Reworked textually abstract, intro, background. Eliminate \emph

examples/technical_report/Isabelle_DOF-Manual/00_Frontmatter.thy

@@ -1,7 +1,7 @@
 (*************************************************************************
  * Copyright (C) 
- *               2019      The University of Exeter 
+ *               2019-20   The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
+ *               2018-2020 The University of Paris-Saclay
  *               2018      The University of Sheffield
  *
  * License:
@@ -42,7 +42,7 @@ text*[abs::abstract,
   A major application of \dof is the integrated development of
   formal certification documents (\eg, for Common Criteria or CENELEC
   50128) that require consistency across both formal and informal
-  arguments.
+  arguments. 
 
   \isadof is integrated into Isabelle's IDE, which
   allows for smooth ontology development as well as immediate
@@ -54,10 +54,13 @@ text*[abs::abstract,
   In this user-manual, we give an in-depth presentation of the design
   concepts of \dof's Ontology Definition Language (ODL) and describe
   comprehensively its major commands. Many examples show typical best-practice
-  applications of the system. \isadof is the
+  applications of the system.
-  first ontology language supporting machine-checked
+
-  links between the formal and informal parts in an LCF-style
+  It is an unique feature of  \isadof  that ontologies may be used to control
-  interactive theorem proving environment.
+  the link between formal and informal content in documents in a machine
+  checked way. These links can connect both text elements as well as formal
+  modelling elements such as terms, definitions, code  and logical formulas,
+  alltogether *\<open>integrated\<close> in a state-of-the-art interactive theorem prover.
 \<close>
 
 (*<*) 

examples/technical_report/Isabelle_DOF-Manual/01_Introduction.thy

@@ -1,7 +1,7 @@
 (*************************************************************************
  * Copyright (C) 
- *               2019      The University of Exeter 
+ *               2019-2020 The University of Exeter 
- *               2018-2019 The University of Paris-Saclay
+ *               2018-2020 The University of Paris-Saclay
  *               2018      The University of Sheffield
  *
  * License:
@@ -33,8 +33,8 @@ have to follow a structure.  In practice, large groups of developers have to pro
 set of documents where the consistency is notoriously difficult to maintain. In particular, 
 certifications are centered around the \<^emph>\<open>traceability\<close> of requirements throughout the entire 
 set of documents. While technical solutions for the traceability problem exists (most notably:
-DOORS~\cite{ibm:doors:2019}), they are weak in the treatment of formal entities (such as formulas and their 
+DOORS~\cite{ibm:doors:2019}), they are weak in the treatment of formal entities (such as formulas 
-logical contexts).
+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
@@ -43,11 +43,12 @@ as \<^emph>\<open>links\<close> between them. A particular link between concepts
 the instances of a subclass to be instances of the super-class.
 
 To adress 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 
+implementation of \dof called \isadof. \dof is designed for building scalable and user-friendly 
-tools on top of interactive theorem provers. \isadof is a novel framework, implemented as extension of 
+tools on top of interactive theorem provers. \isadof is an instance of this novel framework, 
-Isabelle/HOL, to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them during document evolution. Based 
+implemented as extension of Isabelle/HOL, to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them 
-on Isabelle's infrastructures, ontologies may refer to types, terms, proven theorems, code, or 
+during document evolution. Based on Isabelle's infrastructures, ontologies may refer to types, 
-established assertions. Based on a novel adaption of the Isabelle IDE, a document is checked to be 
+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.

examples/technical_report/Isabelle_DOF-Manual/02_Background.thy

@@ -91,9 +91,9 @@ text\<open>
   separate commands from each other.
 
   We distinguish fundamentally two different syntactic levels:
-  \<^item> the \emph{outer-syntax}\bindex{syntax!outer}\index{outer syntax|see {syntax, outer}} (\ie, the 
+  \<^item> the *\<open>outer-syntax\<close>\bindex{syntax!outer}\index{outer syntax|see {syntax, outer}} (\ie, the 
     syntax for commands) is processed by a lexer-library and parser combinators built on top, and
-  \<^item> the \emph{inner-syntax}\bindex{syntax!inner}\index{inner syntax|see {syntax, inner}} (\ie, the 
+  \<^item> the *\<open>inner-syntax\<close>\bindex{syntax!inner}\index{inner syntax|see {syntax, inner}} (\ie, the 
     syntax for \inlineisar|\<lambda>|-terms in HOL) with its own parametric polymorphism type 
     checking.
 
@@ -108,14 +108,14 @@ text\<open>
   \end{isar}
   This will type-set the corresponding text in, for example, a PDF document.  However, this 
   translation is not necessarily one-to-one: text elements can be enriched by formal, \ie, 
-  machine-checked content via \emph{semantic macros}, called antiquotations\bindex{antiquotation}:
+  machine-checked content via *\<open>semantic macros\<close>, called antiquotations\bindex{antiquotation}:
 \begin{isar}
-text\<Open>According to the reflexivity axiom <@>{thm refl}, we obtain in \<Gamma> 
+text\<Open>According to the *\<Open>reflexivity\<Close> axiom <@>{thm refl}, we obtain in \<Gamma> 
       for <@>{term "fac 5"} the result <@>{value "fac 5"}.\<Close>
 \end{isar}
 which is represented in the final document (\eg, a PDF) by:
 \begin{out}
-According to the reflexivity axiom $\mathrm{x = x}$, we obtain in $\Gamma$ for $\operatorname{fac} \text{\textrm{5}}$ the result $\text{\textrm{120}}$.
+According to the \emph{reflexivity} axiom $\mathrm{x = x}$, we obtain in $\Gamma$ for $\operatorname{fac} \text{\textrm{5}}$ the result $\text{\textrm{120}}$.
 \end{out}
   Semantic macros are partial functions of type \inlineisar+\<theta> \<rightarrow> text+; since they can use the
   system state, they can perform all sorts of specific checks or evaluations (type-checks, 

examples/technical_report/Isabelle_DOF-Manual/document/root.bib

@@ -181,7 +181,7 @@
   timestap	= {2008-05-26}
 }
 
-@InProceedings{	  wenzel:asynchronous:2014,
+@InProceedings{wenzel:asynchronous:2014,
   author	= {Makarius Wenzel},
   title		= {Asynchronous User Interaction and Tool Integration in
 		  {Isabelle}/{PIDE}},