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Welcome to the CogPO Wiki!
  
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Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software.
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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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A. SPECIFIC AIMS.  The objective of this proposal is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community.  This cognitive paradigm ontology, CogPO, will be developed through the integration of two well known and established databases, the Functional Imaging Biomedical Informatics Research Network (FBIRN) Human Imaging Database (HID) and the BrainMap database.
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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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Neuroimaging research has produced an enormous amount of data suitable for mining, analysis, and meta-analysis.  As a byproduct of this, new databases are constantly emerging.  Yet until a complete ontology is established and adopted, communication and the exchange of information within and between these neuroimaging databases will be limited.  There are numerous of existing efforts that aim to develop ontologies: RadLex, an ontology of medical imaging acquisition strategies (http://radlex.org); lexicons and ontologies of neuroanatomical regions (e.g., NeuroNames and the Foundational Model of Anatomy (FMA)); full medical ontologies for clinical care concepts, such as the Systematized Nomenclature of Medicine (SNOMED) Ontology, and many others.  In addition, the ontology developed by BIRN, BIRNLex, pulls from all these in developing ontologies of neuroimaging methods and datasets.
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We aim to decompose each condition into its corresponding stimulus, response, and instructions:
  
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Despite the number of ontologies currently being developed, no ontology effort exists to formally define and characterize the cognitive paradigms that are used in functional neuroimaging studies.  Even a brief examination of the literature reveals that a given cognitive paradigm may be encountered under a variety of different names. For example, the “Sternberg task” may also be identified as the “serial item recognition paradigm (SIRP)”, a “delayed match to sample task”, or merely as a “working memory task”.  The latter example is especially confusing as it conflates what the paradigm is intended to study at the time of use, with what it might be understood to characterize later.  That is, applying the label of “working memory task” to data acquired during performance of the “n-back task” presupposes that the data would not be useful in examining “executive function”.  This frequent use of alternate and sometimes competitive terminology makes the formal development of an ontology based solely on paradigm names extremely difficult, if not impossible.
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*[[Stimulus]]
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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]]
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**[[Covert Response]]
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**[[Overt Response]]
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***[[Response Modality]]
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*[[Instructions]]
  
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The design of CogPO concentrates on what can be observed directly: categorization of each paradigm in terms of (1) the stimulus presented to the subjects, (2) the requested instructions, and (3) the returned response.  All paradigms are essentially comprised of these three orthogonal components, and formalizing an ontology around them is a clear and direct approach to describing paradigms.  This type of classification has been a core feature of the BrainMap database since its inception, was endorsed and refined by many reviewers during previous BrainMap workshops (1994-1998), and was part of the BrainMap ontology presentation to the Neuroimaging Informatics Technology Initiative (NIfTI).  Categorization of paradigms according to stimulus, response, and instruction has been shown to allow advanced data retrieval techniques by searching for similarities and contrasts across multiple paradigm levels.  This approach is less susceptible to the whims of conceptual shifting, in that while one’s research interests may progress from “working memory” to “executive function”, one may continue to be interested in paradigms in which (1) a target set of letters were presented, followed by a probe letter, (2) after which subjects indicated if the probe letter matched any target, (3) using a button press response.
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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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Rather than develop a cognitive paradigm ontology in the abstract, the aim of this proposal is to develop and evaluate CogPO in the context of two neuroimaging databases, the FBIRN Human Imaging Database (HID) and the BrainMap database. The FBIRN HID and BrainMap serve very different missions. While the FBIRN HID aims to archive image data prior to publication for re-analysis and mega-analysis, BrainMap’s goal is to archive reduced (coordinate) data for meta-analysis. Because of these fundamental differences, FBIRN HID contains a smaller number of highly focused and finely detailed paradigms, while BrainMap contains a very large number of paradigms represented at a coarser resolution. The present proposal seeks to take advantage of these differences by creating an iterative model of ontological development.
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===Stimulus Modality===
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{|
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|-
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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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Aim 1. Develop the core ontology for the common paradigms in BrainMap and the FBIRN HID. Using the example cognitive paradigms available in both data repositories, and building on our previous work already incorporated into BIRNLex and the BrainMap coding scheme, we will develop and implement the core ontology to fully capture the paradigm characteristics, which are currently contained in both BrainMap and the FBIRN HID, but not ontologically mapped. This will involve defining the hierarchical relationships and instances of stimuli, responses, and instructions in a machine-interpretable and publishable format.
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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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Aim 2. Extend the ontological mapping to the complete list of paradigms contained in BrainMap. We will extend the ontological mapping procedure developed and refined during Aim 1 to encompass all of the paradigms contained in BrainMap. Inclusion of the total list of BrainMap paradigms is an additional, indirect method of involving the community in the development of this ontology, as BrainMap is an open database of neuroimaging results and is therefore potentially represented by any member of the community.
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===Stimulus Role===
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{|
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|-
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| width="200" | [[Feedback]]
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| width="200" | [[Non-Target]]
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|  width="200" | [[Reward]]
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|-
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| [[Target]]
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|
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|}
  
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Aim 3. Enable information exchange between FBIRN HID and BrainMap. The true value of a given ontology can be measured in its ability to facilitate data retrieval. To this end, we will test the efficacy of the ontology developed in Aims 1 and 2 by enabling interoperability and the exchange of information between both databases according to cognitive paradigms of interest. Through combinations of CogPO and other ontologies, the possibility of automated hypothesis testing will be explored.
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===Response Modality===
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{|
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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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Sharing Plan. The present proposal seeks to take advantage of ontological best practices that have shown to be valuable in other projects. Through a series of workshops, we will consult both the domain experts (the neuroimaging research community) and the ontological experts (the National Center for Biomedical Ontology (NCBO) and the BIRN Ontology Task Force (OTF)) as the ontology develops.  We will also allow user input and feedback from the entire neuroimaging community through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC) and the NCBO BioPortal, with links to a Wiki-based presentation of the concepts similar to that used by the Neuroinformatics Framework or the Gene Ontology Consortium.  At the end of funding, we aim to deliver a complete and functioning ontology of cognitive paradigms used in functional neuroimaging in the Protégé-OWL format. These files will contain the concepts, definitions, and relationships of paradigms represented by stimuli, responses, and instructions, and will be distributed through NITRC and the NCBO BioPortal. This ontology will be made available for adoption not only by other fMRI databases, but also for archives of other neuroimaging modalities (e.g., EEG or MEG data), such as the Neural ElectroMagnetic Ontologies (NEMO), and literature neuroinformatics efforts such as the Society for Neuroscience’s PubMed Plus.
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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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===Instructions===
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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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===Paradigm Classes===
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Currently, CogPO has defined 84 classes of paradigms:
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#[[Action Observation Paradigm]]
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#[[Acupuncture Paradigm]]
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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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 +
===CogPO Relationships===
 +
Proper curation of the above concepts required creation of a set of novel relationships:
 +
{|
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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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===Basic Formal Ontology===
 +
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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|-
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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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===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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