JatsTech

JATS XML: Everything a Publisher Needs to Know

XML. JATS. DTD.

Do these look like random acronyms? Or maybe you’ve heard these terms and want to know why and how they matter to you as an academic publisher. In this post, we’ll discuss these terms, their uses, benefits, and implementation.

Index

 

What is JATS XML

(Already know what JATS is? Jump to ‘Benefits of JATS XML for Publishers’)

XML, short for Extensible Markup Language, is a markup language that can encode documents in a format that is:

  1. Machine processable and
  2. Human readable

There are many XML markup languages (see the entire list). Some commonly used XML in academia include CellML, Chemical Markup Language, Graph ML, MathML, ThML and more. The focus of this article is JATS XML which has rapidly become the standard in scholarly publishing.

Journal Article Tag Suite or JATS is an XML tag set designed to ‘model’ journal articles. To elaborate, JATS is a collection of XML attributes and elements that define the semantics and structure of one journal article. So, each article in a journal has its own JATS XML file. JATS cannot be used for other kinds of documents that are published, including entire journals, books, standards, etc.

There are three JATS models that target three different groups in the publishing lifecycle:

  1. Article Authoring Model — for article authors
  2. Journal Article Publishing Model — for publishers, used in the production workflow
  3. Archiving and Interchange Model — for archives and libraries

When JATS first launched in February 2003, it was meant to provide interoperability of article metadata and content between publishers and archives. So, essentially only the third model listed above was in use. It was expected that entities in the scholarly communication cycle (hosters, publishers, archives, etc.) would have their own XML tag sets and would convert articles to JATS XML only for external sharing and display. But JATS has rapidly become the standard in academic publishing. It is used not just by STEM (Scientific, Technical, Engineer, and Medical) journals — who were the early adopters — but also by journals in economics, sociology, humanities, and other fields. Let’s see why.

Benefits of JATS XML for Publishers

JATS is the true standard for journal content. Scholarly communities of small, mid-sized, and large publishers, libraries, public archives like PubMed Central, indexes, hosters and vendors all use JATS XML. While some of the largest publishers still use their internal XML tag sets, they too model their articles to JATS for interchange and deposit. Here’s why many small and mid-sized publishers are creating all their new content in JATS and converting their backfiles too to this markup language:

Production advantages for publishers

JATS XML is declarative and semantic, not behavioral (like HTML). This means that the emphasis is on the structure of the document and content, not on human interaction or styling. Therefore, articles are way easier to process in JATS.

JATS is designed to be customizable, so publishers can easily extend or subset it according to their production needs. Additionally, it is very dynamic and versions with modifications and new features are released regularly in response to users’ requests. So, as your journal grows and needs change, you can bank on JATS being able to scale with your needs.

Best Practice recommendations and tag libraries for JATS XML are extensive with examples and explanations and are freely available online for publishers to refer to. Tag sets (in RNG, DTD and XSD formats) are also freely available, as are some tools for final output generation and QA. Explore the US National Library of Medicine (NLM) website and Github (JATS4R, eLife, etc.) for these resources.

Also, JATS XML enables single source publishing, since a JATS file can be converted to any other output file — PDF, eBook, HTML5, etc. This reduces costs and saves production time.

Increase Readership, Citations and Impact Factor

This is an extremely important benefit of JATS XML. JATS files are machine-readable and searchable. This means that when publishers publish articles as JATS, these files can be accessed, read and indexed by search engines (including Google Scholar, Bing, Google, etc.). Now, whenever someone searches for a keyword that fits your article’s content, then it will show up in the search results.

This is one of the best ways to gain new readership — extremely useful for established publishers and invaluable for new publishers. Also, it is easier for other researchers to find and cite your content. Higher citations = higher impact factor!

Extensive metadata support and record

JATS has the capacity to store rich, extensive metadata with each article. And, this metadata travels with the article to wherever you publish it — your website or repository or when you submit it to indexes or archives. This is great for data mining, context-sensitive searchability (as explained above) and for semantic interchange between publishers, hosters, archives, repositories, and libraries.

Here again, you can see how this is a tremendous readership (and, therefore, citation and IF) advantage for publishers. Users of any commercial or public index or archive or even search engine can search by an author’s name or by specific keywords and find your content.

Metadata supported by JATS includes:

  1. Article-level metadata: This includes data about the article, such as the title, DOI, publisher identifiers, copyrights, arXiv numbers, institution and funder identifiers, keywords, multiple abstracts, detailed information about the research funding, links to resources, etc.
  2. Contributor metadata: Contributors to an article include not just the authors and editors, but also photographers, visualizers, curators, specimen collectors, etc. JATS can store unique external identifiers for contributors, their names, alternative names, roles, and affiliations.
  3. Bibliographic references: JATS can store detailed bibliographic metadata and supports practically all types and styles of reference tagging. For citations, JATS has specific elements including the title of article and journal, issue number, contributor names, date of publication, DOI, etc.

How to convert to JATS XML

So far so good? Now that I’ve shared with you what JATS XML is and what its benefits are, let’s look at how publishers convert documents to JATS for publication.

This is the structure of JATS articles:

Front Matter ()

journal-level metadata

article-level metadata

Body Matter ()

Text of the article, including

paragraphs

sections

figures and graphics

tables (both XHTML and CALS)

equations and quotations

Back Matter ()

appendices

bibliographic reference lists with detailed citation metadata

Publishers generally outsource the conversion of articles received from authors to third-party conversion vendors. The rates charged by these vendors vary. Some publishers may do the conversion in-house or request for JATS submissions from authors (particularly in computer science journals). New journals usually rely on volunteers to help with the conversions.

There are some tools that automate conversion to JATS XML. Typeset is one, there are some others that you may find on Github.

Typeset varies from the other conversion methods — it is far more convenient, quick, automated and, therefore, error proof, and does not call for the endless back-and-forth with third-party vendors.

Learn more on Typeset.io.

Examples of JATS XML Code

This is a full code sample from BMJ:

<front>
    <journal-meta>
      <journal-id journal-id-type="pmc">bmj</journal-id>
      <journal-id journal-id-type="pubmed">BMJ</journal-id>
      <journal-id journal-id-type="publisher">BMJ</journal-id>
      <issn>0959-8138</issn>
      <publisher>
        <publisher-name>BMJ</publisher-name>
      </publisher>
    </journal-meta>
    <article-meta>
      <article-id pub-id-type="other">jBMJ.v324.i7342.pg880</article-id>
      <article-id pub-id-type="pmid">11950738</article-id>
      <article-categories>
        <subj-group>
          <subject>Primary care</subject>
          <subj-group>
            <subject>190</subject>
            <subject>10</subject>
            <subject>218</subject>
            <subject>219</subject>
            <subject>355</subject>
            <subject>357</subject>
          </subj-group>
        </subj-group>
      </article-categories>
      <title-group>
        <article-title>Evolving general practice consultation in Britain: issues of length and context</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <name>
            <surname>Freeman</surname>
            <given-names>George K</given-names>
          </name>
          <role>professor of general practice</role>
          <xref ref-type="aff" rid="aff-a"/>
        </contrib>
        <contrib contrib-type="author">
          <name>
            <surname>Horder</surname>
            <given-names>John P</given-names>
          </name>
          <role>past president</role>
          <xref ref-type="aff" rid="aff-b"/>
        </contrib>
        <contrib contrib-type="author">
          <name>
            <surname>Howie</surname>
            <given-names>John G R</given-names>
          </name>
          <role>emeritus professor of general practice</role>
          <xref ref-type="aff" rid="aff-c"/>      
        </contrib>
        <contrib contrib-type="author">
          <name>
            <surname>Hungin</surname>
            <given-names>A Pali</given-names>
          </name>
          <role>professor of general practice</role>
          <xref ref-type="aff" rid="aff-d"/>
        </contrib>
        <contrib contrib-type="author">
          <name>
            <surname>Hill</surname>
            <given-names>Alison P</given-names>
          </name>
          <role>general practitioner</role>
          <xref ref-type="aff" rid="aff-e"/>
        </contrib>
        <contrib contrib-type="author">
          <name>
            <surname>Shah</surname>
            <given-names>Nayan C</given-names>
          </name>
          <role>general practitioner</role>
          <xref ref-type="aff" rid="aff-b"/>
        </contrib>
        <contrib contrib-type="author">
          <name>
            <surname>Wilson</surname>
            <given-names>Andrew</given-names>
          </name>
          <role>senior lecturer</role>
          <xref ref-type="aff" rid="aff-f"/>
        </contrib>
      </contrib-group>
      <aff id="aff-a">Centre for Primary Care and Social Medicine, 
          Imperial College of Science, Technology
          and Medicine, London W6 8RP</aff>
      <aff id="aff-b">Royal College of General 
          Practitioners, London SW7 1PU</aff>
      <aff id="aff-c">Department of General 
          Practice, University of Edinburgh, Edinburgh EH8 9DX</aff>
      <aff id="aff-d">Centre for Health Studies, 
          University of Durham, Durham DH1 3HN</aff>
      <aff id="aff-e">Kilburn Park Medical 
          Centre, London NW6</aff>
      <aff id="aff-f">Department of General 
          Practice and Primary Health Care, University of Leicester, Leicester 
          LE5 4PW</aff>
      <author-notes>
        <fn fn-type="con">
          <p>Contributors: GKF wrote the paper and revised it after repeated and detailed comments from all of the other authors and feedback from the first referee and from the <italic>BMJ</italic> editorial panel. All other authors gave detailed and repeated comments and cristicisms. GKF is the guarantor of the paper.</p>
        </fn>
        <fn>
          <p>Correspondence to: G Freeman <email>g.freeman@ic.ac.uk</email>
          </p>
        </fn>
      </author-notes>
      <pub-date date-type="pub" publication-format="print"
          iso-8601-date="2002-04-13">
        <day>13</day>
        <month>4</month>
        <year>2002</year>
      </pub-date>
      <volume>324</volume>
      <issue>7342</issue>
      <fpage>880</fpage>
      <lpage>882</lpage>
      <history>
        <date date-type="accepted" iso-8601-date="2002-02-07" 
           publication-format="print">
          <day>7</day>
          <month>2</month>
          <year>2002</year>
        </date>
      </history>
      <permissions>
      <copyright-statement>Copyright © 2002, BMJ</copyright-statement>
      <copyright-year>2002, </copyright-year>
      </permissions>
    </article-meta>
  </front>
  <body>
<p>In 1999 Shah<xref ref-type="bibr" rid="B1">1</xref> and others said that the Royal College of General Practitioners should advocate longer consultations in general practice as a matter of policy. The college set up a working group chaired by A P Hungin, and a systematic review of literature on consultation length in general practice was commissioned. The working group agreed that the available evidence would be hard to interpret without discussion of the changing context within which consultations now take place. For many years general practitioners and those who have surveyed patients' opinions in the United Kingdom have complained about short consultation time, despite a steady increase in actual mean length. Recently Mechanic pointed out that this is also true in the United States.<xref ref-type="bibr" rid="B2">2</xref> Is there any justification for a further increase in mean time allocated per consultation in general practice?</p>
<p>We report on the outcome of extensive debate among a group of general practitioners with an interest in the process of care, with reference to the interim findings of the commissioned systematic review and our personal databases. The review identified 14 relevant papers.
<boxed-text>
        <sec>
          <title>Summary points</title>
          <p>
            <list list-type="bullet">
              <list-item>
                <p>Longer consultations are associated with a range of better patient outcomes</p>
              </list-item>
              <list-item>
                <p>Modern consultations in general practice deal with patients with more serious and chronic conditions</p>
              </list-item>
              <list-item>
                <p>Increasing patient participation means more complex interaction, which demands extra time</p>
              </list-item>
              <list-item>
                <p>Difficulties with access and with loss of continuity add to perceived stress and poor performance and lead to further pressure on time</p>
              </list-item>
              <list-item>
                <p>Longer consultations should be a professional priority, combined with increased use of technology and more flexible practice management to maximise interpersonal continuity</p>
              </list-item>
              <list-item>
                <p>Research on implementation is needed</p>
              </list-item>
            </list>
          </p>
        </sec>
      </boxed-text>
    </p>
    <sec sec-type="subjects">
      <title>Longer consultations: benefits for patients</title>
      <p>The systematic review consistently showed that doctors with longer consultation times prescribe less and offer more advice on lifestyle and other health promoting activities. Longer consultations have been significantly associated with better recognition and handling of psychosocial problems<xref ref-type="bibr" rid="B3">3</xref> and with better patient enablement.<xref ref-type="bibr" rid="B4">4</xref> Also clinical care for some chronic illnesses is better in practices with longer booked intervals between one appointment and the next.<xref ref-type="bibr" rid="B5">5</xref> It is not clear whether time is itself the main influence or whether some doctors insist on more time.</p>
      <p>A national survey in 1998 reported that most (87%) patients were satisfied with the length of their most recent consultation.<xref ref-type="bibr" rid="B6">6</xref> Satisfaction with any service will be high if expectations are met or exceeded. But expectations are modified by previous experience.<xref ref-type="bibr" rid="B7">7</xref> The result is that primary care patients are likely to be satisfied with what they are used to unless the context modifies the effects of their own experience.</p>
    </sec>
    <sec>
      <title>Context of modern consultations</title>
      <p>Shorter consultations were more appropriate when the population was younger, when even a brief absence from employment due to sickness required a doctor's note, and when many simple remedies were available only on prescription. Recently at least five important influences have increased the content and hence the potential length of the consultation.</p>
    </sec>
    <sec>
      <title>Participatory consultation style</title>
      <p>The most effective consultations are those in which doctors most directly acknowledge and perhaps respond to patients' problems and concerns. In addition, for patients to be committed to taking advantage of medical advice they must agree with both the goals and methods proposed. A landmark publication in the United Kingdom was <italic>Meetings Between Experts</italic>, which argued that while doctors are the experts about medical problems in general patients are the experts on how they themselves experience these problems.<xref ref-type="bibr" rid="B8">8</xref> New emphasis on teaching consulting skills in general practice advocated specific attention to the patient's agenda, beliefs, understanding, and agreement. Currently the General Medical Council, aware that communication difficulties underlie many complaints about doctors, has further emphasised the importance of involving patients in consultations in its revised guidance to medical schools.<xref ref-type="bibr" rid="B9">9</xref> More patient involvement should give a better outcome, but this participatory style usually lengthens consultations.</p>
    </sec>
    <sec>
      <title>Extended professional agenda</title>
      <p>The traditional consultation in general practice was brief.<xref ref-type="bibr" rid="B2">2</xref> The patient presented symptoms and the doctor prescribed treatment. In 1957 Balint gave new insights into the meaning of symptoms.<xref ref-type="bibr" rid="B10">10</xref> By 1979 an enhanced model of consultation was presented, in which the doctors dealt with ongoing as well as presenting problems and added health promotion and education about future appropriate use of services.<xref ref-type="bibr" rid="B11">11</xref> Now, with an ageing population and more community care of chronic illness, there are more issues to be considered at each consultation. Ideas of what constitutes good general practice are more complex.<xref ref-type="bibr" rid="B12">12</xref> Good practice now includes both extended care of chronic medical problems—for example, coronary heart disease<xref ref-type="bibr" rid="B13">13</xref>—and a public health role. At first this model was restricted to those who lead change (“early adopters”) and enthusiasts<xref ref-type="bibr" rid="B14">14</xref> but now it is embedded in professional and managerial expectations of good practice.</p>
      <p>Adequate time is essential. It may be difficult for an elderly patient with several active problems to undress, be examined, and get adequate professional consideration in under 15 minutes. Here the doctor is faced with the choice of curtailing the consultation or of reducing the time available for the next patient. Having to cope with these situations often contributes to professional dissatisfaction.<xref ref-type="bibr" rid="B15">15</xref> This combination of more care, more options, and more genuine discussion of those options with informed patient choice inevitably leads to pressure on time.</p>
    </sec>
    <sec>
      <title>Access problems</title>
      <p>In a service free at the point of access, rising demand will tend to increase rationing by delay. But attempts to improve access by offering more consultations at short notice squeeze consultation times.</p>
      <p>While appointment systems can and should reduce queuing time for consultations, they have long tended to be used as a brake on total demand.<xref ref-type="bibr" rid="B16">16</xref> This may seriously erode patients' confidence in being able to see their doctor or nurse when they need to. Patients are offered appointments further ahead but may keep these even if their symptoms have remitted “just in case.” Availability of consultations is thus blocked. Receptionists are then inappropriately blamed for the inadequate access to doctors.</p>
      <p>In response to perception of delay, the government has set targets in the NHS plan of “guaranteed access to a primary care professional within 24 hours and to a primary care doctor within 48 hours.” Implementation is currently being negotiated.</p>
      <p>Virtually all patients think that they would not consult unless it was absolutely necessary. They do not think they are wasting NHS time and do not like being made to feel so. But underlying general practitioners' willingness to make patients wait several days is their perception that few of the problems are urgent. Patients and general practitioners evidently do not agree about the urgency of so called minor problems. To some extent general practice in the United Kingdom may have scored an “own goal” by setting up perceived access barriers (appointment systems and out of hours cooperatives) in the attempt to increase professional standards and control demand in a service that is free at the point of access.</p>
      <p>A further government initiative has been to bypass general practice with new services—notably, walk-in centres (primary care clinics in which no appointment is needed) and NHS Direct (a professional telephone helpline giving advice on simple remedies and access to services). Introduced widely and rapidly, these services each potentially provide significant features of primary care—namely, quick access to skilled health advice and first line treatment.</p>
    </sec>
    <sec>
      <title>Loss of interpersonal continuity</title>
      <p>If a patient has to consult several different professionals, particularly over a short period of time, there is inevitable duplication of stories, risk of naive diagnoses, potential for conflicting advice, and perhaps loss of trust. Trust is essential if patients are to accept the “wait and see” management policy which is, or should be, an important part of the management of self limiting conditions, which are often on the boundary between illness and non-illness.<xref ref-type="bibr" rid="B17">17</xref> Such duplication again increases pressure for more extra (unscheduled) consultations resulting in late running and professional frustration.<xref ref-type="bibr" rid="B18">18</xref>
      </p>
      <p>Mechanic described how loss of longitudinal (and perhaps personal and relational<xref ref-type="bibr" rid="B19">19</xref>) continuity influences the perception and use of time through an inability to build on previous consultations.<xref ref-type="bibr" rid="B2">2</xref> Knowing the doctor well, particularly in smaller practices, is associated with enhanced patient enablement in shorter time.<xref ref-type="bibr" rid="B4">4</xref> Though Mechanic pointed out that three quarters of UK patients have been registered with their general practitioner five years or more, this may be misleading. Practices are growing, with larger teams and more registered patients. Being registered with a doctor in a larger practice is usually no guarantee that the patient will be able to see the same doctor or the doctor of his or her choice, who may be different. Thus the system does not encourage adequate personal continuity. This adds to pressure on time and reduces both patient and professional satisfaction.</p>
    </sec>
    <sec>
      <title>Health service reforms</title>
      <p>Finally, for the past 15 years the NHS has experienced unprecedented change with a succession of major administrative reforms. Recent reforms have focused on an NHS led by primary care, including the aim of shifting care from the secondary specialist sector to primary care. One consequence is increased demand for primary care of patients with more serious and less stable problems. With the limited piloting of reforms we do not know whether such major redirection can be achieved without greatly altering the delicate balance between expectations (of both patients and staff) and what is delivered.</p>
    </sec>
    <sec>
      <title>The future</title>
      <p>We think that the way ahead must embrace both longer mean consultation times and more flexibility. More time is needed for high quality consultations with patients with major and complex problems of all kinds. But patients also need access to simpler services and advice. This should be more appropriate (and cost less) when it is given by professionals who know the patient and his or her medical history and social circumstances. For doctors, the higher quality associated with longer consultations may lead to greater professional satisfaction and, if these longer consultations are combined with more realistic scheduling, to reduced levels of stress.<xref ref-type="bibr" rid="B20">20</xref> They will also find it easier to develop further the care of chronic disease.</p>
      <p>The challenge posed to general practice by walk-in centres and NHS Direct is considerable, and the diversion of funding from primary care is large. The risk of waste and duplication increases as more layers of complexity are added to a primary care service that started out as something familiar, simple, and local and which is still envied in other developed countries.<xref ref-type="bibr" rid="B21">21</xref> Access needs to be simple, and the advantages of personal knowledge and trust in minimising duplication and overmedicalisation need to be exploited.</p>
      <p>We must ensure better communication and access so that patients can more easily deal with minor issues and queries with someone they know and trust and avoid the formality and inconvenience of a full face to face consultation. Too often this has to be with a different professional, unfamiliar with the nuances of the case. There should be far more managerial emphasis on helping patients to interact with their chosen practitioner<xref ref-type="bibr" rid="B22">22</xref>; such a programme has been described.<xref ref-type="bibr" rid="B23">23</xref> Modern information systems make it much easier to record which doctor(s) a patient prefers to see and to monitor how often this is achieved. The telephone is hardly modern but is underused. Email avoids the problems inherent in arranging simultaneous availability necessary for telephone consultations but at the cost of reducing the communication of emotions. There is a place for both.<xref ref-type="bibr" rid="B2">2</xref> Access without prior appointment is a valued feature of primary care, and we need to know more about the right balance between planned and ad hoc consulting.</p>
    </sec>
    <sec>
      <title>Next steps</title>
      <p>General practitioners do not behave in a uniform way. They can be categorised as slow, medium, and fast and react in different ways to changes in consulting speed.<xref ref-type="bibr" rid="B18">18</xref> They are likely to have differing views about a widespread move to lengthen consultation time. We do not need further confirmation that longer consultations are desirable and necessary, but research could show us the best way to learn how to introduce them with minimal disruption to the way in which patients and practices like primary care to be provided.<xref ref-type="bibr" rid="B24">24</xref> We also need to learn how to make the most of available time in complex consultations.</p>
      <p>Devising appropriate incentives and helping practices move beyond just reacting to demand in the traditional way by working harder and faster is perhaps our greatest challenge in the United Kingdom. The new primary are trusts need to work together with the growing primary care research networks to carry out the necessary development work. In particular, research is needed on how a primary care team can best provide the right balance of quick access and interpersonal knowledge and trust.</p>
    </sec>
  </body>
  <back>
    <ack>
      <p>We thank the other members of the working group: Susan Childs, Paul Freeling, Iona Heath, Marshall Marinker, and Bonnie Sibbald. We also thank Fenny Green of the Royal College of General Practitioners for administrative help.</p>
    </ack>
    <ref-list>
      <ref id="B1">
        <label>1</label>
        <element-citation publication-type="journal" publication-format="print">
          <person-group person-group-type="author">
            <name>
              <surname>Shah</surname>
              <given-names>NC</given-names>
            </name>
          </person-group>
          <article-title>Viewpoint: Consultation time—time for a change? Still the “perfunctory work of perfunctory men!”</article-title>
          <source>Br J Gen Pract</source>
          <year iso-8601-date="1999">1999</year>
          <volume>49</volume>
          <fpage>497</fpage>
        </element-citation>
      </ref>
      <ref id="B2">
        <label>2</label>
        <element-citation publication-type="journal" publication-format="print">
          <person-group person-group-type="author">
            <name>
              <surname>Mechanic</surname>
              <given-names>D</given-names>
            </name>
          </person-group>
          <article-title>How should hamsters run? Some observations about sufficient patient time in primary care</article-title>
          <source>BMJ</source>
          <year iso-8601-date="2001">2001</year>
          <volume>323</volume>
          <fpage>266</fpage>
          <lpage>268</lpage>
          <pub-id pub-id-type="pmid">11485957</pub-id>
        </element-citation>
      </ref>
      <ref id="B3">
        <label>3</label>
        <element-citation publication-type="journal" publication-format="print">
          <person-group person-group-type="author">
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              <surname>Howie</surname>
              <given-names>JGR</given-names>
            </name>
            <name>
              <surname>Porter</surname>
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            </name>
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            </name>
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              <surname>Hopton</surname>
              <given-names>JL</given-names>
            </name>
          </person-group>
          <article-title>Long to short consultation ratio: a proxy measure of quality of care for general practice</article-title>
          <source>Br J Gen Pract</source>
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        </element-citation>
      </ref>
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        <label>4</label>
        <element-citation publication-type="journal" publication-format="print">
          <person-group person-group-type="author">
            <name>
              <surname>Howie</surname>
              <given-names>JGR</given-names>
            </name>
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              <surname>Heaney</surname>
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            </name>
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        </element-citation>
      </ref>
      <ref id="B5">
        <label>5</label>
        <element-citation publication-type="journal" publication-format="print">
          <person-group person-group-type="author">
            <name>
              <surname>Kaplan</surname>
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</article> 

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