added sec on term atq, restructuring
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@ -65,7 +65,6 @@ text\<open>
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managers. On a modern Debian system or a Debian derivative (\<^eg>, Ubuntu), the following command
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should install all required \<^LaTeX> packages:
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@{boxed_bash [display]\<open>ë\prompt{}ë sudo aptitude install texlive-full\<close>}
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\<^dof>
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\<close>
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subsubsection*[isadof::technical]\<open>Installing \<^isadof>\<close>
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@ -216,34 +215,31 @@ text\<open>At times, this causes idiosyncrasies like the ones cited in the follo
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\<close>
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section*[scholar_onto::example]\<open>Writing Academic Publications in \<^boxed_theory_text>\<open>scholarly_paper\<close>\<close>
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subsection\<open>Writing Academic Papers\<close>
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subsection\<open>A Selection of major Examples\<close>
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text\<open>
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The ontology \<^verbatim>\<open>scholarly_paper\<close> \<^index>\<open>ontology!scholarly\_paper\<close> is an ontology modeling
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academic/scientific papers, with a slight bias towards texts in the domain of mathematics and
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engineering. We explain first the principles of its underlying ontology, and then we present two
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``real'' examples from our own publication practice.
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\<close>
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text\<open>
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\<^enum> The iFM 2020 paper~@{cite "taha.ea:philosophers:2020"} is a typical mathematical text,
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heavy in definitions with complex mathematical notation and a lot of non-trivial cross-referencing
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between statements, definitions and proofs which are ontologically tracked. However, wrt.
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the possible linking between the underlying formal theory and this mathematical presentation,
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it follows a pragmatic path without any ``deep'' linking to types, terms and theorems,
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deliberately not exploiting \<^isadof> 's full potential with this regard.
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\<^enum> In the CICM 2018 paper~@{cite "brucker.ea:isabelle-ontologies:2018"}, we deliberately
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refrain from integrating references to formal content in order to demonstrate that \<^isadof> is not
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a framework from Isabelle users to Isabelle users only, but people just avoiding as much as
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possible \<^LaTeX> notation.
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\<^enum> The iFM 2020 paper~@{cite "taha.ea:philosophers:2020"} is a typical mathematical text,
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heavy in definitions with complex mathematical notation and a lot of non-trivial cross-referencing
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between statements, definitions and proofs which are ontologically tracked. However, wrt.
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the possible linking between the underlying formal theory and this mathematical presentation, it follows a pragmatic path without any ``deep'' linking to types, terms and theorems,
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deliberately not exploiting \<^isadof> 's full potential with this regard.
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\<^enum> In the CICM 2018 paper~@{cite "brucker.ea:isabelle-ontologies:2018"}, we deliberately
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refrain from integrating references to formal content in order to demonstrate that \<^isadof> is not
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a framework from Isabelle users to Isabelle users only, but people just avoiding as much as
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possible \<^LaTeX> notation.
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The \<^isadof> distribution contains both examples using the ontology \<^verbatim>\<open>scholarly_paper\<close> in
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the directory \<^nolinkurl>\<open>examples/scholarly_paper/2018-cicm-isabelle_dof-applications/\<close> or
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\<^nolinkurl>\<open>examples/scholarly_paper/2020-iFM-CSP\<close>.
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You can inspect/edit the example in Isabelle's IDE, by either
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\<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the
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Isabelle-Icon provided by the Isabelle installation) and loading the file
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\<^nolinkurl>\<open>examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy"\<close>
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\<^item> starting Isabelle/jEdit from the command line by, \<^eg>, calling:
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\<^item> starting Isabelle/jEdit using your graphical user interface (\<^eg>, by clicking on the
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Isabelle-Icon provided by the Isabelle installation) and loading the file
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\<^nolinkurl>\<open>examples/scholarly_paper/2018-cicm-isabelle_dof-applications/IsaDofApplications.thy"\<close>
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\<^item> starting Isabelle/jEdit from the command line by, \<^eg>, calling:
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@{boxed_bash [display]\<open>ë\prompt{\isadofdirn}ë
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isabelle jedit -d . examples/scholarly_paper/2020-iFM-CSP/paper.thy \<close>}
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@ -505,10 +501,9 @@ figure*[figDogfoodVIlinkappl::figure,relative_width="80",src="''figures/Dogfood-
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text\<open>
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An ontological reference application in @{figure "figDogfoodVIlinkappl"}: the
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ontology-dependant antiquotation \<^boxed_theory_text>\<open>@{example \<open>ex1\<close>}\<close> refers to the corresponding
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text-element \<^boxed_theory_text>\<open>ex1\<close>.
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Hovering allows for inspection, clicking for jumping to the definition.
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If the link does not exist or has a non-compatible type, the text is not validated, \<^ie>,
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Isabelle/jEdit will respond with an error.\<close>
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text-element \<^boxed_theory_text>\<open>ex1\<close>. Hovering allows for inspection, clicking for jumping to the
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definition. If the link does not exist or has a non-compatible type, the text is not validated,
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\<^ie>, Isabelle/jEdit will respond with an error.\<close>
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text\<open>We advise users to experiment with different notation variants.
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Note, further, that the Isabelle \<^latex>\<open>@\{cite ...\}\<close>-text-anti-quotation makes its checking
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@ -522,7 +517,7 @@ subsection*["using-term-aq"::technical, main_author = "Some @{author ''bu''}"]
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text\<open>The present version of \<^isadof> is the first version that supports the novel feature of
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\<^dof>-generated term-antiquotations\<^bindex>\<open>term-antiquotations\<close>, \<^ie>, antiquotations embedded
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in HOL-\<open>\<lambda>\<close>-terms possessing arguments that were validated in the ontological context.
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These HOL-\<open>\<lambda>\<close>-terms may occur in definitions, lemmas, or in values to define attributes
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These \<open>\<lambda>\<close>-terms may occur in definitions, lemmas, or in values to define attributes
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in class instances. They have the format:\<close>
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text\<open>\<^center>\<open>\<open>@{name arg\<^sub>1 ... arg\<^sub>n\<^sub>-\<^sub>1} arg\<^sub>n\<close>\<close>\<close>
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