1. Article XML vs. Issue XML
Capturing the Table of Contents under the NLM DTD
Nikos Markantonatos
JATS-Con 2011 / Sep 26, 2011
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

2. JATS has the article at its core
JATS design specifically chose the article as its central element:
Most available DTDs model the article
Article is the most granular publishing entity
Capturing the article content in XML can be challenging
<article> </article>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

3. Articles carry publication context
Most articles are not published independently:
Articles are typically included in issues
Issues belong to journals
Publishers publish journals
Article 1
Article 1
Issue 1
Article 2
Publisher
Journal
Article 3
Article 4
Issue 2
Article 5
Article 6
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

4. Article front matter
Information about this entire structure is captured inside the article XML <front> element:
<article>
<front>
<journal-meta>
<journal-id-type="publisher">Br Med J</journal-id>
<issn> </issn>
<publisher>
<publisher-name>British Medical Journal</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid"> </article-id>
<title-group><article-title>...</article-title></title-group>
<contrib-group>...</contrib-group> <pub-date pub-type="pub">...</pub-date>
<volume>318</volume>
<issue>7187</issue>
<fpage>837</fpage><lpage>841</lpage>
</article-meta>
</front>
</article>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

5. Publication entities
Information is bundled inside article <front> element for completeness purposes, but refers to distinct publication entities:
Article
Issue containing the article
Journal including this issue
Publisher publishing this journal
<front>
Journal
Publisher
Article
Issue
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

6. Metadata referring to the
Article:
Article title
Contributors
Address for correspondence
Abstract
History dates
Article identifiers (doi, pmid)
Article categories
Keywords
Copyright statements
Count statistics
Publishing Context:
Journal title
ISSN
Journal identifiers
Publisher name/location
Volume number
Issue number
Publication date
ToC heading
Issue title
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

7. Limitations of current approach
Articles published in the same issue repeat the same issue and journal metadata:
When these metadata differ, it is hard to tell which version is the correct one
When corrections need to be applied, these must be replicated across all article XMLs
Issue
<front>
<front>
<front>
<front>
<front>
Article 1
Article 2
Article 3
Article 4
Article 5
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

8. Limitations of current approach
To locate all articles belonging to the same issue, an exhaustive search across all article XMLs is necessary:
There is no place where all articles of an issue are explicitly listed
<front>
<front>
Article
Article
<front>
<front>
Article
Article
<front>
<front>
Article
Article
<front>
Article
<front>
Article
<front>
<front>
<front>
Article
Article
Article
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

9. Limitations of current approach
Publishers wishing to present an online version of the Table of Contents need additional metadata:
Nested headings
Issue page range & page count
Cover page & cover caption
Issue self uri and doi
Issue editors
Links to related issues
Supplementary material for the issue
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

10. Limitations of current approach
There is an implicit assumption that an article corresponds to at most one issue, volume, journal and publisher:
<!ELEMENT front (journal-meta?, article-meta,
(def-list|list|notes)*) >
<!ELEMENT journal-meta (journal-id*, journal-title-group*, issn*, isbn*, publisher?, notes?, custom-meta-group?) >
<!ELEMENT article-meta (article-id*, article-categories?, title-group?, (contrib-group | aff | x)*, author-notes?, pub- date*, volume?, volume-id*, volume-series?, issue?, issue-id*, issue-title*, issue-sponsor*, issue-part?, isbn*, supplement?, (((fpage, lpage?)?, page-range?) | elocation-id)?, ( | ext-link | uri | product | supplementary-material)*, history?, permissions?, self-uri*, related-article*, abstract*, trans- abstract*, kwd-group*, funding-group*, conference*, counts?, custom-meta-group?) >
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

11. Article collections
An article may find itself belonging to several collections
Changing the article XML each time is a poor choice
Forthcoming Issue
Online Early Issue
Article
Article
Printed Issue
Article
Online Collection 1
Online Collection 2
Article
Article
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

12. What if…
What if all information not directly related to the article itself, but to its publishing context is extracted out of the article XML, so that:
article XML need only change when information in the article itself changes
information about where the article is published is maintained authoritatively in a single place
metadata about the issue, volume, journal and publisher is not reproduced in each article XML
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

13. Rationale behind Issue XML
Extract all metadata referring to the publishing context out of the article XML and into a separate Issue XML:
Issue
<front>
<front>
<front>
<front>
Article
Article
Article
Article
Issue XML
<front>
<front>
<front>
<front>
Article
Article
Article
Article
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

14. Rationale behind Issue XML
Now it is the Issue XML that points to the articles it contains
Article XMLs include only metadata for the article itself
Issue
Article
Article
Article
Article
Issue XML
Article
Article
Article
Article
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

15. Collection updates
Through the use of Issue XML, you do not need to update the article XML every time the article:
switches from one collection to another
becomes a new member in a collection
drops out of a collection
Another
Collection
Article Collection
Article
Issue XML
Article
Article
Article
Article
Online Collection 2
Article
Article
New
Deleted
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

16. What is Issue XML?
Single authoritative XML file containing metadata for the publishing context of an article:
Journal title/issn
Publisher information
Volume/issue numbers
Cover date
Issue title
Issue editors
Issue doi/self uri
Count statistics
Issue page range
Cover image & caption
Encodes the issue Table of Contents:
First/last issue pages
Article sequence
Nested ToC headings
ToC abstracts
References external resources of the issue:
Issue-wide PDF
Table of Contents PDF
Issue-wide index
Instructions to the authors
Links to other related issues
Supplementary issue
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

17. Top-level Rule Issue XML root element definition: (optional)
<!ELEMENT issue-xml ( journal-meta?, issue-meta, toc+ )>
<issue-xml>
<journal-meta>
</journal-meta>
<issue-meta>
</issue-meta>
<toc>
</toc>
</issue-xml>
(optional)
(exactly one)
(one or more)
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

18. Sample Issue XML <issue-xml> <journal-meta>
<journal-id journal-id-type="publisher-id“>gen</journal-id>
<journal-title-group>
<journal-title>Genesis</journal-title>
</journal-title-group>
<issn pub-type="ppub"> </issn>
<publisher><publisher-name>The MIT Press</publisher-name></publisher>
</journal-meta>
<issue-meta>
<pub-date pub-type="ppub">
<month>July</month><year>2011</year>
</pub-date>
<volume>82</volume>
<issue>7</issue>
<issue-id pub-id-type="doi"> /gen issue-7</issue-id>
</issue-meta>
<toc>
<toc-article-meta>
<article-id pub-id-type="doi"> /article.A</article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /article.B</article-id>
<article-id pub-id-type="doi"> /article.C</article-id>
</toc>
</issue-xml>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

19. Issue XML: <journal-meta>
<journal-meta> is defined directly by JATS:
<ELEMENT journal-meta (journal-id*, journal-title-group*, issn*,
isbn*, publisher?, notes?, custom-meta-group?) >
<issue-xml>
<journal-meta>
<journal-id journal-id-type="publisher-id">gen</journal-id>
<journal-title-group>
<journal-title>Genesis</journal-title>
</journal-title-group>
<issn pub-type="ppub"> </issn>
<publisher><publisher-name>Wiley-Liss</publisher-name></publisher>
</journal-meta>
</issue-xml>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

20. Issue XML: <issue-meta>
<issue-meta> extracts all those elements from <article-meta> that refer to the issue and not to the article itself:
<pub-date>
<volume>/<issue>
<volume-id>
<issue-id>
<issue-title>
<issue-sponsor>
<issue-part>
<series-title>
<issue-meta> also borrows some elements from <article-meta>, but they now refer to the issue level and not to the article level:
<contrib-group>
<author-notes>
<kwd-group>
<fpage>/<lpage>
<page-range>
<self-uri>
<supplement>
<funding-group>
<conference>
<counts>
<custom-meta-group>
<related-issue>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

21. Issue XML: <issue-meta>
<!ELEMENT issue-meta ( contrib-group*, author-notes?, pub-date*, series-title*, series-text?, volume?, volume-id*,
volume-series?, issue?, issue-id*, issue-title*,
issue-sponsor*, issue-part?, supplement?, fpage?, lpage?, page-range?, copyright-statement?, copyright-year?, permissions?, self-uri*, related-issue*, kwd-group*, funding-group*, conference*, counts?, custom-meta-group? ) >
<issue-xml>
<issue-meta>
<pub-date pub-type="ppub">
<month>July</month><year>2011</year>
</pub-date>
<volume>82</volume>
<issue>7</issue>
<issue-id pub-id-type="doi"> /gen issue-7</issue-id>
<self-uri xlink:href=
</issue-meta>
</issue-xml>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

22. Issue XML: <toc>
<!ELEMENT toc ( cover?,
( toc-subject-group | p | toc-article-meta )* )>
<!ELEMENT toc-article-meta ( article-id+ ) ... >
<issue-xml>
<toc>
<toc-article-meta>
<article-id pub-id-type="doi"> /article.A</article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /article.B</article-id>
<article-id pub-id-type="doi"> /article.C</article-id>
</toc>
</issue-xml>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

23. Article references in <toc>
Issue XML includes references to all articles it contains
Only a reference to the article is necessary in the simplest case; article metadata is made available directly out of article XML
Article references may appear as part of one or more issue XMLs
Forthcoming Issue
Article
Issue XML
Issue XML
Article
<toc>
...
</toc>
<toc>
...
</toc>
Article
Article
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

24. Table of Contents example
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

25. Dictate order of articles in ToC
<toc-article-meta>
<article-id pub-id-type="doi"> /article.A</article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /article.B</article-id>
<article-id pub-id-type="doi"> /article.C</article-id>
</toc>
Reordering the article references in <toc> is more intuitive than changing article sequences across all article XMLs.
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

26. Reorder ToC article entries
When ToC headings to appear in the ToC are picked up from <subj-group sub-group-type="heading“>, it is difficult to visualize the ToC with all of its headings
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

27. Embed ToC headings <toc> <toc-subject-group>
<toc-subject-title>
<subject>Cell Biology</subject>
</toc-subject-title>
<toc-article-meta>
<article-id pub-id-type="doi"> /article.A</article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /article.B</article-id>
</toc-subject-group>
<subject>Molecular Biology</subject>
<article-id pub-id-type="doi"> /article.C</article-id>
<article-id pub-id-type="doi"> /article.D</article-id>
</toc>
When ToC headings to appear in the ToC are picked up from <subj-group sub-group-type="heading“>, it is difficult to visualize the ToC with all of its headings
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

28. ToC headings example
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

29. Nested ToC headings
Owing to the recursive nature of <toc-subj-group> headings can be nested at arbitrary depth
In analogy with other recursive elements in JATS
<!ELEMENT toc ( cover?,
( toc-subject-group | p | toc-article-meta )* )>
<!ELEMENT toc-subject-group ( toc-subject-title,
( toc-article-meta | p | toc-subject-group )*) >
<!ELEMENT toc-subject-title ( p*, subject, p*,
trans-toc-subject* ) >
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

30. Embed nested ToC headings
<toc-subject-group>
<toc-subject-title>
<subject>BIOLOGY</subject>
</toc-subject-title>
<subject>Cell Biology</subject>
<toc-article-meta>
<article-id pub-id-type="doi"> /article.A</article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /article.B</article-id>
</toc-subject-group>
<subject>Molecular Biology</subject>
<article-id pub-id-type="doi"> /article.C</article-id>
</toc>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

31. Nested ToC headings
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

32. Multi-lingual headings
Support for multi-lingual headings:
<!ELEMENT toc-subject-title ( p*, subject, p*,
trans-toc-subject* ) >
<toc xml:lang="en">
<toc-subject-group>
<toc-subject-title>
<subject>Cell Biology</subject>
<trans-toc-subject xml:lang="fr">
<subject>Biologie Cellulaire</subject>
</trans-toc-subject>
</toc-subject-title>
<toc-article-meta>
<article-id pub-id-type="doi"> /article.A</article-id>
</toc-article-meta>
</toc-subject-group>
</toc>
Cell Biology / Biologie Cellulaire
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

33. ToC annotations
Support for interspersed paragraphs of text between article entries:
<!ELEMENT toc ( cover?,
( toc-subject-group | p | toc-article-meta )* )>
<!ELEMENT toc-subject-group ( toc-subject-title,
( toc-article-meta | p | toc-subject-group )*) >
Support for paragraphs of text above and below a heading at any nesting level:
<!ELEMENT toc-subject-title ( p*, subject, p*,
trans-toc-subject* ) >
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

34. Annotated ToC headings
Proceedings from the Second International Conference on Human Biology
Session I: Sep 15, 2011
Achieving controlled reprogramming of differentiated cells into a desired cell type would open new opportunities in stem cell biology and regenerative medicine. Experimentation on cell reprogramming requires a model in which cell conversion can be induced and tracked individually. The tiny nematode, Caenorhabditis elegans, owing to its ….
We report on a fetus presenting with an increased nuchal translucency, in which chorionic villus sampling led to the diagnosis of mosaic trisomy 8. Ultrasound scan performed at 15(+6) weeks revealed bilateral cleft lip and palate, flat facial profile, and arrhinia. Pregnancy was terminated at 16(+6) ; postmortem examination showed additional….
Session II: Sep 16, 2011
prdm1 is an important transcriptional regulator that plays diverse roles during development of a wide variety of vertebrate and invertebrate species. prdm1 is required for neural crest specification in zebrafish, but not in mouse embryos. The role of this gene in neural crest formation in other species has not been examined, and its ….
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

35. Special ToC entries
format attribute in <toc-article-meta> allows for article entries in the ToC to be:
specially indented
highlighted
placed inside a box
fine-printed
hidden
placed on a side-table
<!ATTLIST toc-article-meta format CDATA #IMPLIED >
<toc-article-meta format="invisible">
<article-id pub-id-type="doi"> /article-no-ToC</article-id>
</toc-article-meta>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

36. Highlighted ToC entry
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

37. Override article metadata
<toc-article-meta> can do a lot more than reference an article:
Allows for a fully custom ToC article entry
Includes those elements of <article-meta> which make sense in a ToC entry
Any element defined inside <toc-article-meta> is meant to override the corresponding value from the article XML for the purposes of ToC rendering
<!ENTITY toc-article-meta ( article-id+, title-group?,
( contrib-group | aff | %x.class; )*, author-notes?,
((fpage?, lpage?, page-range?) | elocation-id )?,
(%address-link.class;|product|supplementary-material)*,
history?, self-uri*, related-article*, abstract*,
trans-abstract*, toc-graphic*, counts? )" >
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

38. Override ToC authors
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

39. Override ToC authors
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

40. Override ToC authors . . . . <toc-article-meta>
<article-id pub-id-type="doi"> /595693</article-id>
<contrib-group>
<contrib contrib-type="author">
<string-name>
<given-names>B.A.</given-names>
<surname>Chowdhury</surname>
</string-name>
</contrib><x>, </x>
<given-names>S.M.</given-names>
<surname>Seymour</surname>
</contrib><x>, and </x>
<given-names>M.S.</given-names>
<surname>Levenson</surname>
</contrib>
</contrib-group>
</toc-article-meta>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

41. ToC graphic
<!ENTITY toc-article-meta ( article-id+, title-group?,
( contrib-group | aff | %x.class; )*, author-notes?,
((fpage?, lpage?, page-range?) | elocation-id )?,
(%address-link.class;|product|supplementary-material)*,
history?, self-uri*, related-article*, abstract*,
trans-abstract*, toc-graphic*, counts? )" >
<toc-article-meta> uses only elements defined in JATS and used in the content model for <article-meta>
<toc-graphic> forms the only exception:
Associates an image with an article entry in the ToC
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

42. ToC graphic
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

43. Multiple ToCs
<!ELEMENT issue-xml ( journal-meta?, issue-meta, toc+ )>
Publishers occasionally require more than one ToCs for a single issue:
Each ToC may maintain its own article sequence
Each ToC may display its own set of headings
Each ToC may be written in a different language
Each ToC may present its own version of article metadata
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

44. XML for multiple ToCs 1st ToC 2nd ToC 3rd ToC <issue-xml>
<journal-meta>
</journal-meta>
<issue-meta>
</issue-meta>
<toc>
</toc>
</issue-xml>
1st ToC
2nd ToC
3rd ToC
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

45. The Issue XML DTD
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

46. Issue XML for Ahead-of-Print
<journal-meta>
<journal-id journal-id-type="publisher-id">gen</journal-id>
<journal-title-group>
<journal-title>Genesis</journal-title>
</journal-title-group>
<issn pub-type="ppub"> </issn>
<publisher><publisher-name>Wiley-Liss</publisher-name></publisher>
</journal-meta>
<issue-meta issue-type="ahead-of-print">
<issue-id pub-id-type="doi"> /gen.ahead-of-print</issue-id>
<self-uri xlink:href=
</issue-meta>
<toc>
<toc-article-meta>
<article-id pub-id-type="doi"> /gen </article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /gen </article-id>
<article-id pub-id-type="doi"> /gen </article-id>
</toc>
</issue-xml>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

47. Issue XML for Virtual Issue
Virtual issue: ad hoc electronic collection of articles (printed or not) for a specialized readership
Virtual journal: A collection of virtual issues under a journal name with no print counterpart
<issue-xml>
<issue-meta issue-type="virtual">
<issue-id pub-id-type="doi"> /gen.virtual-001</issue-id>
<self-uri xlink:href=
</issue-meta>
<toc>
<toc-article-meta>
<article-id pub-id-type="doi"> /gen </article-id>
</toc-article-meta>
<article-id pub-id-type="doi"> /gen </article-id>
<article-id pub-id-type="doi"> /gen </article-id>
</toc>
</issue-xml>
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

48. Article Interchange Major design objective behind JATS DTDs
Article interchange can still take place with traditional JATS article XML:
Issue metadata
Article
XML
Issue XML
JATS
Article
XML
<stylesheet>
Choice of Issue XML to merge with remains with delivering party and not left to chance
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

49. Issue XML Standardization
Precondition for industry-wide acceptance of Issue XML is incorporation into JATS Suite
Initial prototype must be enhanced to include further functionality and enhancements
Similar efforts by other publishers/aggregators must contribute to a common proposal
Incorporation into JATS will eventually lead to standardization
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

50. In practice Issue XML is not merely an exercise on paper:
Literatum
> 11,600,000 articles
> 650,000 issues
> 6,900 journals
Huge store of Archival & Interchange NLM XML articles hosted on Atypon’s e-publishing platform
All back-content migrated to include Issue XML
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

51. Issue XML in a nutshell A JATS customization which:
Isolates article metadata from issue metadata
Maintains links between an issue and its articles
Accurately encodes the Table of Contents
What do we propose next?
Review this initial prototype
Collect feedback from interested parties
Incorporate final Issue XML proposal into JATS
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

52. Article vs. Issue XML Questions? Thank you. Nikos Markantonatos
Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011