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Article XML vs. Issue XML Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Nikos Markantonatos Capturing.

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Presentation on theme: "Article XML vs. Issue XML Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Nikos Markantonatos Capturing."— Presentation transcript:

1 Article XML vs. Issue XML Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Nikos Markantonatos nikos@atypon.com Capturing the Table of Contents under the NLM DTD JATS-Con 2011 / 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 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 XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Publisher Journal Issue 1 Issue 2 Article 1 Article 2 Article 3 Article 4 Article 5 Article 6 Article 1

4 Article front matter  Information about this entire structure is captured inside the article XML element: Br Med J 0959-8138 British Medical Journal 10092260......... 318 7187 837 841...... Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

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

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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Publishing Context:  Journal title  ISSN  Journal identifiers  Publisher name/location  Volume number  Issue number  Publication date  ToC heading  Issue title

7 Limitations of current approach 1.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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Article 1 Article 2 Article 3 Article 4 Article 5 Issue

8 Limitations of current approach 2.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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Article Article Article Article Article Article Article Article Article Article Article

9 Limitations of current approach 3.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 4.There is an implicit assumption that an article corresponds to at most one issue, volume, journal and publisher:   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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Article Online Early Issue Article Forthcoming Issue Article Printed Issue Article Online Collection 2 Article Online Collection 1

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: Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Article Article Article Article Article Article Article Article Issue XML Issue

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

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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Online Collection 2 Article Article Collection Issue XML Article Another Collection DeletedNew

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

17 ............ Top-level Rule Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  Issue XML root element definition: (optional) (exactly one) (one or more)

18 gen Genesis 1054-7460 The MIT Press July 2011 82 7 10.1002/gen.2011.82.issue-7 10.1002/article.A 10.1002/article.B 10.1002/article.C Sample Issue XML Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

19  is defined directly by JATS: gen Genesis 1054-7460 Wiley-Liss.... Issue XML: Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

20 Issue XML: Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  also borrows some elements from, but they now refer to the issue level and not to the article level:   /   extracts all those elements from that refer to the issue and not to the article itself:   / 

21 .... July 2011 82 7 10.1002/gen.2011.82.issue-7.... Issue XML: Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

22 .... 10.1002/article.A 10.1002/article.B 10.1002/article.C Issue XML: Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

23 Issue XML Article references in  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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Forthcoming Issue Article Issue XML......

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

25 10.1002/article.A 10.1002/article.B 10.1002/article.C 10.1002/article.C 10.1002/article.B 10.1002/article.A Dictate order of articles in ToC Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

26 Reorder ToC article entries Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

27 Cell Biology 10.1002/article.A 10.1002/article.B Molecular Biology 10.1002/article.C 10.1002/article.D Embed ToC 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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  Owing to the recursive nature of headings can be nested at arbitrary depth  In analogy with other recursive elements in JATS

30 BIOLOGY Cell Biology 10.1002/article.A 10.1002/article.B Molecular Biology 10.1002/article.C Embed nested ToC headings 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 Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  Support for multi-lingual headings: Cell Biology Biologie Cellulaire 10.1002/article.A............ Cell Biology / Biologie Cellulaire

33 ToC annotations Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  Support for interspersed paragraphs of text between article entries:  Support for paragraphs of text above and below a heading at any nesting level:

34 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 …. Annotated ToC headings Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 Proceedings from the Second International Conference on Human Biology Session I: Sep 15, 2011 Session II: Sep 16, 2011 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…. 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 ….

35  format attribute in allows for article entries in the ToC to be:  specially indented  highlighted  placed inside a box  fine-printed  hidden  placed on a side-table Special ToC entries Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 10.1002/article-no-ToC

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

37 Override article metadata Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  can do a lot more than reference an article:  Allows for a fully custom ToC article entry  Includes those elements of which make sense in a ToC entry  Any element defined inside is meant to override the corresponding value from the article XML for the purposes of ToC rendering

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 .. 10.1086/595693 B.A. Chowdhury, S.M. Seymour, and M.S. Levenson.. Override ToC authors Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

41 ToC graphic Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  uses only elements defined in JATS and used in the content model for  forms the only exception:  Associates an image with an article entry in the ToC

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

43 Multiple ToCs Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  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

44 .................... XML for multiple ToCs Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011 1st ToC 2nd ToC 3rd ToC

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

46 gen Genesis 1054-7460 Wiley-Liss 10.1002/gen.ahead-of-print 10.1002/gen.100321 10.1002/gen.100340 10.1002/gen.100361 Issue XML for Ahead-of-Print Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011

47 10.1002/gen.virtual-001 10.1002/gen.100321 10.1002/gen.100340 10.1002/gen.100361 Issue XML for Virtual Issue Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  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

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

49 Issue XML Standardization Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  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

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

51 Issue XML in a nutshell Article XML vs. Issue XML - Nikos Markantonatos - Atypon JATS-Con Sep 26, 2011  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

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


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