@STRING{pub-springer={Springer} }
@STRING{pub-springer:adr=""}
@STRING{s-lncs  = "LNCS" }


@Manual{ wenzel:isabelle-isar:2017,
  title =        {The Isabelle/Isar Reference Manual},
  author =    {Makarius Wenzel},
  OPTorganization = {},
  OPTaddress =   {},
  OPTedition =   {},
  OPTmonth =     {},
  year =      {2017},
  note =      {Part of the Isabelle distribution.},
  OPTannote =    {}
}

@Book{            adler:r:2010,
  abstract      = {Presents a guide to the R computer language, covering such
                  topics as the user interface, packages, syntax, objects,
                  functions, object-oriented programming, data sets, lattice
                  graphics, regression models, and bioconductor.},
  added-at      = {2013-01-10T22:39:38.000+0100},
  address       = {Sebastopol, CA},
  author        = {Adler, Joseph},
  isbn          = {9780596801700 059680170X},
  keywords      = {R},
  publisher     = {O'Reilly},
  refid         = 432987461,
  title         = {R in a nutshell},
  year          = 2010
}



@InCollection{    wenzel.ea:building:2007,
  abstract      = {We present the generic system framework of
                  Isabelle/Isarunderlying 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 tactical ML
                  programs. Thus the Isabelle/Isar architecture may be
                  understood as an extension and refinement of the
                  traditional LCF approach, with explicit infrastructure for
                  building derivative systems. To demonstrate the technical
                  potential of the framework, we apply it to a concrete
                  formalmethods tool: the HOL-Z 3.0 environment, which is
                  geared towards the analysis of Z specifications and formal
                  proof of forward-refinements.},
  author        = {Makarius Wenzel and Burkhart Wolff},
  booktitle     = {TPHOLs 2007},
  editor        = {Klaus Schneider and Jens Brandt},
  language      = {USenglish},
  acknowledgement={none},
  pages         = {352--367},
  publisher     = pub-springer,
  address       = pub-springer:adr,
  number        = 4732,
  series        = s-lncs,
  title         = {Building Formal Method Tools in the {Isabelle}/{Isar}
                  Framework},
  doi           = {10.1007/978-3-540-74591-4_26},
  year          = 2007
}

@Misc{w3c:ontologies:2015,
  title={Ontologies},
  organisation={W3c},
  url={https://www.w3.org/standards/semanticweb/ontology},
  year=2018
}

@BOOK{boulanger:cenelec-50128:2015,
  AUTHOR       = "Boulanger, Jean-Louis",
  TITLE        = "{CENELEC} 50128 and {IEC} 62279 Standards",
  PUBLISHER    = "Wiley-ISTE",
  YEAR         = "2015",
  ADDRESS      = "Boston",
  NOTE         = "The reference on the standard."
}

@Booklet{         cc:cc-part3:2006,
  bibkey        = {cc:cc-part3:2006},
  key           = {Common Criteria},
  institution   = {Common Criteria},
  language      = {USenglish},
  month         = sep,
  year          = 2006,
  public        = {yes},
  title         = {Common Criteria for Information Technology Security
                  Evaluation (Version 3.1), {Part} 3: Security assurance
                  components},
  note          = {Available as document
                  \href{http://www.commoncriteriaportal.org/public/files/CCPART3V3.1R1.pdf}
                  {CCMB-2006-09-003}},
  number        = {CCMB-2006-09-003},
  acknowledgement={brucker, 2007-04-24}
}


@Book{            nipkow.ea:isabelle:2002,
  author        = {Tobias Nipkow and Lawrence C. Paulson and Markus Wenzel},
  title         = {Isabelle/HOL---A Proof Assistant for Higher-Order
                  Logic},
  publisher     = pub-springer,
  address       = pub-springer:adr,
  series        = s-lncs,
  volume        = 2283,
  doi           = {10.1007/3-540-45949-9},
  abstract      = {This book is a self-contained introduction to interactive
                  proof in higher-order logic HOL, using the proof
                  assistant Isabelle2002. It is a tutorial for potential
                  users rather than a monograph for researchers. The book has
                  three parts.

                  1. Elementary Techniques shows how to model functional
                  programs in higher-order logic. Early examples involve
                  lists and the natural numbers. Most proofs are two steps
                  long, consisting of induction on a chosen variable followed
                  by the auto tactic. But even this elementary part covers
                  such advanced topics as nested and mutual recursion. 2.
                  Logic and Sets presents a collection of lower-level tactics
                  that you can use to apply rules selectively. It also
                  describes Isabelle/HOL's treatment of sets, functions
                  and relations and explains how to define sets inductively.
                  One of the examples concerns the theory of model checking,
                  and another is drawn from a classic textbook on formal
                  languages. 3. Advanced Material describes a variety of
                  other topics. Among these are the real numbers, records and
                  overloading. Advanced techniques are described involving
                  induction and recursion. A whole chapter is devoted to an
                  extended example: the verification of a security protocol. },
  year          = 2002,
  acknowledgement={brucker, 2007-02-19},
  bibkey        = {nipkow.ea:isabelle:2002},
  tags          = {noTAG},
  clearance     = {unclassified},
  timestap      = {2008-05-26}
}



@InProceedings{	  wenzel:asynchronous:2014,
  author	= {Makarius Wenzel},
  title		= {Asynchronous User Interaction and Tool Integration in
		  Isabelle/{PIDE}},
  booktitle	= {Interactive Theorem Proving (ITP)},
  pages		= {515--530},
  year		= 2014,
  crossref	= {klein.ea:interactive:2014},
  doi		= {10.1007/978-3-319-08970-6_33},
  timestamp	= {Sun, 21 May 2017 00:18:59 +0200},
  abstract	= { Historically, the LCF tradition of interactive theorem
		  proving was tied to the read-eval-print loop, with
		  sequential and synchronous evaluation of prover commands
		  given on the command-line. This user-interface technology
		  was adequate when R. Milner introduced his LCF proof
		  assistant in the 1970-ies, but it severely limits the
		  potential of current multicore hardware and advanced IDE
		  front-ends.
		  
		  Isabelle/PIDE breaks this loop and retrofits the
		  read-eval-print phases into an asynchronous model of
		  document-oriented proof processing. Instead of feeding a
		  sequence of individual commands into the prover process,
		  the primary interface works via edits over a family of
		  document versions. Execution is implicit and managed by the
		  prover on its own account in a timeless and stateless
		  manner. Various aspects of interactive proof checking are
		  scheduled according to requirements determined by the
		  front-end perspective on the proof document, while making
		  adequate use of the CPU resources on multicore hardware on
		  the back-end.
		  
		  Recent refinements of Isabelle/PIDE provide an explicit
		  concept of asynchronous print functions over existing proof
		  states. This allows to integrate long-running or
		  potentially non-terminating tools into the document-model.
		  Applications range from traditional proof state output
		  (which may consume substantial time in interactive
		  development) to automated provers and dis-provers that
		  report on existing proof document content (e.g.
		  Sledgehammer, Nitpick, Quickcheck in Isabelle/HOL).
		  Moreover, it is possible to integrate query operations via
		  additional GUI panels with separate input and output (e.g.
		  for Sledgehammer or find-theorems). Thus the Prover IDE
		  provides continuous proof processing, augmented by add-on
		  tools that help the user to continue writing proofs.
		  }
}

@Proceedings{	  klein.ea:interactive:2014,
  editor	= {Gerwin Klein and Ruben Gamboa},
  title		= {Interactive Theorem Proving - 5th International
		  Conference, {ITP} 2014, Held as Part of the Vienna Summer
		  of Logic, {VSL} 2014, Vienna, Austria, July 14-17, 2014.
		  Proceedings},
  series	= s-lncs,
  volume	= 8558,
  publisher	= pub-springer,
  year		= 2014,
  doi		= {10.1007/978-3-319-08970-6},
  isbn		= {978-3-319-08969-0}
}

@InProceedings{	  bezzecchi.ea:making:2018,
  title		= {Making Agile Development Processes fit for V-style
		  Certification Procedures},
  author	= {Bezzecchi, S. and Crisafulli, P. and Pichot, C. and Wolff,
		  B.},
  booktitle	= {{ERTS'18}},
  abstract	= {We present a process for the development of safety and
		  security critical components in transportation systems
		  targeting a high-level certification (CENELEC 50126/50128,
		  DO 178, CC ISO/IEC 15408).
		  
		  The process adheres to the objectives of an ``agile
		  development'' in terms of evolutionary flexibility and
		  continuous improvement. Yet, it enforces the overall
		  coherence of the development artifacts (ranging from proofs
		  over tests to code) by a particular environment (CVCE).
		  
		  In particular, the validation process is built around a
		  formal development based on the interactive theorem proving
		  system Isabelle/HOL, by linking the business logic of the
		  application to the operating system model, down to code and
		  concrete hardware models thanks to a series of refinement
		  proofs.
		  
		  We apply both the process and its support in CVCE to a
		  case-study that comprises a model of an odometric service
		  in a railway-system with its corresponding implementation
		  integrated in seL4 (a secure kernel for which a
		  comprehensive Isabelle development exists). Novel
		  techniques implemented in Isabelle enforce the coherence of
		  semi-formal and formal definitions within to specific
		  certification processes in order to improve their
		  cost-effectiveness. },
  pdf		= {https://www.lri.fr/~wolff/papers/conf/2018erts-agile-fm.pdf},
  year		= 2018,
  series	= {ERTS Conference Proceedings},
  location	= {Toulouse}
}

@MISC{owl2012,
   title = {OWL 2 Web Ontology Language},
   note={\url{https://www.w3.org/TR/owl2-overview/}, Document Overview (Second Edition)},
   author = {World Wide Web Consortium}
}
    

@MISC{ protege,
  title = {Prot{\'e}g{\'e}},
  note={\url{https://protege.stanford.edu}},
  year = {2018}
}

@MISC{ cognitum,
  title = {Fluent Editor},
  note={\url{http://www.cognitum.eu/Semantics/FluentEditor/}},
  year = {2018}
}

@MISC{ neon,
  title = {The NeOn Toolkit},
  note = {\url{http://neon-toolkit.org}},
  year = {2018}
}

@MISC{ owlgred,
  title = {OWLGrEd},
  note={\url{http://owlgred.lumii.lv/}},
  year = {2018}
}

@MISC{ rontorium,
  title = {R Language Package for FLuent Editor (rOntorion)},
  note={\url{http://www.cognitum.eu/semantics/FluentEditor/rOntorionFE.aspx}},
  year = {2018}
}

@incollection{brucker.ea:isabelle-ontologies:2018,
  abstract = {While Isabelle is mostly known as part of Isabelle/HOL (an interactive theorem prover), it actually provides a framework for developing a wide spectrum of applications. A particular strength of the Isabelle framework is the combination of text editing, formal verification, and code generation.\\\\Up to now, Isabelle's document preparation system lacks a mechanism for ensuring the structure of different document types (as, e.g., required in certification processes) in general and, in particular, mechanism for linking informal and formal parts of a document.\\\\In this paper, we present Isabelle/DOF, a novel Document Ontology Framework on top of Isabelle. Isabelle/DOF allows for conventional typesetting \emph{as well} as formal development. We show how to model document ontologies inside Isabelle/DOF, how to use the resulting meta-information for enforcing a certain document structure, and discuss ontology-specific IDE support.},
  address = {Heidelberg},
  author = {Achim D. Brucker and Idir Ait-Sadoune and Paolo Crisafulli and Burkhart Wolff},
  booktitle = {Conference on Intelligent Computer Mathematics (CICM)},
  doi = {10.1007/978-3-319-96812-4_3},
  keywords = {Isabelle/Isar, HOL, Ontologies},
  language = {USenglish},
  location = {Hagenberg, Austria},
  number = {11006},
  pdf = {https://www.brucker.ch/bibliography/download/2018/brucker.ea-isabelle-ontologies-2018.pdf},
  publisher = {Springer-Verlag},
  series = {Lecture Notes in Computer Science},
  title = {Using The Isabelle Ontology Framework: Linking the Formal with the Informal},
  url = {https://www.brucker.ch/bibliography/abstract/brucker.ea-isabelle-ontologies-2018},
  year = {2018}
}

