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PMC Tagging Guidelines

PMC Tagging Guidelines. A case study in normalization. Abigail Elbow, Breena Krick, Laura Kelly NIH/NLM/NCBI/PMC JATS-Con | 9.27.2011. PMC Overview. But first…. What do those people do with data, anyway?. The PMC process:. 35 schemas Validate against declared DTD

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PMC Tagging Guidelines

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

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

  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. Q: Why have a style checker? 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. Q: So how does anyone know how to tag in PMC style? 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. Q: How do I know if my file is compliant? A: The PMC Style Checker

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

  14. Q: What if I have lots of files? 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 • BreenaKrick • Jeff Beck

  19. Resources: • PMC Tagging Guidelines: • http://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.cgi • Downloadable Style Checker stylesheets and instructions: • http://www.ncbi.nlm.nih.gov/pmc/pmcdoc/tagging-guidelines/stylechecker/stylecheck-README.html • PMC Utilities: • http://www.ncbi.nlm.nih.gov/pmc/pub/validation/ • Tagging Guidelines email list: • http://www.ncbi.nlm.nih.gov/mailman/listinfo/pmc-tagging-guidelines

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