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(*<*)
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theory ConceptsAndImpl
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imports "../../../ontologies/scholarly_paper"
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begin
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open_monitor*[this::article]
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(*>*)
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declare[[strict_monitor_checking=false]]
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title*[tit::title]\<open>A Document Ontology Framework in Isabelle\<close>
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subtitle*[stit::subtitle]\<open>Design and Implementation\<close>
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text*[adb:: author,
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email="''a.brucker@sheffield.ac.uk''",
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orcid="''0000-0002-6355-1200''",
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affiliation="''The University of Sheffield, Sheffield, UK''"]\<open>Achim D. Brucker\<close>
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text*[bu::author,
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email = "''wolff@lri.fr''",
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affiliation = "''Universit\\'e Paris-Sud, Paris, France''"]\<open>Burkhart Wolff\<close>
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text*[abs::abstract,
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keywordlist="[''Semantic Web'',''Document Ontology'',''Formal Document Development'',''Isabelle/DOF'']"]\<open>
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We present an extension of the Isabelle/Isar framework allowing both the
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\<^emph>\<open>modeling\<close> of document ontologies as well as the their *\<open>enforcement\<close> inside theory documents
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by a smooth integration into Isabelle's IDE. The resulting extension \<^verbatim>\<open>Isa_DOF\<close> provides a
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strongly typed ontology definition language allowing to annotate a document element (or ``corpus'')
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with meta-information that is validated during document development and maintenance.
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Ontology definitions provide \<^emph>\<open>concepts\<close>, \<^emph>\<open>is-a\<close> relations and \<^emph>\<open>links\<close> between them,
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as well as \<^emph>\<open>F-links\<close> from concepts to formal content such as types, terms and theorems.
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Documents referring to an ontology are edited, validated and proof-checked within
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Isabelle/HOL. Particular emphasis is put on a deep integration
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into the Isabelle IDE to give immediate ontological feedback to the
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developer of documents containing entities such as text, models,
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formal proofs, and code.
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The IDE animates \<^emph>\<open>links\<close> and \<^emph>\<open>F-links\<close> via hyper-references, and
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controls the document structure by checking a kind of behavioural specification.
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Sufficiently annotated, large documents are easier to be developed collaboratively
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by continuously validating the \<^emph>\<open>coherence\<close> between formal and informal parts, and
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the impact of changes can be better tracked automatically.
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\<close>
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(* Industrial Application ? *)
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(* Support of document ontologies is provided for immediate
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user-feedback when editing large documents with formal and
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semi-formal content, be it for mathematical articles, exercises, or,
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\eg, deliverables in a certified software engineering
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process. *)
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(*
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@inproceedings{DBLP:conf/mkm/BlanchetteHMN15,
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author = {Jasmin Christian Blanchette and
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Maximilian P. L. Haslbeck and
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Daniel Matichuk and
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Tobias Nipkow},
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title = {Mining the Archive of Formal Proofs},
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booktitle = {Intelligent Computer Mathematics - International Conference, {CICM}
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2015, Washington, DC, USA, July 13-17, 2015, Proceedings},
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pages = {3--17},
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year = {2015},
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crossref = {DBLP:conf/mkm/2015},
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url = {https://doi.org/10.1007/978-3-319-20615-8\_1},
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doi = {10.1007/978-3-319-20615-8\_1},
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timestamp = {Fri, 02 Nov 2018 09:40:47 +0100},
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biburl = {https://dblp.org/rec/bib/conf/mkm/BlanchetteHMN15},
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bibsource = {dblp computer science bibliography, https://dblp.org}
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}
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*)
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section*[intro::introduction]\<open> Introduction \<close>
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text*[introtext::introduction]\<open>
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With the maturation and growing power of interactive proof systems, the body of formalized
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mathematics and engineering is dramatically increasing. The Isabelle Archive of Formal Proof (AFP),
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for example, created in 2004, counted in 2015 the number of 215 articles
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@{footnote \<open>... where "articles" are theory developments underlying a submission process
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similar to the mizar journal \cite{}\<close>}, whereas the count stood at 413 only three years later.
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An in-depth empirical analysis shows that both complexity and size increased accordingly
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@{cite "DBLP:conf/mkm/BlanchetteHMN15"}. Since the entire AFP is part of the Isabelle regression
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test suite and therefore maintained for the different releases, this body of knowledge is also
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available in high technical consistency.
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This raises a wider interest in the application of advanced "semantic Web" structuring, query
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and mining techniques. Compared to other scientific disciplines like biology or medicine,
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where large data-bases of genomes or scientific publications have been organized along
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ontologies @{cite "..." and "..." } enabling queries, for example, there are still a number of
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technical and social challenges to overcome in order to leverage this techniques in the
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field of interactive theorem proving. \fixme{avoid ontology here.}
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One of the main use of ontologies is annotation. Let us consider a set of entities available in
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a given corpus. These entities may be sentences or paragraphs in a document, figures, tables,
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definitions or lemmas in a document, etc. By annotation, we denote the link that may exist between
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an ontology concept and a document element of the considered corpus.
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The annotation process consists in defining and running a set of rules leading to the production of
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annotations. This process may be completely automated, semi-automatic with user validation or completely
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interactive.
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\<close>
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text\<open>
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IDEA FOR RELATED WORK: a table with conceptual properties of ontology languages
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Feature | Ontolingua | DAML+OIL | RDFS | OWL | PLIB | XML | Isa_ODL
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------------------------------------------------------------------------
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granularity | Word | | | | | Character | sentence (word)
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relationships | | sentence - concept, is_A, (class-class)
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strong typing | | on attributes and classes
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links | | links , F-links
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algebraic operators | | sets, lists, relations, HOL.
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Constraints | | ML, executable HOL
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CWA vs OWA | | OWA
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Context Modeling | | Context import
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Inheritance | | SINGLE
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Instantiation | | MULTIPLE
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\<close>
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text*[intro_old::introduction]\<open>
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The linking of the \<^emph>\<open>formal\<close> to the \<^emph>\<open>informal\<close> is perhaps the
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most pervasive challenge in the digitization of knowledge and its
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propagation. This challenge incites numerous research efforts
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summarized under the labels ``semantic web'', ``data mining'', or any
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form of advanced ``semantic'' text processing. A key role in
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structuring this linking play \<^emph>\<open>document ontologies\<close> (also called
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\<^emph>\<open>vocabulary\<close> in the semantic web community~@{cite "w3c:ontologies:2015"}),
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\ie, a machine-readable form of the structure of documents as well as
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the document discourse.
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Such ontologies can be used for the scientific discourse within scholarly
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articles, mathematical libraries, and in the engineering discourse
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of standardized software certification
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documents~@{cite "boulanger:cenelec-50128:2015" and "cc:cc-part3:2006"}.
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Further applications are the domain-specific discourse in juridical texts or medical reports.
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In general, an ontology is a formal explicit description of \<^emph>\<open>concepts\<close>
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in a domain of discourse (called \<^emph>\<open>classes\<close>), properties of each concept
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describing \<^emph>\<open>attributes\<close> of the concept, as well as \<^emph>\<open>links\<close> between
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them. A particular link between concepts is the \<^emph>\<open>is-a\<close> relation declaring
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the instances of a subclass to be instances of the super-class.
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The main objective of this paper is to present \isadof, a novel
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framework to \<^emph>\<open>model\<close> typed ontologies and to \<^emph>\<open>enforce\<close> them during
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document evolution. Based on Isabelle infrastructures, ontologies may refer to
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types, terms, proven theorems, code, or established assertions.
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Based on a novel adaption of the Isabelle IDE, a document is checked to be
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\<^emph>\<open>conform\<close> to a particular ontology---\isadof is designed to give fast user-feedback
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\<^emph>\<open>during the capture of content\<close>. This is particularly valuable in case of document
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changes, where the \<^emph>\<open>coherence\<close> between the formal and the informal parts of the
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content can be mechanically checked.
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To avoid any misunderstanding: \isadof is \<^emph>\<open>not a theory in HOL\<close>
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on ontologies and operations to track and trace links in texts,
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it is an \<^emph>\<open>environment to write structured text\<close> which \<^emph>\<open>may contain\<close>
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Isabelle/HOL definitions and proofs like mathematical articles, tech-reports and
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scientific papers---as the present one, which is written in \isadof
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itself. \isadof is a plugin into the Isabelle/Isar
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framework in the style of~@{cite "wenzel.ea:building:2007"}.
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\<close>
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(* declaring the forward references used in the subsequent section *)
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(*<*)
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declare_reference*[bgrnd::text_section]
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declare_reference*[isadof::text_section]
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declare_reference*[ontomod::text_section]
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declare_reference*[ontopide::text_section]
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declare_reference*[conclusion::text_section]
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(*>*)
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text*[plan::introduction]\<open> The plan of the paper is follows: we start by introducing the underlying
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Isabelel sytem (@{docitem (unchecked) \<open>bgrnd\<close>}) followed by presenting the
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essentials of \isadof and its ontology language (@{docitem (unchecked) \<open>isadof\<close>}).
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It follows @{docitem (unchecked) \<open>ontomod\<close>}, where we present three application
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scenarios from the point of view of the ontology modeling. In @{docitem_ref (unchecked) \<open>ontopide\<close>}
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we discuss the user-interaction generated from the ontological definitions. Finally, we draw
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conclusions and discuss related work in @{docitem_ref (unchecked) \<open>conclusion\<close>}. \<close>
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section*[bgrnd::text_section,main_author="Some(@{docitem ''adb''}::author)"]
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\<open> Background: The Isabelle System \<close>
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