JATS & MECA Improvements

Contributors¶

Author Names

We have broken out author name information into <given-names> and <surname> #586

string-name has been removed when there is a better alternative #653

Credit Roles

We are following the JATS4R recommendations (docs) on adding valid JATS roles for 1.2 DTD and above. #650

<role
  vocab="credit"
  vocab-identifier="https://credit.niso.org/"
  vocab-term="Conceptualization"
  vocab-term-identifier="https://credit.niso.org/contributor-roles/conceptualization/">
    Conceptualization
</role>

Bugs were fixed on the vocab-term attribute #649

Non-credit roles are no longer labeled as such, and are simply a <role>

Sections & Abstracts¶

Data Availability

We have added a data-availability part to the <back> element; following JATS4R

<back>
  <sec sec-type="data-availability">
    <title>Data Availability</title>
    <p> ... </p>
  </sec>
  <ref-list>
    ...
  </ref-list>
</back>

Acknowledgements

A stand-alone acknowledgements section can now be added to the <back>

Outstanding, see below, per-author acknowledgements and comments

Multiple abstracts

article.xml

The additional abstracts now have a abstract-type #638

The plain-language-summary is now tagged correctly #648

Key points are added in as an abstract with type "key-points"

<abstract>
  <p>...</p>
</abstract>
<abstract abstract-type="plain-language-summary">
  <title>Plain Language Summary</title>
  <p>...</p>
</abstract>
<abstract abstract-type="key-points">
  <title>Key Points</title>
  <p>...</p>
</abstract>

Keywords¶

Keywords: Keywords are now added to the frontmatter #596

Funding Information¶

Funding: We have added the ability to add funding information and this be passed through to the frontmatter appropriately #596; Added support for open_funder_registry (docs) #654

Custom Manifest¶

EJP does not follow MECA standards for the xlink:href links. We have reprocessed these and left href="" in the manifest.xml file for integration purposes.

Transfer Details¶

EJP does not follow MECA standards for the transfer.xml, we are using the simplified DTD (e.g. role instead or contact-role, title instead of publication-title). We have adopted this DTD for the transfer.xml file for integration purposes. This has also been added to the manifest.xml.

We have added a transfer.xml file:

Full transfer.xml

transfer.xml

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE transfer PUBLIC "-//MECA//DTD Manifest v1.0//en" "https://meca.zip/transfer-ejp.dtd">
<transfer version="1.0" xmlns="https://manuscriptexchange.org/schema/transfer">
  <source>
    <service-provider>
      <provider-name>Curvenote Inc.</provider-name>
      <contact>
        <contact-name>
          <surname>Support</surname>
          <given-names>Curvenote</given-names>
        </contact-name>
        <email>support@curvenote.com</email>
      </contact>
    </service-provider>
    <publication type="submission-system">
      <title>Curvenote Submission System</title>
      <contact>
        <contact-name>
          <surname>Support</surname>
          <given-names>Curvenote</given-names>
        </contact-name>
        <email>support@curvenote.com</email>
      </contact>
    </publication>
  </source>
  <destination>
    <service-provider>
      <provider-name>eJournalPress</provider-name>
      <contact>
        <contact-name>
          <surname>Support</surname>
          <given-names>eJournalPress</given-names>
        </contact-name>
        <email>support@ejournalpress.com</email>
      </contact>
    </service-provider>
    <publication type="journal">
      <title>AGU Journal Test</title>
      <acronym>eatest</acronym>
      <contact>
        <contact-name>
          <surname>Support</surname>
          <given-names>eJournalPress</given-names>
        </contact-name>
        <email>support@ejournalpress.com</email>
      </contact>
    </publication>
  </destination>
  <processing-instructions>
    <comments>Manuscript and notebooks for peer-review</comments>
  </processing-instructions>
</transfer>

Link to original notebooks¶

We have chosen to do add a self-uri for the notebooks in Curvenote. (article.xml)

<self-uri xlink:href="https://agu.curvenote.com/not-a-link-yet?authenticated" content-type="notebooks">Explore reproducible notebooks of this publication in Curvenote.</self-uri>

The link does not currently work (and will be different), but hopefully the XML works for this purpose and follows JATS XML (see docs).

LaTeX Output¶

We have added a single ZIP file in the MECA bundle tex.zip (referenced in the manifest.xml) #630. This has also been added to the manifest.xml.

Miscellaneous¶

Changed the default formatting on XML output
We have updated the names of the meca bundles to end with .meca
Where appropriate, inline math has been simplified to inline elements (simple characters π or super/subscripts)

Planned improvements (by Oct. 31)¶

Add <author-notes> section to frontmatter (comments, notes, coi)
- Conflict of interest statements (per author and grouped) JATS4R
MyST Template improvements (especially around keypoints which are repeated)
Post processing of QMD JATS output to align to same standards
Journal name & identifiers for AGU target journal
Custom ID prefixes for all elements
Submission history

Sept. 2023¶

Additional files in the MECA bundles have been removed (e.g. *.webp)
Abstract is now an XML node #561, #638