(*************************************************************************
 * Copyright (C) 
 *               2019-2023 The University of Exeter 
 *               2018-2023 The University of Paris-Saclay
 *               2018      The University of Sheffield
 *
 * License:
 *   This program can be redistributed and/or modified under the terms
 *   of the 2-clause BSD-style license.
 *
 *   SPDX-License-Identifier: BSD-2-Clause
 *************************************************************************)

(*<*)
theory "M_01_Introduction"
  imports "M_00_Frontmatter"
begin
(*>*)


chapter*[intro::introduction]\<open> Introduction \<close>  
text*[introtext::introduction]\<open> 
The linking of the \<^emph>\<open>formal\<close> to the \<^emph>\<open>informal\<close> is perhaps the most pervasive challenge in the
digitization of knowledge and its propagation. This challenge incites numerous research efforts
summarized under the labels ``semantic web,'' ``data mining,'' or any form of advanced ``semantic''
text processing.  A key role in structuring this linking plays is \<^emph>\<open>document ontologies\<close> (also called
\<^emph>\<open>vocabulary\<close> in the semantic web community~@{cite "w3c:ontologies:2015"}), \<^ie>, a machine-readable
form of the structure of documents as well as the document discourse.

Such ontologies can be used for the scientific discourse within scholarly articles, mathematical 
libraries, and in the engineering discourse of standardized software certification 
documents~@{cite "boulanger:cenelec-50128:2015" and "cc:cc-part3:2006"}. All these
documents contain formal content and have to follow a given structure.  In practice, large groups of developers have to produce a substantial
set of documents where  consistency is notoriously difficult to maintain. In particular, 
certifications are centred around the \<^emph>\<open>traceability\<close> of requirements throughout the entire 
set of documents. While technical solutions for the traceability problem exist (most notably:
DOORS~@{cite "ibm:doors:2019"}), they are weak in the treatment of formal entities (such as formulas 
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>), 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.

Engineering an ontological language for documents that contain both formal and informal elements
as occurring 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 an 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 the 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"}. 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>
(*<*)
declare_reference*[background::text_section]
declare_reference*[isadof_tour::text_section]
declare_reference*[isadof_ontologies::text_section]
declare_reference*[writing_doc::text_section]
declare_reference*[isadof_developers::text_section]
(*>*)
text\<open>
This manual can be read in different ways, depending on what you want to accomplish. We see three
different main user groups: 
\<^enum> \<^emph>\<open>\<^isadof> users\<close>, \<^ie>, users that just want to edit a core document, be it for a paper or a 
  technical report, using a given ontology. These users should focus on 
  @{docitem (unchecked) \<open>isadof_tour\<close>} and, depending on their knowledge of Isabelle/HOL, also on
  @{docitem (unchecked) \<open>background\<close>}. 
\<^enum> \<^emph>\<open>Ontology developers\<close>, \<^ie>,  users that want to develop new ontologies or modify existing 
  document ontologies. These users should, after having gained acquaintance as a user, focus 
  on @{docitem (unchecked) \<open>isadof_ontologies\<close>}. 
\<^enum> \<^emph>\<open>\<^isadof> developers\<close>, \<^ie>, users that want to extend or modify \<^isadof>, \<^eg>, by adding new 
  text-elements. These users should read @{docitem (unchecked) \<open>isadof_developers\<close>}.
\<close>

subsubsection\<open>Typographical Conventions\<close>
text\<open>
  We acknowledge that understanding \<^isadof> and its implementation in all details requires
  separating multiple technological layers or languages. To help the reader with this, we 
  will type-set the different languages in different styles. In particular, we will use 
  \<^item> a light-blue background for input written in Isabelle's Isar language, \<^eg>:
    @{boxed_theory_text [display]
    \<open>lemma refl: "x = x" 
  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 SML-code:
    @{boxed_sml [display] \<open>fun id x = x\<close>}
  \<^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
CHANGELOG.md  CITATION  examples  install  LICENSE  README.md  ROOTS  src\<close>}
\<close>

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 
      Mathematics (CICM)\<close>, number 11006 in Lecture Notes in Computer Science. Springer-Verlag,
      Heidelberg, 2018. \href{https://doi.org/10.1007/978-3-319-96812-4\_3}
      {10.1007/978-3-319-96812-4\_3}.
    \end{quote}
    A \<^BibTeX>-entry is available at: 
    \<^url>\<open>https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelle-ontologies-2018\<close>. 
  \<^item> for the implementation of \<^isadof>~@{cite "brucker.ea:isabelledof:2019"}:
    \begin{quote}\small
      A.~D. Brucker and B.~Wolff. \<^isadof>: Design and implementation. In P.C.~{\"O}lveczky and 
      G.~Sala{\"u}n, editors, \<^emph>\<open>Software Engineering and Formal Methods (SEFM)\<close>, number 11724 in
      Lecture Notes in Computer Science. Springer-Verlag, Heidelberg, 2019.
      \href{https://doi.org/10.1007/978-3-030-30446-1_15}{10.1007/978-3-030-30446-1\_15}.
    \end{quote}
    A \<^BibTeX>-entry is available at: 
    \<^url>\<open>https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelledof-2019\<close>.
  \<^item> for an application of \<^isadof> in the context of certifications:
    \begin{quote}\small
     A.~D. Brucker and B.~Wolff.
     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.
     \<^url>\<open>https://doi.org/10.1007/978-3-030-34968-4_4\<close>.
    \end{quote}
\<close>

(*<*) 
end
(*>*) 
  
