Error guide

Malformed references in JATS XML

The malformed references error groups failures in the <back> block related to bibliographic citations: missing mandatory elements, incorrect publication-type, malformed DOI, or use of <mixed-citation> when the indexer requires parseable structure. It is a leading cause of returns in SciELO and PMC.

References in JATS are not decorative text: they feed citation linking, impact metrics, and discovery in databases. An incomplete <ref-list> can invalidate an article whose body is perfect.

Preferred format: element-citation

SciELO and PMC favor structured citations:

<ref id="ref1">
  <element-citation publication-type="journal">
    <person-group person-group-type="author">
      <name>
        <surname>Garcia</surname>
        <given-names>Maria</given-names>
      </name>
    </person-group>
    <article-title>Cited article title</article-title>
    <source>Scientific Journal</source>
    <year>2024</year>
    <volume>10</volume>
    <issue>3</issue>
    <fpage>45</fpage>
    <lpage>52</lpage>
    <pub-id pub-id-type="doi">10.1234/sj.2024.003</pub-id>
  </element-citation>
</ref>

Each publication-type requires different subelements:

Type	Minimum elements
`journal`	Author, article title, source, year
`book`	Author, title, publisher, year
`web`	Title, URI, access date
`thesis`	Author, title, institution, year

Frequent errors

1. DOI with URL prefix

Incorrect:

<pub-id pub-id-type="doi">https://doi.org/10.1234/example</pub-id>

Correct:

<pub-id pub-id-type="doi">10.1234/example</pub-id>

2. Missing or incorrect publication-type

Incorrect:

<element-citation>
  <article-title>Title</article-title>
  <year>2024</year>
</element-citation>

Correct:

<element-citation publication-type="journal">
  <article-title>Title</article-title>
  <source>Journal</source>
  <year>2024</year>
</element-citation>

3. Reference without year

Citations without <year> fail business-rule validators even when the XSD partially accepts them.

4. mixed-citation without structure

<ref id="ref2">
  <mixed-citation publication-type="journal">
    Perez J, Lopez A. Title. Journal. 2023;12(4):100-110.
  </mixed-citation>
</ref>

Acceptable in some contexts but hinders automatic validation. Migrate to <element-citation> when possible.

5. Duplicate or missing ref ID

Each <ref> cited from the body needs a unique id:

<p>As reported <xref ref-type="bibr" rid="ref1">1</xref>...</p>

Without id="ref1" on the corresponding reference, linking breaks.

Book and book chapter

<ref id="ref3">
  <element-citation publication-type="book">
    <person-group person-group-type="author">
      <name><surname>Smith</surname><given-names>John</given-names></name>
    </person-group>
    <source>Book title</source>
    <publisher-name>Academic Press</publisher-name>
    <year>2022</year>
    <isbn>978-3-16-148410-0</isbn>
  </element-citation>
</ref>

Web resource

<ref id="ref4">
  <element-citation publication-type="web">
    <person-group person-group-type="author">
      <collab>World Health Organization</collab>
    </person-group>
    <article-title>Report title</article-title>
    <year>2025</year>
    <ext-link ext-link-type="uri" xlink:href="https://www.who.int/example">
      https://www.who.int/example
    </ext-link>
    <date-in-citation content-type="access-date">
      <day>01</day><month>06</month><year>2026</year>
    </date-in-citation>
  </element-citation>
</ref>

Bulk correction strategy

Export references to a spreadsheet with columns: author, title, source, year, DOI.
Normalize DOI (no URL prefix).
Assign publication-type per row.
Regenerate <element-citation> from template.
Validate the batch in the JATS validator.
Manually review ambiguous cases (no author, no year, websites).

Relation to other errors

References misplaced in <body> cause invalid document structure. Missing attributes on <ref> are documented in missing required attribute.

For systematic conversion, see JATS XML production or editorial validation.

Conclusion

Malformed references are predictable in Word conversions but avoidable with templates and early validation. Investing in structured <element-citation> improves indexing, citation, and compliance in SciELO and PMC.

Validate your references in the JATS validator and read common JATS errors for full context.