diff --git a/docs/jats.md b/docs/jats.md index 5ec4f17..c12c830 100644 --- a/docs/jats.md +++ b/docs/jats.md @@ -1,108 +1,122 @@ JATS XML Open Dialects ====================== -This page focuses on dialects of JATS XML that are highly relevant to open-source software -development. +This page documents Free Open-Source Software (FOSS) and Open Access (OA) repositories that +establish various *open dialects* of JATS XML. +[Baseprint Document Format (BDF)](bdf/index.md) establishes another JATS open dialect: +*Baseprint JATS*, developed for self-publishing workflows using author-authored JATS XML. +Author-authored JATS demands FOSS that supports WYPISWYP: +What-You-Preview-Is-Semantically-What-You-Publish. -JATS XML Specifications/Recommendations: +JATS XML is formally defined through specifications and recommendations: * * * -## JATS XML Open Corpora +## JATS XML Open Repositories -A corpus of JATS XML articles embodies a particular "dialect" of JATS XML. +* [PubMed Central (PMC) Open Access (OA) Subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/) +* [EPMC Preprints subset](https://europepmc.org/downloads/preprints) +* [eLife article XML repository](https://github.com/elifesciences/elife-article-xml) +* eLife Reviewed Preprints? -Publicly Archived Corpora of JATS XML: -* **PMC XML**: [PubMed Central (PMC) Open Access Subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/) -* **eLife XML**: [eLife article XML repository](https://github.com/elifesciences/elife-article-xml) -* **?**: eLife Reviewed Preprints -* **EPMC XML** CTX? +## Open-source Full-Article XML Transformation -Non-archived Corpora: +"Transformation" is meant in a general sense, and not only [XSLT](https://en.wikipedia.org/wiki/XSLT). -* **bioRxiv preprints** - -## Open-source Full-Article XML Parsing - - +
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Article RepositoryXML Parsing ContextHTML Reading VenueXML Data Source Software Language
PubMed CentralPMCPMC OA Subset ? ?
PubMed CentralPubReader (discontinued 2024)PMC PubReader (discontinued 2024)PMC OA Subset PubReaderJavaScript + XSLXSLT + JavaScript
Europe PMC HTML generationfull-text-xsl + closed-sourceXSL + JavaScriptEurope PMC (EPMC)Preprint serversfull-text-xsl + ?XSLT + ?
Europe PMCinternal workflow after manuscript submission full-text-xsl - + xpub-epmc + EPMC manuscript submission system?internal? + full-text-xsl + xpub-epmc XSLXSLT + JavaScript
eLife Reviewed Preprintsingestion of bioRxiv JATS XMLbioRxiv Encoda TypeScript
Servers using Open Preprint Systems (OPS)?Open Preprint Systems (OPS) serversinternal? OPS PHP
Journals using Open Journal Systems (OJS)?Open Journal Systems (OJS) journalsinternal? OJS PHP
??eLife Lens and derivativesJavaScript
American Mathematical Society (AMS) journalsinternal workflow - [AMS texml-to-html](https://github.com/AmerMathSoc/texml-to-html) - internalAMS texml-to-html JavaScript
Some journals hosted by Centre Mersenneingestion of article data and text into databaseinternal MathDoc platform Python
?HTML generationSciELO?internal? packtoolsPython + XSLXSLT + Python
+ + +## Open-source What-You-Preview-Is-Semantically-What-You-Publish + + - - - - + + + + + + + +
?HTML generationeLife Lens and derivativesJavaScriptToolSoftwareLanguage
FidusWriterFidusWriterPython + JavaScript
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