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Dar Article

NOTE: This document is incomplete and slightly out of date. See latest complete schema here.

This specification defines strict tagging rules for JATS, with the goal of optimising for machine readability, avoiding redundancy and ensuring reusability. The premise is to have exactly one tagging style per use-case. E.g. there is only one way to tag a reference, author or affiliation. Additionally we define a set of optional extensions to model reproducible elements (cells) in JATS. This work is inspired but not related to JATS4R, a similar effort to make JATS more reusable.

Core elements

<aff> <article-meta> <bio> <caption> <contrib-group> <contrib> <disp-quote> <fig> <fn-group> <fn> <inline-formula> <list> <media> <name> <ref> sec table-wrap

Reproducible elements

<code[specific-use=cell]> <fig[fig-type=repro-fig]> <named-content[content-type=inline-cell]>

Core Elements

<aff>

institution[content-type=orgname],
institution[content-type=orgdiv1]?, institution[content-type=orgdiv2]?,
institution[content-type=orgdiv3]?, addr-line[content-type=street-address]?,
addr-line[content-type=complements]?,
city?, state?, postal-code?, country?,
phone?, fax?, email?, uri[content-type=link]?

Example:

<aff id="aff1">
  <institution content-type="orgname">German Primate Center GmbH</institution>
  <institution content-type="orgdiv1">Neurobiology Laboratory</institution>
  <city>Göttingen</city>
  <country>Germany</country>
  <uri content-type="entity">organisation-1</uri>
</aff>

<article-meta>

Please note, that so far only title-group, contrib-group, and abstract are fully specified and editable in Texture.

article-id?, article-categories?, title-group?, contrib-group[content-type=author],
contrib-group[content-type=editor], author-notes?, pub-date*, volume?, issue?,
isbn, (((fpage, lpage?)?, page-range?) | elocation-id)?, history?, permissions?,
self-uri*, (related-article | related-object)*, abstract?, trans-abstract*,
kwd-group*, funding-group*, counts?, custom-meta-group?

Example shows all editable elements:

<article-meta>
  <title-group>
    <article-title>Object vision to hand action in macaque parietal, premotor, and motor cortices</article-title>
  </title-group>
  <contrib-group content-type="author">
    ...
  </contrib-group>
  <contrib-group content-type="editor">
    ...
  </contrib-group>
  <aff id="aff1">
    ...
  </aff>
  <aff id="aff2">
    ...
  </aff>
  <pub-date publication-format="print" date-type="pub" iso-8601-date="1999-01-29">
    <day>29</day>
    <month>01</month>
    <year>1999</year>
  </pub-date>
  <volume>318</volume>
  <issue>7187</issue>
  <fpage>837</fpage>
  <lpage>841</lpage>
  <history>
    ...
  </history>
  <abstract>
    <p>Abstract</p>
  </abstract>
</article-meta>

<bio>

p*

<caption>

title?, p*

<collab>

named-content[content-type=name], uri?, contrib-group?

NOTE: Group authors <collab> are not yet supported in Texture.

<contrib-group>

(contrib[contrib-type=person|group])*

Example for authors / group authors:

<contrib-group content-type="author">
  <contrib contrib-type="person" equal-contrib="yes">
    <name>
      <surname>Church</surname><given-names>Deanna M.</given-names>
    </name>
    <xref ref-type="aff" rid="aff1"/>
  </contrib>
  <!-- NOTE: Group authors are not yet supported by Texture! -->
  <contrib contrib-type="group" equal-contrib="yes">
    <collab>
      <named-content content-type="name">The Mouse Genome Sequencing Consortium</named-content>
      <uri content-type="entity">organisation-25</uri>
      <contrib-group>
        <contrib>
          <name>
            <surname>Kelly</surname><given-names>Laura A.</given-names>
          </name>
        </contrib>
        <contrib>
          <name>
            <surname>Randall</surname><given-names>Daniel Lee</given-names>
            <suffix>Jr.</suffix>
          </name>
        </contrib>
      </contrib-group>
    </collab>
  </contrib>
</contrib-group>

Example for editors:

<contrib-group content-type="editor">
  <contrib contrib-type="person">
    <name>
      <surname>Kastner</surname><given-names>Sabine</given-names>
    </name>
    <xref ref-type="aff" rid="aff1"/>
    <contrib-id contrib-id-type="entity">person-2</contrib-id>
  </contrib>
</contrib-group>

<contrib contrib-type="person">

contrib-id[contrib-id-type=orcid]?, contrib-id[contrib-id-type=entity]?, name, string-name[content-type=alias], bio?, email?, xref*

<contrib contrib-type="group">

collab

<disp-quote>

p+, attrib?

<disp-quote>
  <p>Curabitur vehicula mattis sodales. Orci varius natoque penatibus.</p>
  <attrib>John Doe</attrib>
</disp-quote>

<fig>

object-id[pub-id-type=doi]?, label?, caption?, graphic

NOTE: In Texture <label> is auto-generated and custom labels will be overriden.

<fig id="fig1">
  <object-id pub-id-type="doi">...</object-id>
  <label>Figure 1</label>
  <caption>
    <title>This is the figure that shows everything</title>
    <p>Lorem ipsum</p>
  </caption>
  <graphic xlink:href="images/fig1"/>
</fig>

<fn-group>

fn*

Example:

<fn-group>
  <fn id="fn1">
    <p>Lorem ipsum dolor sit amet, ea ludus intellegat.</p>
  </fn>
</fn-group>

<fn>

@id

p*

<inline-formula>

tex-math

Example:

<p>Math as part of the text <inline-formula content-type="math/tex">
  <tex-math>f\in {\mathcal C}^0([0,+\infty )).</tex-math>
</inline-formula>.</p>

<list>

NOTE: Not implemented in Texture yet.

list-item

Example for bullet list:

<list list-type="bullet">
  <list-item>
    <p>item 1</p>
  </list-item>
  <list-item>
    <list list-type="bullet">
      <list-item>
        <p>item 1.1</p>
      </list-item>
    </list>
  </list-item>
</list>

<list-item>

(list | p)?

NOTE: We allow only one list or paragraph as a child.

<media>

object-id[pub-id-type=doi]?, label?, caption?

NOTE: In Texture <label> is auto-generated and custom labels will be overriden.

Example:

<media id="media1" mime-subtype="mp4" mimetype="video" xlink:href="elife-15278-media1.mp4">
  <object-id pub-id-type="doi">10.7554/eLife.15278.004</object-id>
  <caption>
    <title>Experimental task.</title>
    <p>A monkey grasped and held highly variable objects presented on a PC-controlled turntable. Note: For presentation purposes, the video was captured in the light.
    </p>
  </caption>
</media>

<name>

surname?, given-names?, prefix?, suffix?

<person-group>

(collab | name)*

<ref>

All references are expressed as structured <element-citation> records. Unlike JATS we define a strict pattern for each publication-type value.

Spec for <element-citation>:

publication-type pattern
book person-group[person-group-type=author]?, person-group[person-group-type=editor]?, person-group[person-group-type=translator]?, edition?, year?, month?, day?, source?, publisher-loc*, publisher-name*, page-count?, pub-id[pub-id-type='doi, pmid, isbn']?, volume?, series?
chapter person-group[person-group-type=author]?, person-group[person-group-type=editor]?, person-group[person-group-type=translator]?, edition?, year?, month?, day?, chapter-title?, source?, publisher-loc*, publisher-name*, fpage?, lpage?, page-range?, elocation-id?, pub-id[pub-id-type='doi, pmid, isbn']?, volume?, series?
confproc person-group[person-group-type='author']?, article-title?, year?, month?, day?, source?, fpage?, lpage?, page-range?, elocation-id?, conf-name?, conf-loc?, pub-id[pub-id-type='doi']?
data person-group[person-group-type='author']?, data-title?, source?, year?, month?, day?, pub-id[pub-id-type="accession, ark, doi, archive"]?
magazine person-group[person-group-type=author]?, article-title?, year?, month?, day?, source?, fpage?, lpage?, page-range?, volume?, pub-id[pub-id-type='doi']?
newspaper person-group[person-group-type=author]?, article-title?, year?, month?, day?, source?, fpage?, lpage?, page-range?, volume?, pub-id[pub-id-type='doi']?, edition?, part-title?
journal person-group[person-group-type=author]?, person-group[person-group-type=editor]?, year, month?, day?, article-title, source?, volume?, issue?, fpage?, lpage?, page-range?, elocation-id?, comment?, pub-id[pub-id-type='doi, pmid']?
patent person-group[person-group-type='inventor'], collab[type=assignee]?, article-title?, year?, month?, day?, source?, patent[country='xxx']?
article (aka preprint) person-group[person-group-type=author]?, person-group[person-group-type=editor]?, year, month?, day?, article-title, source?, issue?, elocation-id?, comment?, pub-id[pub-id-type='doi, pmid']?
report person-group[person-group-type='author']?, person-group[person-group-type=sponsor]?, source?, year?, month?, day?, publisher-name*, publisher-loc*, pub-id[pub-id-type='isbn, doi']?, series?
software person-group[person-group-type='author']?, year?, month?, day?, source?, version?, publisher-loc*, publisher-name*, pub-id[pub-id-type='doi']?
thesis person-group[person-group-type='author']?, year?, month?, day?, article-title?, publisher-name*, publisher-loc*, pub-id[pub-id-type='doi']?
webpage person-group[person-group-type='author']?, article-title?, uri?, year?, month?, day?, date-in-citation[iso-8601-date=yyyy-mm-dd], source?

Notes:

  • part-title used to describe a section in a newspaper article
  • series describes things like "Technical Report Series; 949" in reports (note, that there is currently no extra field for the series number)

Example:

<ref id="r1">
  <element-citation publication-type="book">
    <person-group person-group-type="author">
      <collab>National Research Council</collab>
    </person-group>
    <year iso-8601-date="2003">2003</year>
    <source>Guidelines for the Care and Use of Mammals in Neuroscience and Behavioral Research</source>
    <publisher-loc>Washington, D.C</publisher-loc>
    <publisher-name>National Academies Press</publisher-name>
    <pub-id pub-id-type="doi">10.17226/10732</pub-id>
  </element-citation>
</ref>

<sec>

We are much stricter as the original JATS, and only allow supported block-level elements.

title?, (fig | media | table-wrap | list | p | disp-quote | sec)*

<table-wrap>

object-id[pub-id-type=doi]?, label?, caption?, table

NOTE: In Texture <label> is auto-generated and custom labels will be overriden.

<table-wrap id="tbl2" position="float">
  <object-id pub-id-type="doi">10.7554/eLife.10565.006</object-id>
  <label>Table 2.</label>
  <caption>
    <title>Table title</title>
    <p>Sequence identity matrix of the piggyBac inverted terminal repeat sequences and consensus sequences of the MER75 and MER85 human piggyBac-like elements</p>
  </caption>
  <table>...</table>
</table-wrap>

Reproducible Elements

NOTE: These are considered an extension to JATS. It requires a compatible execution engine to be attached. You can open those documents with Stencila.

code[specific-use=cell]

named-content

Example:

<code specific-use="cell">
  <named-content>
    <alternatives>
      <code specific-use="source" language="javascript" code-type="paused"><![CDATA[x = 5*5]]></code>
      <code specific-use="output" language="json"><![CDATA[{ "value_type": "number", "value": 25}]]></code>
    </alternatives>
  </named-content>
</code>

named-content[content-type=inline-cell]

Example:

<p>We got <named-content content-type="inline-cell">
    <alternatives>
      <code specific-use="source" language="javascript"><![CDATA[5*5]]></code>
      <code specific-use="output" language="json"><![CDATA[{ "value_type": "number", "value": 25}]]></code>
    </alternatives>
  </named-content> apples.
</p>

code[specific-use=cell] > named-content:

alternatives

code[specific-use=cell] > named-content > alternatives

code[specific-use=source], code[specific-use=output]

code[specific-use=cell] > named-content > alternatives > code

#PCDATA

fig[fig-type=repro-fig]

object-id[pub-id-type=doi]?, caption?, alternatives

Example:

<fig id="f1" fig-type="repro-fig">
  <caption>
    <title>Biodiversity on Mars</title>
    <p>Lorem ipsum</p>
  </caption>
  <alternatives>
    <code specific-use="source" language="mini" code-type="paused"><![CDATA[plot([11,98])]]></code>
    <code specific-use="output" language="json"><![CDATA[{"execution_time": 1, "value_type": "plot-ly", "value": {...} }]]></code>
  </alternatives>
</fig>

fig[fig-type=repro-fig] > alternatives

code[specific-use=source], code[specific-use=output]

fig[fig-type=repro-fig] > alternatives > code

@code-type paused|''
#PCDATA