1. A case study in normalization Abigail Elbow, Breena Krick, Laura Kelly NIH/NLM/NCBI/PMC JATS-Con | 9.27.2011

2. What do those people do with data, anyway? But first…

3. The PMC process: 35 schemas Validate against declared DTD Transform into JATS XML (Green Archiving DTD) Check validity Run Style Checker Load to PMC database

4. What’s that look like?

5. A: PMC is simply a user of the JATS / NLM DTDs

6. Can you be more specific? More than one way to tag a structure Need for normalization Start with the basic & most inconsistently- tagged: ▫Article metadata ▫Figures ▫Tables RelaxNG schema used first Replaced with XSL stylesheets ▫Allow flexibility, reporting, and varying file output

7. A: The PMC Tagging Guidelines…

8. The Tagging Guidelines HTML prose form of the style rules General Tagging Practice, Document Objects, Elements Introduction and Update History XML backbone Covers PMC, NIHMS, and Bookshelf Covers both 2.3 and 3.0

9. Tagging Guideline XML: @version

10. Tagging Guideline HTML

11. Tagging Guidelines: an element

12. A: The PMC Style Checker

13. Five common style errors MathML tagging and @ ref-type DOIs Empty elements Demo time: http://www.pubmedcentral.nih.gov/utils/style_checker/stylechecker.cgi

14. A: NLM Style Checker stylesheets (v4.3.4)

15. The Style Checker Stylesheets Main file: nlm-stylechecker.xsl It xsl:include(s): ▫stylecheck-match-templates.xsl ▫stylecheck-named-tests.xsl ▫stylecheck-helper-templates.xsl Reports: style-reporter.xsl ▫Generates an HTML Error/Warning report

16. badstyle.XML

17. Another report view: (PMC Production)

18. Special thanks Laura Kelly Breena Krick Jeff Beck

19. Resources: PMC Tagging Guidelines: ▫http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging- guidelines/article/style.htmlhttp://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging- guidelines/article/style.html PMC Online Style Checker: ▫http://www.pubmedcentral.nih.gov/utils/style_checker/stylechecker.cgihttp://www.pubmedcentral.nih.gov/utils/style_checker/stylechecker.cgi Downloadable Style Checker stylesheets and instructions: ▫http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging- guidelines/stylechecker/stylecheck-README.htmlhttp://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging- guidelines/stylechecker/stylecheck-README.html PMC Utilities: ▫http://www.ncbi.nlm.nih.gov/pmc/pub/validation/http://www.ncbi.nlm.nih.gov/pmc/pub/validation/ Tagging Guidelines email list: ▫http://www.ncbi.nlm.nih.gov/mailman/listinfo/pmc-tagging-guidelineshttp://www.ncbi.nlm.nih.gov/mailman/listinfo/pmc-tagging-guidelines