add more JATS software and intro

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:
 
 * <https://jats4r.niso.org/>
 * <https://jats.nlm.nih.gov/>
 * <https://www.niso.org/standards-committees/jats>
 
 
-## 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
-
-<table markdown>
+<table>
 <tr>
-  <th>Article Repository</th>
-  <th>XML Parsing Context</th>
+  <th>HTML Reading Venue</th>
+  <th>XML Data Source</th>
   <th>Software</th>
   <th>Language</th>
 </tr>
 <tr>
-  <td>PubMed Central</td>
+  <td><a href="https://www.ncbi.nlm.nih.gov/pmc/">PMC</a></td>
+  <td>PMC OA Subset</td>
   <td>?</td>
   <td>?</td>
-  <td></td>
 </tr>
 <tr>
-  <td>PubMed Central</td>
-  <td>PubReader (discontinued 2024)</td>
+  <td><a href="https://www.ncbi.nlm.nih.gov/pmc/about/pubreader/">PMC PubReader</a> (discontinued 2024)</td>
+  <td>PMC OA Subset</td>
   <td><a href="https://github.com/ncbi/PubReader">PubReader</a></td>
-  <td>JavaScript + XSL</td>
+  <td>XSLT + JavaScript</td>
 </tr>
 <tr>
-  <td>Europe PMC </td>
-  <td>HTML generation</td>
-  <td><a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">full-text-xsl</a> + closed-source</td>
-  <td>XSL + JavaScript</td>
+  <td>Europe PMC (EPMC)</td>
+  <td>Preprint servers</td>
+  <td><a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">full-text-xsl</a> + ?</td>
+  <td>XSLT + ?</td>
 </tr>
 <tr>
-  <td>Europe PMC</td>
-  <td>internal workflow after manuscript submission</td>
-  <td> <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">full-text-xsl</a>
-       + <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/xpub-epmc">xpub-epmc</a>
+  <td>EPMC manuscript submission system?</td>
+  <td>internal?</td>
+  <td> <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/full-text-xsl">
+       full-text-xsl</a> + <a href="https://gitlab.ebi.ac.uk/literature-services/public-projects/xpub-epmc">xpub-epmc</a>
   </td>
-  <td>XSL</td>
+  <td>XSLT + JavaScript</td>
 </tr>
 <tr>
   <td>eLife Reviewed Preprints</td>
-  <td>ingestion of bioRxiv JATS XML</td>
+  <td>bioRxiv</td>
   <td><a href="https://github.com/stencila/encoda">Encoda</a></td>
   <td>TypeScript</td>
 </tr>
 <tr>
-  <td>Servers using Open Preprint Systems (OPS)</td>
-  <td>?</td>
+  <td>Open Preprint Systems (OPS) servers</td>
+  <td>internal?</td>
   <td><a href="https://pkp.sfu.ca/software/ops/">OPS</a></td>
   <td>PHP</td>
 </tr>
 <tr>
-  <td>Journals using Open Journal Systems (OJS)</td>
-  <td>?</td>
+  <td>Open Journal Systems (OJS) journals</td>
+  <td>internal?</td>
   <td><a href="https://github.com/pkp">OJS</a></td>
   <td>PHP</td>
 </tr>
-<tr markdown>
+<tr>
+  <td>?</td>
+  <td>?</td>
+  <td><a href="https://github.com/elifesciences/lens">eLife Lens</a> and derivatives</td>
+  <td>JavaScript</td>
+</tr>
+<tr>
   <td>American Mathematical Society (AMS) journals</td>
-  <td>internal workflow</td>
-  <td markdown>
-    [AMS texml-to-html](https://github.com/AmerMathSoc/texml-to-html)
-  </td>
+  <td>internal</td>
+  <td><a href="https://github.com/AmerMathSoc/texml-to-html">AMS texml-to-html</a></td>
   <td>JavaScript</td>
 </tr>
 <tr>
   <td>Some journals hosted by <a href="https://www.centre-mersenne.org">Centre Mersenne</a></td>
-  <td>ingestion of article data and text into database</td>
+  <td>internal</td>
   <td><a href="https://gricad-gitlab.univ-grenoble-alpes.fr/mathdoc/ptf">MathDoc platform</a></td>
   <td>Python</td>
 </tr>
 <tr>
-  <td>?</td>
-  <td>HTML generation</td>
+  <td><a href"https://scielo.org">SciELO</a>?</td>
+  <td>internal?</td>
   <td><a href="https://github.com/scieloorg/packtools">packtools</a></td>
-  <td>Python + XSL</td>
+  <td>XSLT + Python</td>
 </tr>
+</table>
+
+
+## Open-source What-You-Preview-Is-Semantically-What-You-Publish
+
+<table>
 <tr>
-  <td>?</td>
-  <td>HTML generation</td>
-  <td>eLife Lens and derivatives</td>
-  <td>JavaScript</td>
+  <th>Tool</th>
+  <th>Software</th>
+  <th>Language</th>
+</tr>
+<tr>
+  <td><a href="https://www.fiduswriter.org">FidusWriter</td>
+  <td><a href="https://github.com/fiduswriter/fiduswriter">FidusWriter</a></td>
+  <td>Python + JavaScript</td>
 </tr>
 </table>
+