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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>Automatically Generating Human Readable Documentation for Ontology Design Patterns</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Cogan Shimizu</string-name>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Data Semantics Lab, Kansas State University</institution>
          ,
          <country country="US">USA</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Keeping documentation consistent across deliverables is frequently a hassle. This program is a method for extracting and utilizing the common documentation annotations and those more speci c to ontology design patterns from OWL les and rendering via LaTeX to provide a human readable, shareable PDF.</p>
      </abstract>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>Motivation</title>
      <p>Documentation is a critically important component of any system. This
especially holds true as the complexity of that system grows. As knowledge graphs
(KG) grow both in size and complexity, and commensurately popularity, it is
important to meet the demand for in-depth documentation of the KG's schema
in order to promote its (re)use. This program is used to generate human readable
documentation (in the form of a pdf) from the annotations that are traditionally
used for documentation purposes within an OWL le.</p>
      <p>
        Automatic documentation generators are not new (e.g., [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ]). The added
bene t of this particular software is a focus on pattern-based ontologies (e.g. those
produced by composing ontology design patterns [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ] through the Modular
Ontology Modeling methodology [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ]) and the speci c annotations that describe their
modular structure [
        <xref ref-type="bibr" rid="ref7">7</xref>
        ], and the extended annotation vocabulary that describes
the intended and empirical uses of the modules [
        <xref ref-type="bibr" rid="ref6">6</xref>
        ].
This program is implemented in Python and depends on the RDFlib library. It
expects an OWL le and extracts the relevant annotations to the OWL le from
the Ontology Design Pattern Representation Language (OPLa) [
        <xref ref-type="bibr" rid="ref6 ref7">7,6</xref>
        ] in order
to generate the sections of the documentation. The annotations can be done
manually (e.g. through Protege1), but can also be generated using tools such
0 Copyright © 2020 for this paper by its authors. Use permitted under Creative
      </p>
      <p>
        Commons License Attribution 4.0 International (CC BY 4.0)
1 See https://protege.stanford.edu/.
as the OPLaTab [
        <xref ref-type="bibr" rid="ref12">12</xref>
        ] or CoModIDE [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ]. The output is a well-formed LATEX
document.
      </p>
      <p>The current structure is the title page, populated with top level annotations
such as dc:creator, a primer chapter talking about schema diagrams and axioms
(authored by Pascal Hitzler and can be con gured o ), and then generates the
following sections, when the appropriate annotations are present. Where
appropriate, it will also attempt to nd gures, such as Schema Diagrams and
examples, via the opla-sd:hasSchemaDiagram, opla-sd:hasShortcutDiagram,
oplasd:hasExampleDiagram annotations.</p>
      <p>
        { Overview: is generated using the opla-cp: annotation. The overview section
describes the overall purpose of the ontology (or pattern).
{ Use cases: is generated using the opla-cp:hasScenario annotation. The
program currently expects the title of the use case to be separated from the text
of the use case by a newline character. Use cases are the context of expected
interactions between agents (e.g., users or programs) and the ontology.
{ Competency Questions: is generated using the
opla-cp:hasCompetencyQuestion annotation. The program will create an enumerated (alphabetized)
list of the competency questions for the ontology. Competency questions are
the fundamental interactions that constitute a use case.
{ Formalization: is generated using the opla-core:Axiom opla-core:isNativeTo
owl:Ontology annotation pattern. Currently we support the formalization
and explanation of 17 the axiom patterns that can be found in [
        <xref ref-type="bibr" rid="ref2 ref9">9,2</xref>
        ].
{ Submodules: is generated using the opla-core:isNativeTo annotation. The
program identi es any submodules and links to the appropriate section in
the documentation. A submodule can be considered to be a fully de ned and
described component of the ontology.
{ Views: is generated using the opla-core:hasShortcut annotation. Shortcuts
are \optional" role chains throughout the ontology that may help for
alignments or data publishers. These are described in the same manner as the
Formalization section.
{ Entanglements: is generated using the opla-cp:hasEntanglement
annotation. Entanglements may be viewed as alignments or implementations. This
section is generally more useful for patterns where multiple implementations
may exist (e.g., SOSA/SSN [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ] vs. RealEstateCore [
        <xref ref-type="bibr" rid="ref5">5</xref>
        ]).
{ Examples: is generated using the opla-cp:hasExample annotation. These are
just example triples encoded into a literal and represented in a Verbatim
environment.
{ Remarks, Questions, Issues, Known Problems: is generated using the
opla-cp:hasConsequence, opla-cp:hasRemark, or rdfs:Comment annotations. This
a catchall section.
      </p>
      <p>Additional information on the implementation, installation, and use of these
tools (including CoModIDE) can be found in our online portal.2 The source
2 See http://daselab.org/content/modular-ontology-engineering-portal.
(documentation-generator/), licensing (license.txt), and example execution(documentation/),
containing two working patterns, for this demonstration can be found on GitHub.3
3</p>
    </sec>
    <sec id="sec-2">
      <title>Demonstration</title>
      <p>We expect to provide a live demonstration of the program's functionality in a
tutorial-like format. We will provide several additional pre-annotated patterns
beyond what is currently included in the online repository for this demonstration
in order to show how di erent annotations result in changed documentation. In
particular, we will walk potential users through the execution process of this
program, customize the nal output, and illustrate integration with the surrounding
tool-suite.
4</p>
    </sec>
    <sec id="sec-3">
      <title>Next Steps</title>
      <p>
        There are many additional directions that we may take this work. First and
foremost, we intend to incorporate additional insights from [
        <xref ref-type="bibr" rid="ref8">8</xref>
        ] on how to
better document ontology design patterns to potential users. This includes a more
comprehensive modeling of use-cases and competency questions and the
provenance and lineage thereof. We also wish to see how it may be used to document
so-called Modular Ontology Design Libraries [
        <xref ref-type="bibr" rid="ref13">13</xref>
        ] where many patterns may
interrelate (e.g., through opla-core:hasRelatedPattern).
      </p>
      <p>While this program represents a prototypical demonstration of the ability
to generate useful, human-readable documentation from annotations, there are
several ways to improve this process: for better code quality and improved,
resultant machine-readable (and human-readable) documentation. For the former,
by separating static portions of the documentation (e.g., the primer chapter or
LATEX speci c formatting) For the latter, by outputting to HTML. Finally, we
expect to support additional documentation annotations.</p>
      <p>Acknowledgement. The authors acknowledge support by the National Science
Foundation under Grant 2033521 A1: KnowWhereGraph: Enriching and Linking
Cross-Domain Knowledge Graphs using Spatially-Explicit AI Technologies.
3 See https://github.com/KnowWhereGraph/documentation-generator.</p>
    </sec>
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