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

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

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

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  1. JATS for Korean medical journal databases Choon Shil Lee Sookmyung

    Women’s University Committee for Information Management, KAMJE
  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
  3. KAMJE • Korean Association of Medical Journal Editors • as

    of October 2015 251 members (member journals) • Medical society journals published in Korea
  4. 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.
  5. Databases provided by KAMJE • Cover Korean medical journals •

    Information in English • All information Free/Open Access
  6. 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
  7. 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
  8. 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
  9. KAMJE Press • E-journal platform services for individual member society

    journals • 71 journals • Customized Synapse platform for journal identity • Synapse XML (JATS)
  10. 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)
  11. 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
  12. • 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.
  13. • 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.
  14. 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)
  15. 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
  16. 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
  17. Some of the errors pointed out in PMC Evaluation Reports

    • Remove duplicate tagging of <collab> in reference 21. • Remove extraneous punctuation in <article-title>. • Correct typo in <title>. • Correct typo in <label> tagging. • Correct typo in keywords. • Graphic file names do not match callouts in XML. • Incorrect character entity. • Per the PDF, contributor <given-names> incorrect. • Per the PDF, received <day> 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 <on-behalf-of> element. • The footnote “FN1” is referred to but never defined.
  18. 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?
  19. 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
  20. 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
  21. 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
  22. Accepted Manuscript Typesetting Journal Publishing/Production Workflow (1): From Final Print

    version PDF to JATS XML JATS <XML> üCut & Paste manually from PDF üOnline publication delayed till print PDF version is available
  23. 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.
  24. 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.
  25. 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.
  26. 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)