revision of front, intro and bachgrnd (incomplete)

Isabelle_DOF/ontologies/scholarly_paper/scholarly_paper.thy

@@ -448,7 +448,7 @@ fun doc_cmd kwd txt flag key =
 in
 
 val _ = doc_cmd \<^command_keyword>\<open>Definition*\<close> "Freeform Definition" 
-                Definition_default_class \<^const_name>\<open>defn\<close>;
+                 Definition_default_class \<^const_name>\<open>defn\<close>;
 
 val _ = doc_cmd \<^command_keyword>\<open>Lemma*\<close>      "Freeform Lemma Description" 
                  Lemma_default_class \<^const_name>\<open>lemm\<close>;
@@ -554,6 +554,7 @@ print_doc_classes
 print_doc_class_template "definition" (* just a sample *)
 print_doc_class_template "lemma" (* just a sample *)
 print_doc_class_template "theorem" (* just a sample *)
+print_doc_class_template "premise" (* just a sample *)
 
 
 subsection\<open>Structuring Enforcement in Engineering/Math Papers \<close>

Isabelle_DOF/thys/manual/M_00_Frontmatter.thy

@@ -30,6 +30,7 @@ define_shortcut* TeXLive \<rightleftharpoons> \<open>\TeXLive\<close>
                  BibTeX  \<rightleftharpoons> \<open>\BibTeX{}\<close> 
                  LaTeX   \<rightleftharpoons> \<open>\LaTeX{}\<close>
                  TeX     \<rightleftharpoons> \<open>\TeX{}\<close>
+                 dofurl  \<rightleftharpoons> \<open>\dofurl\<close>
                  pdf     \<rightleftharpoons> \<open>PDF\<close>
 
 text\<open>Note that these setups assume that the associated \<^LaTeX> macros 

Isabelle_DOF/thys/manual/M_01_Introduction.thy

@@ -38,26 +38,34 @@ and their logical contexts).
 
 Further applications are the domain-specific discourse in juridical texts or medical reports.  
 In general, an ontology is a formal explicit description of \<^emph>\<open>concepts\<close> in a domain of discourse
-(called \<^emph>\<open>classes\<close>), properties of each concept describing \<^emph>\<open>attributes\<close> of the concept, as well 
-as \<^emph>\<open>links\<close> between them. A particular link between concepts is the \<^emph>\<open>is-a\<close> relation declaring 
+(called \<^emph>\<open>classes\<close>), components (called \<^emph>\<open>attributes\<close>) of the concept, and properties (called 
+\<^emph>\<open>invariants\<close>) on concepts. Logically, classes are represented by a type (the class type) and
+particular terms representing \<^emph>\<open>instances\<close> of them. Since components are typed, it is therefore
+possible to express \<^emph>\<open>links\<close> like \<open>m\<close>-to-\<open>n\<close> relations between classes. 
+Another form of link between concepts is the \<^emph>\<open>is-a\<close> relation declaring 
 the instances of a subclass to be instances of the super-class.
 
-To address this challenge, we present the Document Ontology Framework (\<^dof>) and an 
-implementation of \<^dof> called \<^isadof>. \<^dof> is designed for building scalable and user-friendly 
-tools on top of interactive theorem provers. \<^isadof> is an instance of this novel framework, 
-implemented as extension of Isabelle/HOL, to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them 
-during document evolution. Based on Isabelle's infrastructures, ontologies may refer to types, 
-terms, proven theorems, code, or established assertions. Based on a novel adaption of the Isabelle 
-IDE (called PIDE, @{cite "wenzel:asynchronous:2014"}), a document is checked to be 
-\<^emph>\<open>conform\<close> to a particular ontology---\<^isadof> is designed to give fast user-feedback \<^emph>\<open>during the 
-capture of content\<close>. This is particularly valuable in case of document evolution, where the 
-\<^emph>\<open>coherence\<close> between the formal and the informal parts of the content can be mechanically checked.
+Engineering an ontological language for documents that contain both formal and informal elements
+as occuring in formal theories is a particular challenge. To address this latter, we present 
+the Document Ontology Framework (\<^dof>) and an implementation of \<^dof> called \<^isadof>.
+ \<^dof> is designed for building scalable and user-friendly  tools on top of interactive theorem 
+provers. \<^isadof> is an instance of this novel framework,  implemented as extension of Isabelle/HOL, 
+to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them  during document evolution. Based on Isabelle's 
+infrastructures, ontologies may refer to types, terms, proven theorems, code, or established 
+assertions. Based on a novel adaption of the Isabelle IDE (called PIDE, @{cite "wenzel:asynchronous:2014"}), 
+a document is checked to be \<^emph>\<open>conform\<close> to a particular ontology---\<^isadof> is designed to give fast 
+user-feedback \<^emph>\<open>during the capture of content\<close>. This is particularly valuable in case of document 
+evolution, where the \<^emph>\<open>coherence\<close> between the formal and the informal parts of the content can 
+be mechanically checked.
 
 To avoid any misunderstanding: \<^isadof>  is \<^emph>\<open>not a theory in HOL\<close> on ontologies and operations to 
 track and trace links in texts, it is an \<^emph>\<open>environment to write structured text\<close> which 
 \<^emph>\<open>may contain\<close> Isabelle/HOL definitions and proofs like mathematical articles, tech-reports and
 scientific papers---as the present one, which is written in \<^isadof> itself. \<^isadof> is a plugin 
-into the Isabelle/Isar framework in the style of~@{cite "wenzel.ea:building:2007"}.\<close>
+into the Isabelle/Isar framework in the style of~@{cite "wenzel.ea:building:2007"}. However,
+ \<^isadof> will generate from ontologies a theory infrastructure consisting of types, terms, theorems
+and code that allows both interactive checking as well as formal reasoning over meta-data
+related to annotated documents.\<close>
 
 subsubsection\<open>How to Read This Manual\<close>
 (*<*)
@@ -91,9 +99,9 @@ text\<open>
   by simp\<close>}
   \<^item> a green background for examples of generated document fragments (\<^ie>, PDF output):
     @{boxed_pdf [display] \<open>The axiom refl\<close>}
-  \<^item> a red background for (S)ML-code:
+  \<^item> a red background for SML-code:
     @{boxed_sml [display] \<open>fun id x = x\<close>}
-  \<^item> a yellow background for \LaTeX-code:
+  \<^item> a yellow background for \<^LaTeX>-code:
     @{boxed_latex [display] \<open>\newcommand{\refl}{$x = x$}\<close>}
   \<^item> a grey background for shell scripts and interactive shell sessions:
     @{boxed_bash [display]\<open>ë\prompt{}ë ls
@@ -104,6 +112,15 @@ subsubsection\<open>How to Cite \<^isadof>\<close>
 text\<open>
   If you use or extend \<^isadof> in your publications, please use 
   \<^item> for the \<^isadof> system~@{cite "brucker.ea:isabelle-ontologies:2018"}:
+    \begin{quote}\small
+      A.~D. Brucker, I.~Ait-Sadoune, N. Méric, and B.~Wolff. Using Deep Ontologies in Formal 
+      Software Engineering. In \<^emph>\<open>International Conference on Rigorous State-Based Methods (ABZ 2023)\<close>, 
+      To appear in Lecture Notes in Computer Science. Springer-Verlag,
+      Heidelberg, 2023. \href{https://doi.org/???} {10.1007/????????}.
+    \end{quote}
+    A \<^BibTeX>-entry is available at: 
+    \<^url>\<open>https://www.lri.fr/~wolff/bibtex/wolff.html\<close>. 
+  \<^item> an older description of the system~@{cite "brucker.ea:isabelle-ontologies:2018"}:
     \begin{quote}\small
       A.~D. Brucker, I.~Ait-Sadoune, P.~Crisafulli, and B.~Wolff. Using the {Isabelle} ontology 
       framework: Linking the formal with the informal. In \<^emph>\<open>Conference on Intelligent Computer 
@@ -128,13 +145,13 @@ text\<open>
      Using Ontologies in Formal Developments Targeting Certification. 
      In W. Ahrendt and S. Tarifa, editors. \<^emph>\<open>Integrated Formal Methods (IFM)\<close>, number 11918.
      Lecture Notes in Computer Science. Springer-Verlag, Heidelberg, 2019.
-     \href{https://doi.org/10.1007/978-3-030-34968-4\_4}.
+     \<^url>\<open>https://doi.org/10.1007/978-3-030-34968-4_4\<close>.
     \end{quote}
 \<close>
 subsubsection\<open>Availability\<close>
 text\<open>
   The implementation of the framework is available at 
-  \url{\dofurl}. The website also provides links to the latest releases. \<^isadof> is licensed 
+  \url{\<^dofurl>}. The website also provides links to the latest releases. \<^isadof> is licensed 
   under a 2-clause BSD license (SPDX-License-Identifier: BSD-2-Clause).
 \<close>
 

Isabelle_DOF/thys/manual/M_02_Background.thy

@@ -1,7 +1,7 @@
 (*************************************************************************
  * Copyright (C) 
- *               2019-2022 The University of Exeter 
- *               2018-2022 The University of Paris-Saclay
+ *               2019-2023 The University of Exeter 
+ *               2018-2023 The University of Paris-Saclay
  *               2018      The University of Sheffield
  *
  * License:
@@ -30,8 +30,8 @@ While Isabelle is widely perceived as an interactive theorem
 prover for HOL (Higher-order Logic)~@{cite "nipkow.ea:isabelle:2002"}, we would like to emphasize
 the view that Isabelle is far more than that: it is the \<^emph>\<open>Eclipse of Formal Methods Tools\<close>.  This 
 refers to the ``\<^emph>\<open>generic system framework of Isabelle/Isar underlying recent versions of Isabelle.  
-Among other things, Isar provides an infrastructure for Isabelle plug-ins, comprising extensible 
-state components and extensible syntax that can be bound to ML programs. Thus, the Isabelle/Isar 
+Among other things, Isabelle provides an infrastructure for Isabelle plug-ins, comprising extensible 
+state components and extensible syntax that can be bound to SML programs. Thus, the Isabelle 
 architecture may be understood as an extension and refinement of the traditional `LCF approach', 
 with explicit infrastructure for building derivative systems.\<close>''~@{cite "wenzel.ea:building:2007"} 
 
@@ -49,9 +49,13 @@ The Isabelle system architecture shown in @{docitem \<open>architecture\<close>}
 with Standard ML (SML) at the bottom layer as implementation  language. The architecture actually 
 foresees a \<^emph>\<open>Nano-Kernel\<close> (our terminology) which resides in the SML structure \<^boxed_sml>\<open>Context\<close>. 
 This structure provides a kind of container called \<^emph>\<open>context\<close> providing an identity, an 
-ancestor-list as well as typed, user-defined state for components (plugins) such as \<^isadof>. 
+ancestor-list as well as typed, user-defined state for plugins such as \<^isadof>. 
 On top of the latter, the LCF-Kernel, tactics, automated proof procedures as well as specific 
-support for higher specification constructs were built.\<close>
+support for higher specification constructs were built.
+\<^footnote>\<open>We use the term \<^emph>\<open>plugin\<close> for a collection of HOL-definitions, SML and Scala code in order
+to distinguish it from the official Isabelle term \<^emph>\<open>component\<close> which implies a particular 
+format and support by the Isabelle build system.\<close>
+\<close>
 
 section*[dof::introduction]\<open>The Document Model Required by \<^dof>\<close>
 text\<open>
@@ -72,13 +76,13 @@ declare_reference*["fig:dependency"::figure]
 text\<open>
   The Isabelle Framework is based on a \<^emph>\<open>document-centric view\<close>\<^bindex>\<open>document-centric view\<close> of 
   a document, treating the input in its integrality as set of (user-programmable) \<^emph>\<open>document element\<close> 
-  that may mutually depend on and link to each other; A \<^emph>\<open>document\<close> in our sense is what is configured in a set of 
-  \<^verbatim>\<open>ROOT\<close>- and \<^verbatim>\<open>ROOTS\<close>-files.
+  that may mutually depend on and link to each other; A \<^emph>\<open>document\<close> in our sense is what is configured 
+  in a set of  \<^verbatim>\<open>ROOT\<close>- and \<^verbatim>\<open>ROOTS\<close>-files.
 
   Isabelle assumes a hierarchical document model\<^index>\<open>document model\<close>, \<^ie>, an \<^emph>\<open>integrated\<close> document 
   consist of a hierarchy of \<^emph>\<open>sub-documents\<close>  (files); dependencies are restricted to be
   acyclic at this level. 
-  Sub-documents can have different document types in order to capture documentations consisting of 
+  Document parts can have different document types in order to capture documentations consisting of 
   documentation, models, proofs, code of various forms and other technical artifacts.  We call the 
   main sub-document type, for historical reasons, \<^emph>\<open>theory\<close>-files.  A theory file\<^bindex>\<open>theory!file\<close>
   consists of a \<^emph>\<open>header\<close>\<^bindex>\<open>header\<close>, a \<^emph>\<open>context definition\<close>\<^index>\<open>context\<close>, and a body 
@@ -108,9 +112,9 @@ contains characters and a special notation for semantic macros \<^bindex>\<open>
 (here \<^theory_text>\<open>@{term "fac 5"}).\<close>
 \<close>
 
-text\<open>While we concentrate in this manual on \<^theory_text>\<open>text\<close>-document elements --- this is the main
-use of \<^dof> in its current stage --- it is important to note that there are actually three
-families of ``ontology aware'' document elements with analogous 
+text\<open>While \<^theory_text>\<open>text\<close>- elements play a major role in this manual on
+--- this is the main use of \<^dof> in its current stage --- it is important to note that there 
+are actually three families of ``ontology aware'' document elements with analogous 
 syntax to standard ones. The difference is a bracket with meta-data of the form:
 @{theory_text [display,indent=5, margin=70] 
 \<open>
@@ -123,7 +127,8 @@ Depending on the family, we will speak about \<^emph>\<open>(formal) text-contex
 \<^emph>\<open>(ML) code-contexts\<close>\<^index>\<open>code-contexts\<close> and \<^emph>\<open>term-contexts\<close>\<^index>\<open>term-contexts\<close> if we refer 
 to sub-elements inside the \<open>\<open>...\<close>\<close> cartouches of these command families. Note that the Isabelle
 framework allows for nesting cartouches that permits to support switching into a different
-context. In general, this has also the effect that the evaluation of antiquotations changes.
+context, albeit not all combinations are actually supported. 
+In general, nesting contexts has the effect that the evaluation of antiquotations changes.
 \<^footnote>\<open>In the literature, this concept has been referred to \<open>Cascade-Syntax\<close> and was used in the 
 Centaur-system and is existing in some limited form in some Emacs-implementations these days. \<close>  
 \<close>