October 5, 2015

What's New in Edifix 2.3

Computer on a table with autumn leaves in the background

Autumn has arrived in New England. Leaves are turning, apples are baking, and Edifix is updating!

JATS XML Exports

In parallel with the HTML and Word doc export options, the JATS XML export option is now View-dependent! This means that you can export your references to JATS XML with or without the annotated changes and warnings.

JATS (the Journal Article Tag Suite) is the latest version of what was known as the NLM Journal Publishing XML DTD, an XML DTD that has been widely adopted by a large number of publishers of scholarly journals. It defines XML elements and attributes that describe the content and metadata of journal articles, including bibliographic references. JATS XML does not define the presentational style of the reference; it identifies the semantic meaning of each element of the reference, allowing the reference to be rendered in any style.

You can use the JATS XML from Edifix in different production workflows, such as in depositing your published references to PubMed Central or transforming your articles from XML to ePub, HTML, or PDF!

For those who want more flexibility from the Edifix-generated XML, this latest update is for you!

Examples

The following reference can be exported to three different variations of JATS XML:

  1. Van Luit JE, Van der Molen MJ. The effectiveness of Korean number naming on insight into numbers in Dutch students with mild intellectual disabilities. Res Dev Disabil. 2011;32(5):1822-1828. http://dx.doi.org/10.1016/j.ridd.2011.03.014. PMID:21498042.

PubMed reports that reference 1 "Van Luit, Van der Molen, 2011" was retracted in "Res Dev Disabil. 2011 Nov-Dec;32(6):3018".

All variations include the following <front> block at the beginning of the XML, which details statistics such as the editorial style, the number of journal references parsed, and the number of references linked to PubMed.

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Journal Archiving and Interchange DTD v1.0 20120330//EN" "JATS-archivearticle1.dtd">
<article xmlns:xlink="http://www.w3.org/1999/xlink" xml:lang="en" dtd-version="1.0" article-type="reference-list">
<front>
<article-meta>
<custom-meta-group>
<custom-meta><meta-name>TotalReferences</meta-name><meta-value>1</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesParsed</meta-name><meta-value>1</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesBillable</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>LinkServices</meta-name><meta-value>pubmed-crossref</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesLinked</meta-name><meta-value>1</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesLinkedDOI</meta-name><meta-value>1</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesLinkedPMID</meta-name><meta-value>1</meta-value></custom-meta>
<custom-meta><meta-name>JournalReferences</meta-name><meta-value>1</meta-value></custom-meta>
<custom-meta><meta-name>BookReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>BookChapterReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>ConferenceReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>ElectronicReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>DissertationReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>LegalReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>StandardReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>OtherReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>UnknownReferences</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesSemiParsed</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>ReferencesBookUnparsed</meta-name><meta-value>0</meta-value></custom-meta>
<custom-meta><meta-name>EditorialStyle</meta-name><meta-value>AMA</meta-value></custom-meta>
</custom-meta-group>
</article-meta>
</front>

The XML for each reference then reflects what is displayed on each view.

From the Show Changes view, the XML includes the tracked changes and warnings in the <annotation> element:

<back>
<ref-list>
<ref id="b1"><label>1. </label><mixed-citation publication-type="journal" specific-use="restruct"><?corrected-journal-title Research in Developmental Disabilities?><?corrected-abbrev-journal-title Res. Dev. Disabil.?><person-group person-group-type="author"><string-name><surname>Van Luit</surname> <given-names>JE</given-names></string-name>, <string-name><surname>Van der Molen</surname> <given-names>MJ</given-names></string-name></person-group>. <article-title>The effectiveness of Korean number naming on insight into numbers in Dutch students with mild intellectual disabilities.</article-title> <source>Res Dev Disabil</source>. <year>2011</year>;<volume>32</volume>(<issue>5</issue>):<fpage>1822</fpage>-<lpage>1828</lpage>. <pub-id pub-id-type="doi">10.1016/j.ridd.2011.03.014</pub-id><pub-id pub-id-type="pmid">21498042</pub-id><issn>0891-4222</issn><annotation>
<p content-type="diff">1.<strike> J. E.</strike> Van Luit<underline> JE</underline>,<strike> M.J.</strike> Van der Molen<underline> MJ</underline>. The effectiveness of Korean number naming on insight into numbers in Dutch students with mild intellectual disabilities. Res<strike>.</strike> Dev<strike>.</strike> Disabil. <underline>2011;</underline>32<strike>, </strike><underline>(5):</underline>1822<strike> </strike><underline>-</underline><strike>(201</strike>1<strike>)</strike><underline>828.</underline></p>
<p content-type="warning">PubMed reports that reference 1 "Van Luit, Van der Molen, 2011" was retracted in "Res Dev Disabil. 2011 Nov-Dec;32(6):3018".</p></annotation></mixed-citation></ref>
</ref-list>
</back>
</article>

From the References + Links/Comments view, the XML includes warnings but not the tracked changes:

<back>
<ref-list>
<ref id="b1"><label>1. </label><mixed-citation publication-type="journal" specific-use="restruct"><person-group person-group-type="author"><string-name><surname>Van Luit</surname> <given-names>JE</given-names></string-name>, <string-name><surname>Van der Molen</surname> <given-names>MJ</given-names></string-name></person-group>. <article-title>The effectiveness of Korean number naming on insight into numbers in Dutch students with mild intellectual disabilities.</article-title> <source>Res Dev Disabil</source>. <year>2011</year>;<volume>32</volume>(<issue>5</issue>):<fpage>1822</fpage>-<lpage>1828</lpage>. <pub-id pub-id-type="doi">10.1016/j.ridd.2011.03.014</pub-id><pub-id pub-id-type="pmid">21498042</pub-id><issn>0891-4222</issn><annotation><p content-type="warning">PubMed reports that reference 1 "Van Luit, Van der Molen, 2011" was retracted in "Res Dev Disabil. 2011 Nov-Dec;32(6):3018".</p></annotation></mixed-citation></ref>
</ref-list>
</back>
</article>

From the References Only view, the XML does not include any tracked changes or comments:

<back>
<ref-list>
<ref id="b1"><label>1. </label><mixed-citation publication-type="journal" specific-use="restruct"><person-group person-group-type="author"><string-name><surname>Van Luit</surname> <given-names>JE</given-names></string-name>, <string-name><surname>Van der Molen</surname> <given-names>MJ</given-names></string-name></person-group>. <article-title>The effectiveness of Korean number naming on insight into numbers in Dutch students with mild intellectual disabilities.</article-title> <source>Res Dev Disabil</source>. <year>2011</year>;<volume>32</volume>(<issue>5</issue>):<fpage>1822</fpage>-<lpage>1828</lpage>. <pub-id pub-id-type="doi">10.1016/j.ridd.2011.03.014</pub-id><pub-id pub-id-type="pmid">21498042</pub-id><issn>0891-4222</issn></mixed-citation></ref>
</ref-list>
</back>
</article>

Overage charges

If your volume of work does not fit neatly into one of our many subscription options, you can always subscribe to the lower subscription tier and take advantage of our Overage References system.

When you exceed your reference allowance, you are prompted to process the additional references for a per-reference fee. You can now choose to accept this per-reference fee automatically, decreasing the number of clicks between you and your beautifully Edifixed references.

The next time you are prompted to accept the per-reference fee, you can choose to process all references over your reference allowance for an additional per reference fee without being prompted by checking the box at the bottom of the dialog:

Overage charge dialog

If you choose to automatically accept the overage charges that are accrued when you Edifix references in excess of your allowance, you will not be prompted to accept any estimated overage fees. When your overage fees have accrued to meet or exceed the cost of your reference subscription, you will be prompted to submit a payment for these charges. Otherwise, you will be billed for your overage charge balance when your subscription renews.

You can change your mind at any time and disable this option on your Settings page.

Email subscriptions

In addition to the overage charges option, there are more email subscription options available on your Settings page. You can now choose to opt-out of newsletters, product offers, technical updates, or all of the above!

Have new features to request or bugs to report for our next release cycle? We're always happy to hear from you.


Link: http://www.edifix.com/blog/blog/What%27s-new-in-Edifix-2.3.html