title>C21 H49 Al Cl7 N7 O7 Tc</data-title>,
  version <version>130981</version>. From
  <source>Crystallography Open Database</source>,
  accession <pub-id pub-id-type='accession' 
    assigning-authority='crystallography open database'
    xlink:href='http://www.crystallography.net/cod/1517518.html'>1517518</pub-id>.
</mixed-citation>
                

Record from the Protein Data Bank

This example is of the RCSB Protein Data Bank[22] record 102l.

<mixed-citation publication-type='data'>
  <name><surname>Heinz</surname><given-names>D.W.</given-names></name>,
  <name><surname>Baase</surname><given-names>W.A.</given-names></name>,
  <etal>et. al.</etal>
  <data-title>How amino-acid insertions are allowed in an alpha-helix of T4 
  lysozyme</data-title>.
  <source>RCSB Protein Data Bank</source>,
  accession <pub-id pub-id-type='accession' assigning-authority='pdb'
    xlink:href='http://www.rcsb.org/pdb/explore/explore.do?structureId=102l'>102l</pub-id>.
  <pub-id pub-id-type='doi'
    xlink:href='http://dx.doi.org/10.2210/pdb102l/pdb'>10.2210/pdb102l/pdb</pub-id>
</mixed-citation>

Data record from FigShare

<mixed-citation>
  <name><surname>Mulvany</surname><given-names>Ian</given-names></name>,
  <data-title>citing-dataset-elements</data-title>.
  <source>FigShare</source>, 
  <date-in-citation content-type=’pub-date’ 
    iso-8601-date='2014-06-30'><day>30</day><month>06</month>
  <year>2014</year></date-in-citation>,
  <pub-id pub-id-type='doi' xlink:href='http://dx.doi.org/10.6084/m9.figshare.1088363'
    assigning-authority='figshare'>10.6084/m9.figshare.1088363</pub-id>.
</mixed-citation>

Page from Encyclopedia of Life

<mixed-citation>
  <person-group person-group-type='curator'>
    <name><surname>Frankis</surname><given-names>Michael</given-names></name>
  </person-group>, curator.
  "<data-title>Mountain bluebird</data-title>."
  <source>Encyclopedia of Life</source>, available from 
  <ext-link ext-link-type='uri' 
    xlink:href='http://eol.org/pages/1177542'>http://eol.org/pages/1177542</ext-link>.
  Accessed 30 Mar 2015.
</mixed-citation>

Add Health

The following shows how one might tag a citation for the Add Health data set:[23]

<mixed-citation>
  <name><surname>Harris</surname><given-names>Kathleen Mullan</given-names></name>.
  <date-in-citation content-type="pub-date"><year>2009</year></date-in-citation>.
  <data-title>The National Longitudinal Study of Adolescent to Adult Health (Add Health),
    Waves I & II, 1994–1996; Wave III, 2001–2002; Wave IV, 2007-2009</data-title>
  [machine-readable data file and documentation].
  <publisher-loc>Chapel Hill, NC</publisher-loc>:
  <publisher-name>Carolina Population Center, University of North Carolina at
    Chapel Hill</publisher-name>. 
  DOI: <pub-id pub-id-type='doi'
    xlink:href='http://dx.doi.org/10.3886/ICPSR27021.v9'>10.3886/ICPSR27021.v9</pub-id>
</mixed-citation>

Conclusions

Data citation serves to establish provenance, to assign scientific credit and to increase data discoverability. Machine readability can enhance its utility for all of these functions. JATS already is the de-facto standard for exchanging journal article content in a machine readable fashion, and from a strong basis in biomedicine, it is continuously expanding into other areas as journals, publishers or repositories are adjusting their workflows to this standard.

In parallel, data citation is increasingly becoming an element of data-related policies. For example, the NIH recently released its Public Access Plan, which states[24] that “NIH will explore ways to advance data as a legitimate form of scholarship through data citation and other means”. By integrating data citation mechanisms into JATS, a technical foundation is provided, on the basis of which such data citation policies can be implemented in practice.

While the trigger for the changes reported here was data citation, some of these changes extend JATS in ways that are useful beyond data citations. For instance, the <version> element could also be used for citing software, and the new linking attributes added to <pub-id> are yet more general.

The group closely coordinated with the wider Data Citation Implementation Group at Force11, and it will continue to monitor developments of data citation as well as usage of the new JATS infrastructure for data citation. In doing so, it will collaborate with the JATS4R Working group[25] that assesses tagging practices and issues guidelines on how to tag specific items in JATS such that the potential for reuse of the tagged content is maximized.

References

1.
Force11 Joint Declaration of Data Citation Principles: http://www​.force11.org/datacitation .
2.
Force11 Data Citation Implementation Group: https://www​.force11.org​/datacitationimplementation.
3.
CODATA-ICSTI Task Group on Data Citation Standards and Practices: http://dx​.doi.org/10.2481/dsj.OSOM13-043.
4.
Research Data Alliance (RDA): https://rd-alliance​.org/node/141.
5.
Starr J, Castro E, Crosas M, Dumontier M, Downs RR, Duerr R, Haak L, Haendel M, Herman I, Hodson S, Hourclé J, Kratz JE, Lin J, Nielsen LH, Nurnberger A, Pröll S, Rauber A, Sacchi S, Smith AP, Taylor M, Clark T. (2015) Achieving human and machine accessibility of cited data in scholarly publications. PeerJ PrePrints 3:e697v4 https://dx​.doi.org/10​.7287/peerj.preprints.697v4. [PMC free article: PMC4498574] [PubMed: 26167542]
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The Royal Society (2012) "Science as an open enterprise." Available: http://royalsociety​.org​/policy/projects/science-public-enterprise.
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Final report - Science as an open enterprise. 21 June 2012. https:​//royalsociety​.org/policy/projects​/science-public-enterprise/Report/
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Catapano T. TaxPub: An Extension of the NLM/NCBI Journal Publishing DTD for Taxonomic Descriptions. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2010 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010. Available from: http://www​.ncbi.nlm.nih​.gov/books/NBK47081/
9.
Penev L, Catapano T, Agosti D, et al. Implementation of TaxPub, an NLM DTD extension for domain-specific markup in taxonomy, from the experience of a biodiversity publisher. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2012 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2012. Available from: http://www​.ncbi.nlm.nih​.gov/books/NBK100351/
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CRediT- Contributor Role Taxonomy: http:​//projectcredit.net/
18.
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Crystallography Open Database: http://www​.crystallography.net/
22.
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25.
Beck J, Chodacki J, Eaton A, et al.; JATS4R Working Group. Improving the reusability of JATS. In: Journal Article Tag Suite Conference (JATS-Con) Proceedings 2015 [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2015. Available from: http://www​.ncbi.nlm.nih​.gov/books/NBK279901/
26.
NISO JATS Standing Committee Recommended Changes Between NISO/JATS 1.0 and JATS 1.1, in Response to Comments to on NISO Z39.96-2012, September 2013 through October 2014. December, 2014, http://www​.niso.org/apps​/group_public/download​.php/14128/JATS-SC-JATS-1​.1d2-Chg-Hist.pdf .

Standing Committee Responses

The following are the verbatim responses from the JATS Standing Committee to the recommendations presented by the Data Citation group.[26]

Comment 534: Add Two New Elements to Citations for Citing Data

Standing Committee Recommendation

  • The <version> element will be added to the list of citation-content elements, for inclusion in citations, product descriptions, et al. This element will be defined as “The precise version number of the data or software being cited”. This element is similar to, but not the same as, the current JATS <edition> element.
  • The <data-title> element (for the name of the data piece being referenced) will be added to the list of citation-content elements, for inclusion in citations, product descriptions, et al.

Standing Committee Documentation Recommendation

  • The <data-title> is the formal title of the data source or part of the data source being cited (may include applicable dates). The scope of the <data-title> is intended to be more like the scope of <article-title> than like the scope of <source>. The documentation must make these levels clear, since both <data-title> and <source> might be applicable for a cited dataset.
  • The <version> element is the version number of a software package or data site being cited. Examples for both software and data sources should be given, if possible.

Comment 538: Add Attribute @assigning-authority for <ext-link> and <pub-id>

Standing Committee Recommendation

  • Add the new attribute @assigning-authority to the elements <ext-link> and <pub-id>. The @pub-id-type can then state that the element content is, for example a “DOI” and the assigning authority is ‘crossref” or “figshare” (note lower case values). This attribute may also be used to lessen the semantic overloading of the @pub-id-type attribute say that the @authority for the content is an organization such as “PDB” or “GenBank”.
  • Note: This new attribute makes better semantic sense for <pub-id>. The @authority on <ext-link> will probably be rarely used, but covers the case in which an <ext-link> (a link by definition) codes an identifier, as can happen with DOIs.

Comment 535: Add Linking Attributes to Element <pub-id>

Standing Committee Recommendatio

  • The might-link attributes will be added to <pub-id>, so that a <pub-id> that is a DOI can carry the linking attributes and be made into a live link. In this use of <pub-id>, the identifier acts as a link as well as an identifier.

Comment 536: Add a New Value for Attribute @publication-type

Standing Committee Recommendation

The attribute @publication-type is currently used on the citation elements <mixed-citation> and <element-citation> to record the type of publication being cited, for example, "book", "journal", or "standard". The data-specific value “data” will be added to the non-normative suggested value lists for the attribute @publication-type, with the meaning: “a dataset or other research data collection such as a spreadsheet”.

Comment 537: Add a New Value for Attribute @person-group-type

Standing Committee Recommendation

The @person-group-type attribute is used on the <person-group> element to indicate the role of the contributors named in the group, for example, "author", "compiler", "editor", et al. For the purposes of citing datasets and art, the value “curator” will be added to this list.

Comment 539: Additional Identifier Values for the @pub-id-type Attribute

Standing Committee Recommendation

  • The attribute @pub-id-type is defined as the “Type of publication identifier or the organization or system that defined the identifier”. In Publishing and Authoring, this is a restricted list of values. In Archiving, this is a suggested list of values. The following identifier-type values will be added to these values list: 'accession', 'ark', and 'handle'.
  • The CrossRef metadata for ORCIDs for authors has a boolean attribute named @authenticated with a default value 'false'. The new @authenticated attribute will be added to <contrib-id>, as an optional Boolean value.
The copyright holders grant the U.S. National Library of Medicine permission to archive and post a copy of this paper on the Journal Article Tag Suite Conference proceedings website.
Bookshelf ID: NBK280240

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