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
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 and Korean Medical Journal Databases
4. KAMJE • Korean Association of Medical Journal Editors • as of October 2015 251 members (member journals) • Medical society journals published in Korea
5. 252 KAMJE Journals
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.
8. Databases provided by KAMJE • Cover Korean medical journals • Information in English • All information Free/Open Access
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
11. 213 KoreaMed Journals
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
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
17. 136 Synapse Journals
18. KAMJE Press • E-journal platform services for individual member society journals • 71 journals • Customized Synapse platform for journal identity • Synapse XML (JATS)
21. 71 KAMJE Press Journals
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)
24. Database Workflows
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
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.
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.
28. Synapse & its byproduct/derivative databases
31. KoreaMed borrows “Figures & Tables” from Synapse Synapse borrows “MeSH terms”from KoreaMed
32. 96 PubMed Central Journals
33. 100 PubMed Journals
34. 20 MEDLINE Journals
35. 34 SCI Journals
36. How we began
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)
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
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
40. PMC Evaluation Reports
42. 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.
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?
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
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
47. JATS tagging example records in Korean
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
50. 2-day classes on Introduction to XML Tagging Mulberry Technologies April 29-30, 2009
51. JATS-Con every year! Technical meeting with PMC Production Team
52. Current Journal Publishing/Production Workflows
53. 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
54. Journal Publishing/Production Workflow (2): One JATS XML for Web and Typesetting Accepted Manuscript JATS <XML>
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.
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.
57. http://www.ncbi.nlm.nih.gov/pmc/about/new-in-pmc/
58. PubReader implemented in Synapse in January 15, 2013
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.
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)
63. Thank you! E-journal Database Ecosystem XMLink office image wall