PMC Tagging GuidelinesA case study in normalization

Abigail Elbow, Breena Krick, Laura Kelly NIH/NLM/NCBI/PMCJATS-Con | 9.27.2011

PMC OverviewWhat do those people do with data, anyway?

But first…

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

What’s that look like?

Q: Why have a style checker?A: PMC is simply a user of the JATS / NLM DTDs

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

Q: So how does anyone know how to tag in PMC style?A: The PMC Tagging Guidelines…

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

Tagging Guideline XML: @version

Tagging Guideline HTML

Tagging Guidelines: an element

Q: How do I know if my file is compliant?A: The PMC Style Checker

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

Q: What if I have lots of files?A: NLM Style Checker stylesheets (v4.3.4)

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

badstyle.XML

Another report view: (PMC Production)

Special thanks

•Laura Kelly•Breena Krick•Jeff Beck

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-guideline

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