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Welcome to the CogPO Wiki!
 
Welcome to the CogPO Wiki!
  
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Here is where we will come to a consensus on the initial terms that will be included in CogPO.  We will start by defining the terms associated with the [[BrainMap Taxonomy]].  Also taken from BrainMap are entries that correspond to [[Paradigm Class]] and [[Behavioral Domain]].
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Here is where we will come to a consensus on the initial terms that will be included in our ontology of cognitive paradigms.  Our starting point are the terms associated with the [[BrainMap Taxonomy]].
  
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In creating an ontology of cognitive paradigms we aim to decompose each condition into:
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In CopPO, a cognitive [[paradigm]] is represented by the concept of [[Behavioral Experimental Paradigm]]. Each [[Behavioral Experimental Paradigm]] is characterized by one or more [[Behavioral Experimental Paradigm Condition]]s and [[Behavioral Experimental Paradigm Condition Contrast]]s.
  
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*[[Stimulus Modality]]
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We aim to decompose each condition into its corresponding stimulus, response, and instructions:
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*[[Stimulus|Stimulus Type]]
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*[[Response Modality]]
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*[[Stimulus]]
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*[[Response|Response Type]]
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**[[Stimulus Role]]
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**[[Implicit Stimulus]]
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**[[Explicit Stimulus]]
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***[[Stimulus Modality]]
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*[[Response]]
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**[[Response Role]]
 +
**[[Covert Response]]
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**[[Overt Response]]
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***[[Response Modality]]
 
*[[Instructions]]
 
*[[Instructions]]
  
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For more information, please see the [[Aims of the CogPO Project]].
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Each of these terms is categorized by a set of classes, which will increase in size as CogPO evolves.
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The initial representation of the domain is as follows, though it will be modified as we flesh this out:
 
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[[image:CogPO1.jpg]]
 
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==CogPO Policies==
 
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Draft 1.0, 10/07/2009
 
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The whole point of having a Wiki is to allow concepts to be identified and fleshed out collaboratively before becoming "official."  A concept is entered into the official CogPO Protege/OWL files when it's been hammered out a bit on the Wiki and shows no sign of going away. Definitions and other properties can change once the concept is entered into CogPO, of course. But the general ideas are as follows:
 
  
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# Any member of the research community can create new concepts or edit concepts.  Create a log in and start making suggestions. All edits are reviewed by CogPO curators, who reserve the right to undo them if it is not in keeping with best practices or ontological clarity.
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===Stimulus Modality===
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# A new concept MUST include the required properties noted below. Optional properties are also listed in the Annotation Properties file.
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{|
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# Please use the Search box before you make a new concept to identify if the term or a related term has already been given a wiki page. We also recommend searching NeuroLex and the NCBO Bioportal for related terms so you can see what concepts other experts have created that might be what you need.
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|-
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# You can also suggest new relationships. The guidelines for defining relationships are coming soon.
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| width="200" | [[Auditory Modality]]
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|  width="200" | [[Interoceptive Modality]]
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|  width="200" | [[Tactile Modality]]
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|-
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| [[Gustatory Modality]]||[[Olfactory Modality]]||[[Visual Modality]]
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|}
  
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<b>Defining a concept in CogPO: required properties </b>
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===Explicit Stimulus===
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{|
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|-
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|  width="200" | [[3D Objects]]
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|  width="200" | [[Fixation Point]]
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|  width="200" | [[Painful Stimulation]]
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|-
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| [[Abstract Patterns]]||[[Flashing Checkerboard]]||[[Points of Light]]
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|-
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| [[Acupuncture]]||[[Food]]||[[Pseudowords]]
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|-
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| [[Asian Characters]]||[[Fractals]]||[[Random Dots]]
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|-
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| [[Braille Dots]]||[[Heat]]||[[Reversed Speech]]
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|-
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| [[Breathable Gas]]||[[Infrared Laser]]||[[Shapes]]
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|-
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| [[Chord Sequences]]||[[Infusion]]||[[Syllables]]
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|-
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| [[Clicks]]||[[Letters]]||[[Symbols]]
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|-
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| [[Digits]]||[[Music]]||[[TMS]]
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|-
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| [[Electrical Stimulation]]||[[Noise]]||[[Tactile Stimulation]]
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|-
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| [[Eye Puffs]]||[[Nonverbal Vocal Sounds]]||[[Tones]]
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|-
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| [[Faces]]||[[Nonvocal Sounds]]||[[Vibratory Stimulation]]
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|-
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| [[False Fonts]]||[[Odor]]||[[Words]]
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|-
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| [[Film Clips]]||[[Pictures]]
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|}
  
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In keeping with best practices from NeuroLex, the Neural ElectroMagnetic Ontology (NEMO), and others, concepts in CogPO must have the following annotation properties defined:
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===Stimulus Role===
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*COGPO_annotation_properties:definition – A natural language definition that adheres to Aristotelian constraints (A is a B that C's). Equivalent to core:definition. <i>Example:</i> The auditory modality is a sensory modality that involves the auditory nervous system.
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{|
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*COGPO_annotation_properties:preferredlabel -- An underscore-delimited, human-readable label for a concept. Equivalent to rdfs:label and core:prefLabel. this is the most common way for humans to refer to the concept. <i>Example:</i> The preferred label for the concept "Auditory Modality" is "Auditory_Modality".
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|-
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*COGPO_annotation_properties:hasURI -- This property defines the CogPO URI for a concept. The URI is a non-human-readable label that also provides a stable web address for accessing the concept. For an imported term, the URI should be the source ontology URI (if possible?). MIREOT recommends that the source term URI be included specifically. This only is filled in when the concept is curated.
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|  width="200" | [[Feedback]]
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*COGPO_annotation_properties:createdDate -- [YYYY-MM-DD] The date when the current concept was created. Equivalent to the same term in NeuroLex.
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|  width="200" | [[Non-Target]]
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*COGPO_annotation_properties:curator -- This property defines the CogPO ontology curators who've contributed to the definition of a class.  In the case of multiple curators, the individual curator name may also be associated with the definition, if that person was primarily responsible for it.
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|  width="200" | [[Reward]]
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*COGPO_annotation_properties:hasCurationStatus -- This provides specific info on the level of curation a given class has received, and is specifically designed to promote automated reporting on the status of classes in an ontology.  It is a type of skos_editorial_note. For a full listing of the possible values for Curation Status, see the full COGPO Annotation Properties.
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|-
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| [[Target]]
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|
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|}
  
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Also required are:  
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===Response Modality===
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# the direct superclass concept, either from within CogPO or from another ontology.
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{|
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# the most granular concept from BFO that is applicable. Everything is either a continuant or an occurrent, but it would be better to suggest a branch a little lower in the BFO tree than that top level. The curators will also do their best to fill this term in.
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|-
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|  width="200" | [[Arm]]
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|  width="200" | [[Hand]]
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| width="200" | [[Pelvis]]
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|-
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| [[Eye]]||[[Leg]]||[[Shoulder]]
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|-
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| [[Face]]||[[Mouth]]||[[Torso]]
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|-
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| [[Foot]]||
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|}
  
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===Overt Response===
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{| {{table}}
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|-
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|  width="200" | [[Blink]]
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|  width="200" | [[Finger Tapping]]
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|  width="200" | [[Saccades]]
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|-
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| [[Breathe Response]]||[[Flexion or Extension]]||[[Smile Response]]
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|-
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| [[Breath-Hold Response]]||[[Grasp]]||[[Speech]]
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|-
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| [[Button Press]]||[[Manipulate]]||[[Swallow]]
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|-
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| [[Draw]]||[[Micturate]]||[[Whistle]]
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|-
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| [[Drink]]||[[Point]]|||[[Write]]
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|}
  
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===Recent Tasks===
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===Instructions===
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*Logo? (Angie)
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{|
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|-
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|  width="200" | [[Attend]]
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| width="200" | [[Fixate]]
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|  width="200" | [[Recall]]
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|-
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| [[Breathe Instructions]]||[[Generate]]||[[Repeat]]
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|-
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| [[Breath-Hold Instructions]]||[[Imagine]]||[[Rest]]
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|-
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| [[Count]]||[[Move]]||[[Sing]]
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|-
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| [[Detect]]||[[Name]]||[[Smile Instructions]]
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|-
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| [[Discriminate]]||[[Read]]||[[Track]]
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|-
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| [[Encode]]
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|}
  
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*Add details to website (Angie)
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===Paradigm Classes===
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**short description of PNAS paper as a motivation? (Jess says yes)
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Currently, CogPO has defined 84 classes of paradigms:
  
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*Begin discussion of some concepts/information with BFO, Neurolex (Jess)
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#[[Action Observation Paradigm]]
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**e.g., sound and tones, various stimulus types and response types (behaviors)
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#[[Acupuncture Paradigm]]
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**save stimulus and response roles for smaller discussions
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#[[Anti-Saccades Paradigm]]
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#[[Braille Reading Paradigm]]
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#[[Breath-Holding Paradigm]]
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#[[Chewing or Swallowing Paradigm]]
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#[[Classical Conditioning Paradigm]]
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#[[Counting or Calculation Paradigm]]
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#[[Cued Explicit Recognition Paradigm]]
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#[[Deception Task Paradigm]]
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#[[Deductive Reasoning Paradigm]]
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#[[Delay Discounting Task Paradigm]]
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#[[Delayed Match To Sample Paradigm]]
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#[[Delayed Non Match To Sample Paradigm]]
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#[[Divided Auditory Attention Paradigm]]
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#[[Drawing Paradigm]]
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#[[Eating or Drinking Paradigm]]
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#[[Encoding Paradigm]]
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#[[Episodic Recall Paradigm]]
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#[[Face Monitor or Discrimination Paradigm]]
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#[[Film Viewing Paradigm]]
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#[[Finger Tapping Paradigm]]
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#[[Fixation Paradigm]]
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#[[Flanker Task Paradigm]]
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#[[Flashing Checkerboard Paradigm]]
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#[[Flexion or Extension Paradigm]]
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#[[Free Word List Recall Paradigm]]
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#[[Go/No-Go Paradigm]]
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#[[Grasping Paradigm]]
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#[[Imagined Movement Paradigm]]
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#[[Imagined Objects or Scenes Paradigm]]
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#[[Isometric Force Paradigm]]
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#[[Mental Rotation Paradigm]]
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#[[Micturition Task Paradigm]]
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#[[Music Comprehension or Production Paradigm]]
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#[[n-back Paradigm]]
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#[[Naming (Covert) Paradigm]]
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#[[Naming (Overt) Paradigm]]
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#[[Non-Painful Electrical Stimulation Paradigm]]
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#[[Non-Painful Thermal Stimulation Paradigm]]
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#[[Oddball Discrimination Paradigm]]
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#[[Olfactory Monitor or Discrimination Paradigm]]
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#[[Orthographic Discrimination Paradigm]]
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#[[Pain Monitor or Discrimination Paradigm]]
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#[[Paired Associate Recall Paradigm]]
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#[[Passive Listening Paradigm]]
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#[[Passive Viewing Paradigm]]
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#[[Phonological Discrimination Paradigm]]
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#[[Pitch Monitor or Discrimination Paradigm]]
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#[[Pointing Paradigm]]
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#[[Posner Task Paradigm]]
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#[[Reading (Covert) Paradigm]]
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#[[Reading (Overt) Paradigm]]
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#[[Recitation or Repetition (Covert) Paradigm]]
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#[[Recitation or Repetition (Overt) Paradigm]]
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#[[Rest Paradigm]]
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#[[Reward Task Paradigm]]
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#[[Saccades Paradigm]]
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#[[Semantic Monitor or Discrimination Paradigm]]
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#[[Sequence Recall or Learning Paradigm]]
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#[[Simon Task Paradigm]]
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#[[Sleep Paradigm]]
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#[[Spatial or Location Discrimination Paradigm]]
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#[[Sternberg Task Paradigm]]
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#[[Stroop Task Paradigm]]
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#[[Subjective Emotional Picture Discrimination Paradigm]]
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#[[Syntactic Discrimination Paradigm]]
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#[[Tactile Monitor or Discrimination Paradigm]]
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#[[Task Switching Paradigm]]
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#[[Theory of Mind Task Paradigm]]
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#[[Tone Monitor or Discrimination Paradigm]]
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#[[Tower of London Paradigm]]
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#[[Transcranial Magnetic Stimulation Paradigm]]
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#[[Vibrotactile Monitor or Discrimination Paradigm]]
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#[[Video Games Paradigm]]
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#[[Visual Distractor or Visual Attention Paradigm]]
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#[[Visual Pursuit or Tracking Paradigm]]
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#[[Whistling Paradigm]]
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#[[Wisconsin Card Sorting Test Paradigm]]
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#[[Word Generation (Covert) Paradigm]]
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#[[Word Generation (Overt) Paradigm]]
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#[[Word Stem Completion (Covert) Paradigm]]
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#[[Word Stem Completion (Overt) Paradigm]]
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#[[Writing Paradigm]]
  
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*Begin discussion with Jeff et al. about what it would take to use NIF to query BrainMap and HID using CogPO terms (and how much of that can be done before the ontology is complete) (Jess)
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===CogPO Relationships===
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** NIF people working on this, Jess to touch base with them next week (9/1/09)
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Proper curation of the above concepts required creation of a set of novel relationships:
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** Now having regular calls with NIF/NeuroLex every other Monday.
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{|
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|-
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|  width="200" | [[has_stimulus]]
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|  width="200" | [[has_response]]
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|  width="200" | [[has_instructions]]
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|-
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| [[has_stimulus_modality]]||[[has_response_modality]]||[[has_contrast]]
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|-
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| [[included_in_contrast]]||[[includes_condition]]||[[related_to]]
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|}
  
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*Work out an experiment model with KFED and OBI (Jess)
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===Basic Formal Ontology===
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**Can discuss stimulus and response roles, modality qualities etc. here
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CogPO uses a number of terms from Basic Formal Ontology ([http://www.ifomis.org/bfo/ BFO]), Ontology for Biomedical Investigations ([http://obi-ontology.org/page/Main_Page OBI]), and the Information Artifact Ontology ([http://code.google.com/p/information-artifact-ontology/ IAO]):
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**Working on this: Have downloaded OBI, made contact with OBI people, joined the OBI-developers mailing list, etc.
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{|
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|-
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|  width="200" | [[action specification]]
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|  width="200" | [[fiat object part]]
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|  width="200" | [[object aggregate]]
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|-
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| [[planned process]]||[[process aggregate]]||[[quality]]
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|-
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| [[role]]
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|}
  
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*Submit book proposal: Done and approved. Now we have to write it.
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===For More Information===
 +
Please see the [[Aims of the CogPO Project]] or [[CogPO's Wiki Policies]].

Latest revision as of 12:02, 22 July 2015

Welcome to the CogPO Wiki!

Here is where we will come to a consensus on the initial terms that will be included in our ontology of cognitive paradigms. Our starting point are the terms associated with the BrainMap Taxonomy.

In CopPO, a cognitive paradigm is represented by the concept of Behavioral Experimental Paradigm. Each Behavioral Experimental Paradigm is characterized by one or more Behavioral Experimental Paradigm Conditions and Behavioral Experimental Paradigm Condition Contrasts.

We aim to decompose each condition into its corresponding stimulus, response, and instructions:

Each of these terms is categorized by a set of classes, which will increase in size as CogPO evolves.

Stimulus Modality

Auditory Modality Interoceptive Modality Tactile Modality
Gustatory Modality Olfactory Modality Visual Modality

Explicit Stimulus

3D Objects Fixation Point Painful Stimulation
Abstract Patterns Flashing Checkerboard Points of Light
Acupuncture Food Pseudowords
Asian Characters Fractals Random Dots
Braille Dots Heat Reversed Speech
Breathable Gas Infrared Laser Shapes
Chord Sequences Infusion Syllables
Clicks Letters Symbols
Digits Music TMS
Electrical Stimulation Noise Tactile Stimulation
Eye Puffs Nonverbal Vocal Sounds Tones
Faces Nonvocal Sounds Vibratory Stimulation
False Fonts Odor Words
Film Clips Pictures

Stimulus Role

Feedback Non-Target Reward
Target

Response Modality

Arm Hand Pelvis
Eye Leg Shoulder
Face Mouth Torso
Foot

Overt Response

Blink Finger Tapping Saccades
Breathe Response Flexion or Extension Smile Response
Breath-Hold Response Grasp Speech
Button Press Manipulate Swallow
Draw Micturate Whistle
Drink Point Write

Instructions

Attend Fixate Recall
Breathe Instructions Generate Repeat
Breath-Hold Instructions Imagine Rest
Count Move Sing
Detect Name Smile Instructions
Discriminate Read Track
Encode

Paradigm Classes

Currently, CogPO has defined 84 classes of paradigms:

  1. Action Observation Paradigm
  2. Acupuncture Paradigm
  3. Anti-Saccades Paradigm
  4. Braille Reading Paradigm
  5. Breath-Holding Paradigm
  6. Chewing or Swallowing Paradigm
  7. Classical Conditioning Paradigm
  8. Counting or Calculation Paradigm
  9. Cued Explicit Recognition Paradigm
  10. Deception Task Paradigm
  11. Deductive Reasoning Paradigm
  12. Delay Discounting Task Paradigm
  13. Delayed Match To Sample Paradigm
  14. Delayed Non Match To Sample Paradigm
  15. Divided Auditory Attention Paradigm
  16. Drawing Paradigm
  17. Eating or Drinking Paradigm
  18. Encoding Paradigm
  19. Episodic Recall Paradigm
  20. Face Monitor or Discrimination Paradigm
  21. Film Viewing Paradigm
  22. Finger Tapping Paradigm
  23. Fixation Paradigm
  24. Flanker Task Paradigm
  25. Flashing Checkerboard Paradigm
  26. Flexion or Extension Paradigm
  27. Free Word List Recall Paradigm
  28. Go/No-Go Paradigm
  29. Grasping Paradigm
  30. Imagined Movement Paradigm
  31. Imagined Objects or Scenes Paradigm
  32. Isometric Force Paradigm
  33. Mental Rotation Paradigm
  34. Micturition Task Paradigm
  35. Music Comprehension or Production Paradigm
  36. n-back Paradigm
  37. Naming (Covert) Paradigm
  38. Naming (Overt) Paradigm
  39. Non-Painful Electrical Stimulation Paradigm
  40. Non-Painful Thermal Stimulation Paradigm
  41. Oddball Discrimination Paradigm
  42. Olfactory Monitor or Discrimination Paradigm
  43. Orthographic Discrimination Paradigm
  44. Pain Monitor or Discrimination Paradigm
  45. Paired Associate Recall Paradigm
  46. Passive Listening Paradigm
  47. Passive Viewing Paradigm
  48. Phonological Discrimination Paradigm
  49. Pitch Monitor or Discrimination Paradigm
  50. Pointing Paradigm
  51. Posner Task Paradigm
  52. Reading (Covert) Paradigm
  53. Reading (Overt) Paradigm
  54. Recitation or Repetition (Covert) Paradigm
  55. Recitation or Repetition (Overt) Paradigm
  56. Rest Paradigm
  57. Reward Task Paradigm
  58. Saccades Paradigm
  59. Semantic Monitor or Discrimination Paradigm
  60. Sequence Recall or Learning Paradigm
  61. Simon Task Paradigm
  62. Sleep Paradigm
  63. Spatial or Location Discrimination Paradigm
  64. Sternberg Task Paradigm
  65. Stroop Task Paradigm
  66. Subjective Emotional Picture Discrimination Paradigm
  67. Syntactic Discrimination Paradigm
  68. Tactile Monitor or Discrimination Paradigm
  69. Task Switching Paradigm
  70. Theory of Mind Task Paradigm
  71. Tone Monitor or Discrimination Paradigm
  72. Tower of London Paradigm
  73. Transcranial Magnetic Stimulation Paradigm
  74. Vibrotactile Monitor or Discrimination Paradigm
  75. Video Games Paradigm
  76. Visual Distractor or Visual Attention Paradigm
  77. Visual Pursuit or Tracking Paradigm
  78. Whistling Paradigm
  79. Wisconsin Card Sorting Test Paradigm
  80. Word Generation (Covert) Paradigm
  81. Word Generation (Overt) Paradigm
  82. Word Stem Completion (Covert) Paradigm
  83. Word Stem Completion (Overt) Paradigm
  84. Writing Paradigm

CogPO Relationships

Proper curation of the above concepts required creation of a set of novel relationships:

has_stimulus has_response has_instructions
has_stimulus_modality has_response_modality has_contrast
included_in_contrast includes_condition related_to

Basic Formal Ontology

CogPO uses a number of terms from Basic Formal Ontology (BFO), Ontology for Biomedical Investigations (OBI), and the Information Artifact Ontology (IAO):

action specification fiat object part object aggregate
planned process process aggregate quality
role

For More Information

Please see the Aims of the CogPO Project or CogPO's Wiki Policies.

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