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  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>CoTOn: A Cognitive Theory Ontology for Representing Diverging Conceptualizations of Cognitive Concepts</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Anna Ravenschlag</string-name>
          <email>annanatali.ravenschlag@plus.ac.at</email>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Bianca Löhnert</string-name>
          <email>bianca.loehnert@plus.ac.at</email>
          <xref ref-type="aff" rid="aff1">1</xref>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Giancarlo Guizzardi</string-name>
          <email>g.guizzardi@utwente.nl</email>
          <xref ref-type="aff" rid="aff3">3</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Maria das Graças da Silva Teixeira</string-name>
          <email>maria.teixeira@ufes.br</email>
          <xref ref-type="aff" rid="aff0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Monique Denissen</string-name>
          <email>monique.denissen@plus.ac.at</email>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Florian Hutzler</string-name>
          <email>florian.hutzler@plus.ac.at</email>
          <xref ref-type="aff" rid="aff2">2</xref>
        </contrib>
        <aff id="aff0">
          <label>0</label>
          <institution>Universidade Federal do Espírito Santo, Departamento de Computação e Eletrônica</institution>
          ,
          <country country="BR">Brazil</country>
        </aff>
        <aff id="aff1">
          <label>1</label>
          <institution>University of Salzburg, Department of Computer Science, Database Research Group</institution>
          ,
          <country country="AT">Austria</country>
        </aff>
        <aff id="aff2">
          <label>2</label>
          <institution>University of Salzburg, Department of Psychology, Centre for Cognitive Neuroscience</institution>
          ,
          <country country="AT">Austria</country>
        </aff>
        <aff id="aff3">
          <label>3</label>
          <institution>University of Twente, Department of Mathematics and Computer Science</institution>
          ,
          <country country="NL">The Netherlands</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Cognitive neuroscience is a data-intensive and theory-driven discipline that seeks to explain how human experience and behavior is related to physiological, behavioral, and neural measurements. The investigated cognitive concepts (e.g., memory or attention) are, however, latent, unobservable constructs that are assessed via observable and objectifiable measurements obtained in carefully designed experimental settings. Because their definitions and assumed interrelations may vary depending on the underlying cognitive theories, cognitive concepts must be defined and interpreted in the context of those theories. For communication, however, the cognitive neuroscience community is accustomed to use the same linguistic terms for denoting cognitive concepts that have varying definitions in diferent theories, efectively introducing terminological ambiguity. An ontology for the domain of cognitive neuroscience thus needs to be capable of representing these varying definitions of cognitive concepts that depend on diferent theories while preserving the relation to their linguistic terms to meet the communication needs of the community. To address this problem, we propose a Cognitive Theory Ontology (CoTOn) that provides the means to represent and relate 1. the objectifiable knowledge about observable entities of the experimental setting, 2. the theory-dependent conceptualizations of latent cognitive concepts, and 3. the community-specific use of the same linguistic terms for diferently defined cognitive concepts. In this paper, we ontologically analyse the relevant entities in the cognitive neuroscience domain and derive a reference model and an operational version of CoTOn on the level of general types. We implement this initial version of CoTOn in Protégé and show its applicability for retrieving objectifiable as well as theory-dependent knowledge.</p>
      </abstract>
      <kwd-group>
        <kwd>eol&gt;cognitive neuroscience</kwd>
        <kwd>domain analysis</kwd>
        <kwd>reference model</kwd>
        <kwd>operational ontology</kwd>
        <kwd>SABiO</kwd>
        <kwd>UFO</kwd>
      </kwd-group>
    </article-meta>
  </front>
  <body>
    <sec id="sec-1">
      <title>1. Introduction</title>
      <p>
        Cognitive neuroscience is a data-intensive and theory-driven discipline that seeks to explain how
human experience and behavior is related to physiological, behavioral and neural measurements.
Importantly, the objects of interest being investigated, i.e. cognitive concepts like memory or
attention, are latent, only indirectly observable constructs [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ]. To assess these latent cognitive
concepts, they are operationalized via observable measurements that are obtained in carefully
designed experimental settings.
      </p>
      <p>
        Since cognitive concepts are constructs that are not directly observable, cognitive
neuroscientists work with assumptions about them. These assumptions are provided by various theories
that propagate potentially diferent definitions for these constructs. In practice, the latent
nature of cognitive concepts and their subsequent definitions by diferent theories often result
in ambiguous terminology. Accordingly, the same linguistic terms may be assigned to divergent
cognitive concepts, or diferent linguistic terms are used for putatively identical concepts [
        <xref ref-type="bibr" rid="ref1">1</xref>
        ].
      </p>
      <p>
        Because the definitions and assumed interrelations of concepts may vary depending on the
underlying theoretical framework, cognitive concepts must be defined and interpreted in the
context of those theories [
        <xref ref-type="bibr" rid="ref2">2</xref>
        ]. This is also highly relevant when it comes to providing
adequate metadata for annotating neurocognitive datasets (obtained with e.g. functional magnetic
resonance imaging, electroencephalography or magnetoencephalography), since a cognitive
neuroscientist’s research question is defined by the theoretical perspective taken. The research
question, in turn, determines the details of the experimental setting in which a dataset is
collected [
        <xref ref-type="bibr" rid="ref3">3</xref>
        ]. Consequently, the theoretical framework is essential for understanding the scientist’s
intent, for interpreting neurocognitive data, and thus for the interoperability of the data.
      </p>
      <p>Making the domain knowledege in cognitive neuroscience explicit and negotiating its meaning
necessitates an ontological domain analysis that is grounded in a top-level ontology. Deriving
a domain ontology from this analysis ofers powerful means for structuring this knowledge,
resulting in a human-understable as well as machine-readable representation.
Problem statement. From an ontological perspective, the co-existence of competing
theories implies diverging conceptualizations of reality, thus propagating diferent ontological
commitments. In terms of representational adequacy, an ontology for the domain of cognitive
neuroscience thus needs to be capable of representing these varying definitions while
preserving their relation to commonly used linguistic terms in order to meet the communication
needs of the community. These fundamental requirements have not been captured before in
existing knowledge representation projects in the field. Hence, this paper aims to develop
an ontology solving the problem of representing diverging conceptualizations of cognitive
concepts put forward by co-existing theories while preserving their relation to commonly
applied terminology.</p>
      <p>Contribution. To address this problem, we propose a Cognitive Theory Ontology (CoTOn)
that provides the means to represent and relate 1. the objectifiable knowledge about observable
entities of the experimental setting, 2. the theory-dependent conceptualizations of latent
cognitive concepts, and 3. the community-specific use of the same linguistic terms for diferently
defined cognitive concepts.</p>
      <p>The remainder of this paper is organized as follows. Section 2 introduces related work on
knowledge representation in cognitive neuroscience that we aim to reuse as a basis for CoTOn.
In Section 3 we provide an ontological analysis for the domain of cognitive neuroscience,
identifying the relevant entities and how they relate to each other. In Section 4, we present an
initial operational version of CoTOn covering a selection of general types that are populated
with domain-specific instances. Further, we execute exemplary queries for knowledge retrieval
on the operational version of CoTOn. Lastly, in Section 5, we summarize our contributions and
provide an outlook on planned future developments.</p>
    </sec>
    <sec id="sec-2">
      <title>2. Related Work</title>
      <p>
        The need for structured knowledge representation in cognitive neuroscience is reflected in
the growing number of knowledge representation projects covering diferent aspects of the
domain [
        <xref ref-type="bibr" rid="ref4">4</xref>
        ]. One of the few projects that focuses on the most challenging aspect, i.e. the
representation of cognitive concepts, is the Cognitive Atlas [
        <xref ref-type="bibr" rid="ref5 ref6">5, 6</xref>
        ]. It is a collaborative
knowledgebuilding project that was initiated to capture the current state of knowledge in cognitive
neuroscience with the goal of agreeing on unique definitions for cognitive concepts. To bridge
the gap between cognitive concepts and the experiments performed to assess them, the Cognitive
Atlas uses the concept of tasks which in turn is reused from the Cognitive Paradigm Ontology
[
        <xref ref-type="bibr" rid="ref7 ref8">7, 8</xref>
        ]. The conceptualization of the Cognitive Atlas asserts that cognitive concepts can be
subkinds or parts of other cognitive concepts. Tasks, on the other hand, consist of one or
more conditions that define the relevant experimental manipulations. These conditions have
indicators, such as behavioral or neural measures, that are recorded for analysis. Related
cognitive concepts are in turn either assessed via the indicator value for a specific condition
or, following a subtraction logic commonly used in neuroimaging, isolated by contrasting the
indicator values of multiple conditions.
      </p>
      <p>With currently 886 entries for cognitive concepts and 788 entries for tasks, the Cognitive Atlas
is the most comprehensive compilation of these entities available. Subsequent iterations have
added concepts of phenotypes (i.e., mental disorders, personality traits, and behaviors), theories,
and task batteries. With the exception of mental disorders with 221 entries, the remaining
additions have not yet been fully embraced by the broader community as the number of entries
for these concepts on the Cognitive Atlas website are comparatively small.</p>
      <p>Of conceptual relevance to the present manuscript is that in the Cognitive Atlas, each cognitive
concept can only be assigned with one unique definition. Accordingly, it does not provide the
means to represent divergening definitions of cognitive concepts and how they relate to each
other as proposed by competing theories. For CoTOn, we build on the Cognitive Atlas by reusing
the definitions for the entities Theory, Cognitive Concept, Task, Condition, and Indicator as well
as by adopting the linguistic terms used by the community for cognitive concepts. However, we
address the limitations of the Cognitive Atlas with respect to the theory-driven representation
of cognitive concepts by enabling diverging definitions of cognitive concepts although they are
assigned the same linguistic term.</p>
    </sec>
    <sec id="sec-3">
      <title>3. Ontological Domain Analysis</title>
      <p>
        As stated above, a particular challenge for the domain of cognitive neuroscience lies in balancing
the need for a shared vocabulary (to ensure interoperability and machine readability) while
reflecting scholarly disagreement as a driver and necessity for scientific progress. The Cognitive
Theory Ontology CoTOn, which we present as a possible solution, represents and relates
theory-specific definitions of cognitive concepts to their commonly used linguistic terms and
objectifiable measurements. CoTOn is grounded in the Unified Foundation Ontology (UFO [
        <xref ref-type="bibr" rid="ref9">9</xref>
        ]),
so the notions of Endurant, Event, Aspect, Quality, Disposition, Quality Space and Quality Value
as well as the relations involving them (e.g., inherence, instantiation, historical and existential
dependence) should be interpreted as they are defined in that ontology. We recognize that many
of these notions could be found in other top-level ontologies such as DOLCE [
        <xref ref-type="bibr" rid="ref10">10</xref>
        ] and BFO [
        <xref ref-type="bibr" rid="ref11">11</xref>
        ].
      </p>
      <p>Subsequently, we follow a convention where the concepts from a top-level ontology are
underlined and those of the Cognitive Theory Ontology (CoTOn) are represented in bold.
For the running example in Section 3.3 we use italic letters to represent the instances of selected
CoTon concepts.</p>
      <sec id="sec-3-1">
        <title>3.1. Top-Level Ontological Distinctions</title>
        <p>
          We employ the top-level ontological distinctions put forward by UFO [
          <xref ref-type="bibr" rid="ref9">9</xref>
          ], i.e. we assume the
following: Firstly, there are Endurants and Perdurants (Events). Endurants can be Objects or
Aspects, the latter inhering (and, thus, being existentially dependent) in the former. Aspects
can be either Intrinsic Aspects - which inhere in a single individual, or Relators - which are
existentially dependent on multiple individuals, thus, binding them. Intrinsic Aspects can be
either Qualities or Dispositions. Qualities are aspects of individuals that are associated with
(and can be measured on) Quality Values in specific Quality Spaces. Dispositions, in contrast,
are Aspects that are manifested in certain situations as Events. Complementarily, Events are
always manifestations of Dispositions. Lastly, Agents are Objects with intentionality.
        </p>
      </sec>
      <sec id="sec-3-2">
        <title>3.2. CoTOn: A Cognitive Theory Ontology</title>
        <p>As mentioned before, the domain of cognitive neuroscience comprises theory-dependent
knowledge on cognitive concepts, community-specific usage of linguistic terms denoting these, and
objectifiable knowledge on experimental settings. With respect to these three areas, we
subsequently identify their relevant entities and how they relate to each other.</p>
        <p>Theory-dependent knowledge. A Cognitive Theory is an Artifact created by an Author,
who is a Creator. Thus, the theory is historically dependent on that author, meaning that it
could not have existed without this author having existed before. Artifact creators are Agents,
which can be Individual Agents or Collective Agents. A Cognitive Theory can define a
number of Cognitive Concepts and can re-use concepts defined by other theories. Importantly,
if a concept A is defined in theory T then A is existentially dependent on that theory, i.e., it
cannot exist without that theory. Further, a Cognitive Concept can be notionally dependent
on other concepts. If a concept A is notionally dependent on a concept B then A cannot be
defined without reference to B. As an Agent, a Cognitive Subject bears a number of Cognitive
Aspects (Cognitive Qualities and Cognitive Dispositions), including Cognitive Capacities
(which are Cognitive Dispositions). The theory being tested hypothesizes the existence of
Cognitive Aspects in that subject that are instances of Cognitive Concepts of that theory.
Community-specific terminology use. A Scientific Community is a collective agent
whose members are Scientists. The Scientific Community uses Linguistic Terms, i.e.
sequences of letters, as a symbol to denote Cognitive Concepts. Terminological Usage is a
relator that connects a Scientific Community , Linguistic Terms, and Cognitive Concepts.
As such, Terminological Usage represents the collective consensus of a Scientific
Community to refer to diferent conceptualizations of Cognitive Concepts defined in diferent
Cognitive Theories by a common Linguistic Term.</p>
        <p>Objectifiable knowledge. Cognitive Tasks are types of experiments designed to test
hypotheses formulated about Cognitive Concepts constituting a Cognitive Theory. A
Cognitive Task can yield multiple Cognitive Task Executions. A Cognitive Task Execution
is a complex event in which at least a Cognitive Subject (who is also an Individual Agent)
participates. Further, a Cognitive Task is characterized by a number of Task Conditions,
designed to test the presence of the hypothesized Cognitive Aspects inhering in a Cognitive
Subject. A Task Condition has Indicators whose instances can be used to measure properties
associated to these Cognitive Concepts. A Cognitive Task Execution (a run of the designed
experiment) has as parts events termed Task Condition Executions that are instantiations of
each of the Task Conditions prescribed by that Cognitive Task. Task Condition Executions
are interpreted as manifestations of the hypothesized Cognitive Dispositions tested by the
experiment (the Cognitive Task).</p>
        <p>A Task Condition Execution also has as parts Indicator Measurements, which are
events that produce Data Items that represent qualities associated with those Task Condition
Executions. A collective of Data Items composes a Dataset. Those Data Items can be
either Indication Data Items or Indication Contrast Data Items. Indication Data Items
result from Indications that are created by Indicator Measurements and are instances of
the Indicators associated with the Cognitive Theory being tested and which can have their
measurements (termed Cognitive Quality Measured Value) measured in a Quality Space
associated with a Quality of a Task Condition Execution. An Indication Contrast Data
Item is a Data Item that represents a Cognitive Indication Contrast which is a relator
connecting two diferent Indications.</p>
      </sec>
      <sec id="sec-3-3">
        <title>3.3. Running Example</title>
        <p>To better illustrate the problem statement and our proposed solution, we introduce the following
examples. Cognitive concepts to which Scientists commonly refer to as working memory have
been extensively studied in psychology and cognitive neuroscience. This resulted in several
co-existing Cognitive Theories. Here, we introduce three influential theories that, while
refering to the same Linguistic Term working memory, propagate diferent conceptualizations
of diferent Cognitive Concepts.</p>
        <p>
          The Modal model [
          <xref ref-type="bibr" rid="ref12">12</xref>
          ], a Cognitive Theory created by the Authors R. Atkinson and R. Shifrin ,
defines the Cognitive Concept of short-term store as the capacity to maintain information for a
brief period of time and explicitly equates it with the Linguistic Term of working memory. Based
on that, working memory can be assessed via the forward condition (a Task Condition) of the
digit span task (a Cognitive Task), in which Cognitive Subjects are presented with a sequence
of numbers and are asked to recall them in the same order immediately after presentation. The
number of correctly remembered digits is interpreted as an Indicator of short-term store.
        </p>
        <p>
          The Multicomponent model [
          <xref ref-type="bibr" rid="ref13 ref14">13, 14</xref>
          ] (created by A. Baddeley and G. Hitch), on the other hand,
defines the Cognitive Concept of working memory as the capacity to maintain and manipulate
information. In this conceptualization, working memory has as parts other Cognitive Concepts,
i.e. the phonological loop, visuospatial sketchpad, episodic bufer , and central executive. According
to its defintion, working memory cannot be measured with the forward condition of the digit
span task because no manipulation of information is required. Instead, working memory as
defined by this model must be assessed with more complex Task Conditions, such as the
sequencing condition of the digit span task, in which Cognitive Subjects must mentally arrange
the numbers presented to them in ascending order before reporting them.
        </p>
        <p>
          In the Cognitive Theory Embedded-process model [
          <xref ref-type="bibr" rid="ref15">15</xref>
          ], the Author N. Cowan explicitly
refers to working memory as a Linguistic Term for communication. This term, in turn, points
to the Cognitive Concept of activated memory. As such, activated memory is defined as
maintaining old and novel information in an accessible state that is suitable for manipulation
during the performance of interfering tasks. Here, the Cognitive Concept of short-term
memory is explicitly defined as a subcomponent of activated memory. A Cognitive Task
that assesses working memory as defined in this Cognitive Theory is the reading-span task,
in which Cognitive Subjects are instructed to remember the last word of a sentence while
simultaneously making judgements about the content of the sentences.
4. CoTOn: Reference Model and Initial Implementation
The traditional two-level schema in conceptual modeling (i.e. the level of types or classes and
the level of instances [
          <xref ref-type="bibr" rid="ref16">16</xref>
          ]) does not fully sufice the representational complexity needed for
the domain of cognitive neuroscience. As explicated in the previous section, the type-level of
CoTOn (e.g. containing the classes Cognitive Concept and Cognitive Task) is instantiated again
by types (e.g. working memory and digit span task). According to [
          <xref ref-type="bibr" rid="ref16">16</xref>
          ], this means that the
former are second-order types, i.e. types whose instances are first-order types, and the latter are
in turn first-order types, i.e. types whose instances are individuals that cannot play the role of
types in the instantiation relation. Ultimately, those individuals are the neurocognitive datasets,
e.g. the particular Cognitive Task Execution of a digit span task that measures the Cognitive
Aspect working memory in a particular Cognitive Subject as an instantiation of a respective
Cognitive Concept.
        </p>
        <p>We acknowledge that this additional layer of complexity requires a multi-level modeling
approach which will be adressed in future work with respect to neurocognitive data annotation
(see Section 5). As a first step, however, it is necessary to derive an ontological representation that
is capable to disambiguate the conflation of linguistic terminology use and theory-dependent
conceptualizations of cognitive concepts. As the purpose of the current paper is to address
this first step, in the following we will model selected second-order types as classes and the
ifrst-order types as individuals instantiating those classes.</p>
        <p>
          The development process described in the subsequent sections was guided by the Systematic
Approach for Building Ontologies (SABiO, [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ]). In accordance with the SABiO guidelines, we
employ the term reference model for denoting the domain reference ontology, i.e. a
solutionindependent conceptual model describing and organizing a selection of relevant domain entities.
The term operational ontology in turn refers to an implemented, machine-readable version of
the reference model.
        </p>
      </sec>
      <sec id="sec-3-4">
        <title>4.1. Purpose Identification and Requirement Elicitation</title>
        <p>The intended use of CoTOn targets two main aspects, i.e. knowledge representation and data
annotation. Regarding knowledge representation, we aim to capture objectifiable knowledge
on the experimental settings (i.e. Cognitive Tasks, Task Conditions, and Indicators) as well as
theory-dependent knowledge on Cognitive Concepts, their assumed interrelations, and their
connection to common Linguistic Terms. With respect to Cognitive Concepts, an essential
aspect is that we do not aim to provide a (subjective) intersection of current (heterogeneous)
thinking, but rather to allow the representation of the co-existing heterogeneity of Cognitive
Concepts - embedded in their respective defining Cognitive Theories. For the purpose of this
paper, we will apply CoTOn for knowledge retrieval. Exploiting its reasoning capabilities
for knowledge discovery (e.g., by finding implicit commonalities across Cognitive Theories,
Cognitive concepts, or Cognitive Tasks) as well as neurocognitve data annotation will be part
of future work.</p>
        <p>
          To describe the functional requirements that the initial version of CoTOn must satisfy, we
followed the SABiO guidelines [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ] and formulated seven competency questions (CQ) based
on the running example. We again highlight classes in bold, and the respective inidividuals
of interest in italics. In terms of evaluation, these competency questions are used as example
queries on the operational ontology in Section 4.4.
        </p>
        <p>• CQ1: Which Cognitive Theories define Cognitive Concepts that are denoted with
the Linguistic Term Working memory?
• CQ2: Which Authors created the Cognitive Theory Modal model?
• CQ3: Which Cognitive Concepts are denoted with the Linguistic Term Working
memory?
• CQ4: What are parts of the Cognitive Concept that is denoted with the Linguistic</p>
        <p>Term Working memory as defined by the Cognitive Theory Multicomponent model?
• CQ5: What are parts of the Cognitive Concept that is denoted with the Linguistic</p>
        <p>Term Working memory as defined by Cognitive Theory Embedded-process model?
• CQ6: Which Indicators measure the Cognitive Concept that is denoted with the</p>
        <p>Linguistic Term Working memory as defined by the Cognitive Theory Modal model?
• CQ7: Which Indicators measure the Cognitive Concept that is denoted with the
Linguistic Term Working memory as defined by the Cognitive Theory Multicomponent
model?</p>
      </sec>
      <sec id="sec-3-5">
        <title>4.2. Reference Model</title>
        <p>
          Based on these competency questions, we derived a reference model (Figure 1) that employs a
selection of CoTOn concepts and their interrelations that were identified and described in the
ontological domain analysis in Section 3. The reference model was designed in OntoUML [
          <xref ref-type="bibr" rid="ref18">18</xref>
          ], a
conceptual modeling language that is specifically developed to reflect the ontological distinctions
put forward by UFO. In accordance with SABiO [
          <xref ref-type="bibr" rid="ref17">17</xref>
          ], we use the reference model as the basis
for implementing an operational version of CoTOn.
        </p>
        <p>For the initial operational version (see Section 4.3), we implement the CoTOn concepts
Cognitive Theory, Author, Cognitive Concept, Linguistic Term, Cognitive Task, Task Condition,
and Indicator as classes (highlighted in blue in Figure 1). Table 1 shows definitions for those
classes as well as exemplary instances. Note that for those classes, we reuse definitions provided
by the Cognitive Atlas and the American Psychological Association Dictionary, a widely accepted
knowledge source in the cognitive neuroscience community, whenever possible.</p>
      </sec>
      <sec id="sec-3-6">
        <title>4.3. Operational Ontology</title>
        <p>
          We use Protégé [
          <xref ref-type="bibr" rid="ref20 ref21">20, 21</xref>
          ] to implement the initial operational version of CoTOn in OWL [
          <xref ref-type="bibr" rid="ref22">22</xref>
          ], the
Web Ontology Language 1. This operational version currently contains the seven second-order
types Cognitive Theory, Author, Linguistic Term, Cognitve Concept, Cognitive Task, Task
Condition, and Indicator that are instantiated with the respective first-order types. Figure 2
depicts exemplary class instantiations for the Multicomponent model (i.e. an instance of a
Cognitive Theory).
1An aplha release of the current development status of CoTOn is availabe via
https://gitlab.com/ccns/neurocog/neurodataops/anc/classification/cognitive-ontology/-/releases/alpha-release
        </p>
        <sec id="sec-3-6-1">
          <title>Definition Example</title>
          <p>
            A principle or body of interrelated principles Multi-component model,
that purports to explain or predict a number of Modal model
interrelated phenomena [
            <xref ref-type="bibr" rid="ref19">19</xref>
            ]
The creator of a Cognitive Theory A. Baddeley, N. Cowan
A latent unobservable construct postulated by Activated memory,
a psychological theory [
            <xref ref-type="bibr" rid="ref5">5</xref>
            ] Phonological bufer
A colloquial name used by the cognitive neuro- Working memory
science community to denote Cognitive
Concepts
A prescribed activity meant to engage or ma- Digit span task, Reading
nipulate mental function in an efort to gain span task
insight into the underlying Cognitive Concepts
[
            <xref ref-type="bibr" rid="ref5">5</xref>
            ]
Subsets of an experiment that define the rele- Digit span task: forward
vant experimental manipulation [
            <xref ref-type="bibr" rid="ref5">5</xref>
            ] condition, Digit span task:
sequencing condition
Number of items
remembered correctly
A specific quantitative or qualitative variable
that is recorded under a particular condition
for analysis [
            <xref ref-type="bibr" rid="ref5">5</xref>
            ]
          </p>
          <p>Since the Cognitive Atlas database provides a list of commonly used linguistic terms for
cognitive concepts, we reuse them by selectively importing (owl:import) these terms as
instances of the class Linguistic Term into our ontology. Note that the decision to model the
entity Linguistic Term as a class rather than an annotation property of Cognitive Concepts
indicating synonymy (e.g., skos:altLabel) was driven by the necessity to confine the list of
selectable terms to a predefined range of options. This guarantees that only the terms imported
from the Cognitive Atlas (or future extensions thereof) can be assigned as Linguistic Terms of
Cognitive Concepts rather than arbitrary annotation strings. This is especially important for
CoTOn’s purpose to reflect our community’s communication habits (i.e. the Linguistic Terms
used by our Scientific Community) that are then further disambiguated via Cognitive Theories
that define the respective Congitive Concepts.</p>
          <p>To distinguish diferently defined instances of the class Cognitive Concept that have identical
display names (and thus, connect to the same instance of the Linguistic Term class) we assign
unique Internationalized Resource Identifiers (IRIs) that contain the theory name. In order to
enable more exhaustive representation of the knowledge that theories encapsulate, we plan
to elevate the current Cognitive Concept instances to second-level types, i.e. classes in the
operational ontology, in future work.</p>
          <p>isPartOf
LinTgeurmistic isLinguisticTermOf CCoognncietipvte</p>
          <p>Central
executive</p>
          <p>Visuospatial
sketchpad</p>
          <p>Phonological</p>
          <p>loop</p>
        </sec>
      </sec>
      <sec id="sec-3-7">
        <title>4.4. Ontology Application</title>
        <p>The operational version of CoTOn can now be applied to answer the competency questions
stated in Section 4.1. For answering these questions, we use the built-in function for description
logic (DL) queries in Protégé and provide an overview of the results in Table 2.</p>
        <p>The first three competency questions ask for objectifiable knowledge (adressing the first
requirement for CoTOn, i.e. representing objectifiable knowledge) about theories that define
a concept that is commonly termed working memory (CQ1), the authors of one of those
theories (CQ2), and concepts that are denoted with the linguistic term working memory
(CQ3). In contrast, CQ4 to CQ7 require theory-dependent knowledge about the diverging
conceptualizations of cognitive concepts that are commonly termed working memory and which
indicators are eligible for measuring these concepts as defined by particular theories. Note that,
while CQ4 and CQ5 as well as CQ6 and CQ7 ask for the same kind of knowledge, the queries
return diferent instances depending on the theoretical context - thus satisfying the second
and third requirements CoTOn was developed to address (i.e., representing theory-dependent
knowledge and its relation to linguistic terms used in the cognitive neuroscience community).</p>
        <p>The importance of the three requirements we formulated for CoTOn can be particularly well
observed when comparing the query results for CQ3 and CQ5. Consider the similar sounding
cognitive concepts of short-term store (result for CQ3) and short-term memory (result for CQ5).
Short-term store is a cognitive concept that is defined in the modal model (see Section 3.3)
and is commonly denoted with the linguistic term working memory. Short-term memory,
however, is a cognitive concept defined in the embedded-process model. Importantly, here
short-term memory itself is not denoted with the linguistic term working memory, but is part
CQ2
CQ3
CQ4</p>
        <p>Author and creates value Modal model
Cognitive Concept and hasLinguisticTerm value
Working memory
Cognitive Concept and isPartOf some
(hasLinguisticTerm value Working memory and
isDefinedBy value Multicomponent model)
CQ5 Cognitive Concept and isPartOf some
(hasLinguisticTerm value Working memory and
isDefinedBy value Embedded-process model)
CQ6 Indicator and measures some
(hasLinguisticTerm value Working memory and
isDefinedBy value Modal model)
CQ7 Indicator and measures some
(hasLinguisticTerm value Working memory and
isDefinedBy value Multicomponent model)</p>
        <sec id="sec-3-7-1">
          <title>Results</title>
          <p>Embedded-process model
Modal model
Multicomponent model
Atkinson
Shifrin
Activated memory
Short-term store
Working memory
Central executive
Episodic bufer
Phonological loop
Visuospatial sketchpad
Short-term memory
Digit span task Forward
Number correct
Digit span task Sequencing
Number correct
of the cognitive concept that is commonly termed working memory in this theory, namely
activated memory.</p>
        </sec>
      </sec>
    </sec>
    <sec id="sec-4">
      <title>5. Conclusion and Future Work</title>
      <p>In this paper, we provided a solution for representing diverging theoretical assumptions of
the latent cognitive concepts studied in cognitive neuroscience. With CoTOn, we proposed
a Cognitive Theory Ontology to represent and relate 1. the objectifiable knowledge about
observable entities of the experimental setting, 2. the theory-dependent conceptualizations of
latent cognitive concepts, and 3. the community-specific use of the same linguistic terms for
diferently defined cognitive concepts. Further, we presented an ontological analysis, grounded
in UFO, for the domain of cognitive neuroscience. Based on this analysis, we derived a reference
model and implemented an initial operational version of CoTOn on the type-level in Protégé.
Lastly, we exemplified and evaluated its application for knowledge retrieval by answering
the competency questions we formulated during the development process. In contrast to
existing knowledge representation projects in the field such as the Cognitive Atlas, CoTOn is
capable of representing diferent theory-dependent conceptualization of cognitive concepts and
disambiguate their conflation with linguisitic terms commonly used by our community.</p>
      <p>In future work, we aim to extend the operational version of CoTOn by including additional
entities as identified in the ontological domain analysis and use its reasoning capacities for
knowledge discovery. Further, we intend to use CoTOn to annotate neurocognitive datasets
with domain-specific metadata, allowing researchers to deeply evaluate the characteristics of
a dataset. We expect that domain-specific, machine-readable annotations will facilitate data
search, integration, and reuse by enabling the discovery and combination of datasets based on
desired characteristics for purposes beyond those for which they were originally collected.</p>
      <p>
        To address the need for data annotation, we aim to apply a multi-level modeling approach
to represent this additional layer of complexity. We believe that incorporating neurocognitive
data instances as an additional level will help to address two longstanding issues in cognitive
neuroscience, i.e. 1) estimating how well theories explain existing data, ultimately allowing
empirically based judgments between competing theories, and 2) addressing the unsolved
problem of reverse inference, i.e. inferring the presence of cognitive processes from neural
activation patterns [
        <xref ref-type="bibr" rid="ref23 ref24">23, 24</xref>
        ].
      </p>
      <p>Acknowledgments This work was supported by: Austrian Federal Ministry of Education,
Science and Research (BMBWF) under grant number 2920 (Austrian NeuroCloud); Federal State
of Salzburg under grant number 20102-F2101143-FPR (Digital Neuroscience Initiative); Austrian
Science Fund (FWF) under grant number W1233-B (Doctoral College “Imaging the Mind”). We
thank Mateusz Pawlik and Barbara Strasser-Kirchweger for their feedback and support.</p>
    </sec>
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