JATS for Korean medical journal databases: Synapse, KoreaMed and KoMCI / JATS-Con-Asia-20151019-06-Choon-Shil-Lee

JATS-Con Asia
Monday, October 19, 2015
http://jats-con-asia.strikingly.com/

General Session:
Speaker 4 "JATS for Korean medical journal databases: Synapse, KoreaMed and KoMCI"
-Choon Shil Lee, Sookmyung Women's University
Abstract: http://jats-con-asia.strikingly.com/#speakers
Materials: https://speakerdeck.com/jatsconasiasc/jats-con-asia-20151019-06-choon-shil-lee
Video: https://vimeo.com/150522126

Transcript

1. JATS
   for Korean medical journal databases
   Choon Shil Lee
   Sookmyung Women’s University
   Committee for Information Management, KAMJE
   

   View Slide

2. Agenda
   • KAMJE and Korean Medical Journal
   Databases
   • Database Workflows
   • How We Began
   • Current Journal Publishing/Production
   Workflows (1) & (2)
   • Lessons Learned and JATS’ Advantages
   

   View Slide

3. KAMJE and Korean Medical
   Journal Databases
   

   View Slide

4. KAMJE
   • Korean Association of Medical Journal
   Editors
   • as of October 2015
   251 members (member journals)
   • Medical society journals published in
   Korea
   

   View Slide

5. 252 KAMJE Journals
   

   View Slide

6. KAMJE
   • Producer and service provider of three
   eminent databases of Korean biomedical
   journals.
   • Major data provider to PubMed Central
   and PubMed/MEDLINE for Korean
   journals.
   • Subsidiary company, XMLink, for
   database development and XML file
   production.
   

   View Slide

7. View Slide

8. Databases provided by KAMJE
   • Cover Korean medical journals
   • Information in English
   • All information Free/Open Access
   

   View Slide

9. KoreaMed
   http://koreamed.org
   • Since 1997
   • Abstract database
   • PubMed equivalent
   • PubMed XML compatible
   • 221 journals
   • Over 230,000 records
   • MeSH
   • LinkOut to Synapse, KoMCI & Journals
   • CrossRef/DOI linking
   • Cited-by Metrics
   

   View Slide

10. View Slide

11. 213 KoreaMed Journals
    

    View Slide

12. KoMCI
    http://komci.org
    • Since 2000
    • Citation Index
    Abstracts & Cited References
    • Web of Science & JCR equivalents
    • 221 journals
    • Over 230,000 records
    700,000 cited references
    • LinkOut to KoreaMed, Synapse & Journals
    

    View Slide

13. View Slide

14. View Slide

15. Synapse
    http://synapse.koreamed.org
    • Since 2007
    • Full text e-journal database/digital archive
    • PMC equivalent
    • PMC XML à now JATS
    • DOI landing/Reference linking platform
    • 139 journals
    • Over 68,000 records
    • LinkOut to KoreaMed, KoMCI & Journals
    • MeSH
    • Cited-by Metrics
    

    View Slide

16. View Slide

17. 136 Synapse Journals
    

    View Slide

18. KAMJE Press
    • E-journal platform services for individual
    member society journals
    • 71 journals
    • Customized Synapse platform for journal
    identity
    • Synapse XML (JATS)
    

    View Slide

19. View Slide

20. View Slide

21. 71 KAMJE Press Journals
    

    View Slide

22. Korean Medical Journal Information
    • Since 2008
    • Journal bibliographic information
    • US NLM’s Journals database (NLM
    Catalog) equivalent
    • Over 700 journals
    • Over 3,000 records (journal title changes)
    

    View Slide

23. View Slide

24. Database Workflows
    

    View Slide

25. KAMJE databases are
    • Internally integrated
    – Various database services from a database file
    – Journal DB for set-up & check-up journal info.
    • Generated from “Synapse XML files”
    – JATS 1.0 XML files
    – The same XML files submitted to PMC
    – Synapse XML files = PMC XML files
    

    View Slide

26. • An XML file is faithfully marked up as
    described in the PubMed Central Tagging
    Guidelines, previously in NLM DTD 2.3,
    now in JATS 1.0.
    

    View Slide

27. • Then the file is used for the creation and
    generation of records for each and every
    databases mentioned above.
    • The same file is submitted to PubMed
    Central (and PubMed).
    • A CrossRef DOI deposit XML file is also
    extracted from the JATS full text XML file.
    

    View Slide

28. Synapse & its byproduct/derivative databases
    

    View Slide

29. View Slide

30. View Slide

31. KoreaMed borrows “Figures & Tables” from Synapse
    Synapse borrows “MeSH terms”from KoreaMed
    

    View Slide

32. 96 PubMed Central Journals
    

    View Slide

33. 100 PubMed Journals
    

    View Slide

34. 20 MEDLINE Journals
    

    View Slide

35. 34 SCI Journals
    

    View Slide

36. How we began
    

    View Slide

37. The 1st PMC Journal from KAMJE
    Journal of Korean Medical Science
    2007.4 PMC application
    2007.4 Stage 1: PMC's Scientific Quality
    Standard
    2007.6 DOI prefixes assigned
    2007.7 Stage 2: Technical Requirements Test
    (73 sample articles)
    2007.8 Evaluation report (1)
    2007.11 Evaluation report (2)
    2008.2 Evaluation report (3)
    

    View Slide

38. 2008.2 Stage 3: Journal set up
    2008.2 DOI deposit
    2008.7 PMC Agreement
    2008.8 PMC banners & final file ftp
    2008.11 JKMS Live in PMC
    2008.11 Current issue ftp (v23 n6)
    2008.12 PMC Data QA report
    2008 3 KAMJE journals in PMC
    

    View Slide

39. In plain words,
    • It took almost 2 years before we were
    convinced that we are able to produce
    quality XML files acceptable to PMC.
    • PMC has been a big helping hand for a
    novice to decipher journal article tag sets
    and self-study tagging guidelines.
    – PMC Evaluation Reports
    – Technical meeting with PMC Production Team
    

    View Slide

40. PMC Evaluation Reports
    

    View Slide

41. View Slide

42. Some of the errors pointed out in
    PMC Evaluation Reports
    • Remove duplicate tagging of in reference 21.
    • Remove extraneous punctuation in .
    • Correct typo in .
    • Correct typo in tagging.
    • Correct typo in keywords.
    • Graphic file names do not match callouts in XML.
    • Incorrect character entity.
    • Per the PDF, contributor incorrect.
    • Per the PDF, received incorrect.
    • Pagination incorrect.
    • Contributor affiliation labels missing.
    • Inconsistent paragraph tagging. (Multiple instances.)
    • Per the PDF, the math figures occurring between these paragraphs are missing.
    • Remove extraneous character in entity tagging. (Multiple instances)
    • When a contributor has written or edited a work “on behalf of” an organization or group,
    use element.
    • The footnote “FN1” is referred to but never defined.
    

    View Slide

43. What it meant:
    to have a few KAMJE journals in PMC
    • Yes:
    – We now have basic knowledge and skills on
    article XML tagging.
    – We may start operating a reliable system
    comparable to other databases.
    – It made Korean medical journal editors to go
    with PMC XML whatever that is.
    • But:
    – Quality assurance?
    – Production efficiency?
    

    View Slide

44. Yet to be resolved:
    • To educate & train XML production staff
    (not available in domestic markets then)
    • Low production costs expected
    (low journal publication budget)
    • Manual cut & paste jobs for XML file
    production from print version PDFs
    

    View Slide

45. Progresses since then
    2010.10 PMC Publisher Preview Site
    2013.1 PubReader format
    2013.5 XML file Production in JATS 1.0
    2013.12 CrossMark
    2014.12 ePub format
    Text and Data Mining License info. to
    Crossref (ALI: Access License Indicators)
    2015.3 MathML (Equation, Formula, Matrix)
    Table XML
    2015.3 JATS 1.1d3 announced (not yet using it)
    2015 96 journals in PMC
    

    View Slide

46. View Slide

47. JATS tagging example records in Korean
    

    View Slide

48. View Slide

49. Learning and Networking
    Workshops & technical meetings attended
    2009.4 2-day classes on
    “Introduction to XML Tagging”
    (Mulberry Technologies)
    Since 2010 (each year)
    * JATS-Con
    * Technical meeting with PMC Production Team
    

    View Slide

50. 2-day classes on
    Introduction to
    XML Tagging
    Mulberry Technologies
    April 29-30, 2009
    

    View Slide

51. JATS-Con every year!
    Technical meeting with PMC Production Team
    

    View Slide

52. Current Journal
    Publishing/Production Workflows
    

    View Slide

53. Accepted
    Manuscript Typesetting
    Journal Publishing/Production Workflow (1):
    From Final Print version PDF to JATS XML
    JATS
    
    üCut & Paste
    manually from
    PDF
    üOnline publication delayed till
    print PDF version is available
    

    View Slide

54. Journal Publishing/Production Workflow (2):
    One JATS XML for Web and Typesetting
    Accepted
    Manuscript
    JATS
    
    

    View Slide

55. JATS’ Advantages
    • We can easily look for/study/follow on
    what/how other journals/databases
    do/deal/think with/about article
    markup/marked up articles.
    • Many/various tagging examples are
    available in PMC (records).
    • JATS-list is a good information source.
    

    View Slide

56. JATS’ Advantages
    • If a particular feature is implemented in a
    database, we may also attempt to provide
    the same service to our users.
    • If they can do it,
    we can also do/solve/resolve it.
    

    View Slide

57. http://www.ncbi.nlm.nih.gov/pmc/about/new-in-pmc/
    

    View Slide

58. PubReader implemented in Synapse
    in January 15, 2013
    

    View Slide

59. View Slide

60. Lessons Learned
    • JATS certainly is a journal article tag suite.
    • JATS is a standard.
    Interoperability, Compatibility, Collaboration
    • JATS is an excellent guide which
    elaborates on the best practices in tagging
    journal articles.
    

    View Slide

61. Other Standards
    in KAMJE Databases
    • DOI (Digital Object Identifier)
    • ORCID (Open Researcher and Contributor ID)
    • FundRef (Funder Id)
    • Greatly facilitate the discoverability and visibility
    of Korean medical journal articles in global scale
    • Provides easy access (Click!) to Korean medical
    journal articles
    • Can easily grasp what’s going on in Korean
    medical research front (What articles by what
    authors with what funding)
    

    View Slide

62. View Slide

63. Thank you! E-journal Database Ecosystem
    XMLink office image wall
    

    View Slide

64. View Slide