2007-03-05 2007-03-05 BIRNLex-CogBehavior The BIRN Ontology Task Force 1.2 Bill Bug The current (2006-10-10) members of the BIRN Ontology Task Force are listed here as the primary curators of the main BIRNLex ontology. Others from within BIRN labs and directly collaborating with BIRN labs have also contributed to specific classes and class properties. Effort is made to provide attribution for each class, where appropriate. Jessica Turner Carol Bean The BIRN project lexicon+ontology The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project, covering anatomy, disease, data collection, project management and experimental design. It is built using the organizational framework provided by the foundational Basic Formal Ontology (BFO). It uses an abstract biomedical layer on top of that - OBO-UBO which has been constructed as a proposal to the OBO Foundry. This is meant to support creating a sharable view of core biomedical objects such as biomaterial_entity, and organismal_entity that all biomedical ontologies are likely to need and want to use with the same intended meaning. The BIRNLex-Main.owl ontology imports the several domain specific ontology modues required to construct a formal ontology for the multiscale investigation of neurological disease. This particular module contains entities related to the behavior and cognitive capabilities and actions of organisms (BB:2007-03-05). David Kennedy Jeff Grethe Maryann Martone Amarnath Gupta Christine Fennema-Notestine uncurated Discrimination_function Bill Bug 2007-03-06 2007-03-06 Discrimination_function 2007-03-06 Pain_stimulus_triggered_activity Pain_stimulus_triggered_activity 2007-03-06 uncurated Bill Bug Jessica Turner UMLS uncurated Happiness 2006-06-01 Happiness 2007-03-11 C0018592 C0018592 Highly pleasant emotion characterized by outward manifestations of gratification; joy Bill Bug A behavioral function supporting immediate sensory-motor integration with minimal nervous system processing (BB:2007-03-05). Skeletomotor_reflex_function 2007-03-06 uncurated Skeletomotor_reflex_function 2007-03-06 2007-03-06 Inductive_reasoning_function Bill Bug 2007-03-06 Inductive_reasoning_function uncurated Generative_verbal_activity Generative_verbal_activity 2007-03-06 Bill Bug 2007-03-06 uncurated C0002957 Anger Anger MeSH C0002957 2006-06-01 A strong emotional feeling of displeasure aroused by being interfered with, injured or threatened (MeSH). Jessica Turner uncurated 2007-03-05 UMLS C0561843 uncurated Memory that involves the conscious recall or recognition of one‚Äôs own life. Autobiographical_memory 2006-05-15 Jessica Turner Autobiographical_memory 2007-03-05 2007-03-06 Bill Bug 2007-03-06 Verbal_function uncurated Verbal_function Abductive_reasoning_function uncurated Bill Bug 2007-03-06 2007-03-06 Abductive_reasoning_function Bill Bug 2007-03-05 2007-03-05 _birnlexCogBehavior_retired_class These are classes for whom the represented entities are now described using a different class. A class is deprecated if it's semantic meaning required alteration or its entity is now represented directly in an imported foundational ontology. These original classes maintain their original identifiers and are included to provide support for previous applications using this ontology class prior to its being deprecated. _birnlexCogBehavior_retired_class Drawing 2007-03-06 2007-03-06 Drawing Bill Bug uncurated Auditory_stimulus_triggered_activity 2007-03-06 Bill Bug Auditory_stimulus_triggered_activity 2007-03-06 uncurated The cognitive process of encoding, storing and retrieving past experience Memory 2006-05-15 Jessica Turner 2007-03-05 uncurated Memory BF_T0000216 Requested as opposed to free (BB:2007-03-05). 2007-03-05 Requested_recall 2007-03-05 Bill Bug Requested_recall uncurated Abductive reasoning is a type of reasoning in which a hypothesis is chosen to best explain the relevant evidence - also called 'inference to the best explanation'. Abduction starts from a set of accepted facts and infers to their most likely, or best, explanations. The term abduction is also sometimes used to just mean the generation of hypotheses to explain observations or conclusions. Abductive reasoning allows inferring 'a' as an explanation of 'b'. Because of this, abduction allows the precondition 'a' of 'a entails b' to be inferred from the consequence, and, as such, such abduction is formally equivalent to the logical fallacy 'affirming the consequent.' (Wikipedia - BB:2007-03-05). Bill Bug 2007-03-06 2007-03-06 Abductive_reasoning_activity Wikipedia Abductive_reasoning_activity uncurated Bill Bug 2007-03-06 Discrimination_activity uncurated Discrimination_activity 2007-03-06 uncurated 2007-03-06 Bill Bug Saccadic_eye_movement Rapid eye movement relative to an initial target 2007-03-06 Saccadic_eye_movement uncurated 2006-05-15 Memory_recall 2007-03-05 Bill Bug Recall as opposed to storage (BB:2007-03-05). Memory_recall Bill Bug 2007-03-06 uncurated Interpretive_vision_based_reading Interpretive_vision_based_reading 2007-03-06 _birnlexCogBehavior_limbo_class 2007-03-05 Bill Bug 2007-03-05 class in limbo since major refactoring of foundational community ontologies (e.g., BFO, OBI, SKOS). (BB:2007-03-05). _birnlexCogBehavior_limbo_class Behavioral_process 2007-03-05 Behavioral_process uncurated BIRN OTF 2006-05-15 uncurated Verbal_activity 2007-03-06 2007-03-06 Bill Bug Verbal_activity A behavioral activity employing verbal function to either generate or interpreting meaningful spoken or writen words or symbols. If generating verbal output, a motor system is invoked. If interpreting verbal input, typically a sensory system is invoked, though certain interpretive activity involves movement of the sensory organ - e.g., eye movements during reading (BB:2007-03-05). uncurated 2007-03-05 2006-06-01 UMLS Jessica Turner MeSH C0003467 Anxiety Persistent feeling of dread, apprehension, and impending disaster (MeSH). C0003467 Anxiety 2007-03-06 uncurated Eye_movement Bill Bug Eye_movement 2007-03-06 2007-03-06 Smoking uncurated Smoking 2007-03-06 Bill Bug Memory_function 2007-03-06 2007-03-06 Bill Bug uncurated Memory_function Cognitive_process BIRN OTF 2007-03-05 uncurated Cognitive_process 2006-05-15 Reasoning_function 2007-03-06 Reasoning_function 2007-03-06 uncurated Bill Bug 2007-03-06 2007-03-06 Behavioral_function uncurated Behavioral_function Bill Bug Behavioral functions consist of the variety of emergent operations for which the organism's nervous system is the primary enabling organ system and as such behavioral functions can be said to inhere in the nervous system. Behavioral functions may lead to action via a physiological actuation system such as the skeleto-muscular system or give rise to actions only percieved internally by the individual in which the function inheres (BB). 2007-03-06 2007-03-06 Inidividual_body_part_movement Bill Bug Inidividual_body_part_movement uncurated C0233486 Sadness BIRN OTF Bill Bug Sadness In what way is this related to Happiness? Is there in fact a single underlying Cognitive_entity for which Happiness and Sadness are just either end of the quality gamut describing that entity as experienced by an individual (BB)? Can you experience both Happiness and Sadness simultaneously (BB)? 2007-03-05 2006-06-01 uncurated 2007-03-06 2007-03-06 Interpretive_listening Bill Bug Interpretive_listening uncurated 2007-03-06 uncurated Bill Bug Verbal_speaking 2007-03-06 Verbal_speaking Bill Bug Olfactory_stimulus_triggered_activity 2007-03-06 2007-03-06 uncurated Olfactory_stimulus_triggered_activity Bill Bug Deductive_reasoning_function 2007-03-06 Deductive_reasoning_function 2007-03-06 uncurated Cognitive_state 2006-06-01 Bill Bug Moved under bfo:Disposition, as these are states toward which the organisms in which they inhere are disposed (BB:2007-03-05). Cognitive_state Maryann Martone 2007-03-05 Moved from base of hiearchy to a subclass of bfo:realizable_entity (BB). Describes entities related to cognitive processes. At some point, this will have to be merged with the OBR but for now I think it's best kept separate (MM). uncurated Sensory_stimulus_triggered_activity 2007-03-06 Sensory_stimulus_triggered_activity Bill Bug uncurated 2007-03-06 2007-03-06 Visual_stimulus_triggered_activity uncurated 2007-03-06 Bill Bug Visual_stimulus_triggered_activity 2006-05-15 The process of focusing on certain aspects of current experience to the exclusion of others. It is the act of heeding or taking notice or concentrating. (MeSH) Attention 2007-03-05 uncurated Attention MeSH-UMLS Jessica Turner C0004268 uncurated Lateralized_activity 2007-03-06 Laterality may actually be most effectively expressed as a measured quality via PATO (BB:2007-03-05). A behavioral activity expressing a behavioral function that is differentially supported across the two cerebrain hemispheres in the vertebrate brain (BB:2007-03-05). Bill Bug Lateralized_activity 2007-03-06 2007-03-06 uncurated Bill Bug Moral_reasoning_activity Moral_reasoning_activity 2007-03-06 Moral reasoning is individual or collective practical reasoning about what, morally, one ought to do (Stanford Encyclopedia of Philosphy). Inductive_reasoning_activity uncurated Wikipedia inductive reasoning is a type of reasoning in which the premises of an argument are believed to support the conclusion but do not ensure it. It is used to ascribe properties or relations to types based on tokens (i.e., on one or a small number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns. Induction is used, for example, in USING SPECIFIC PROPOSITIONS such as:'this ice is cold'; 'a billiard ball moves when struck with a cue' TO INFER GENERAL PROPOSITIONS such as:'all ice is cold'; 'all billiard balls struck with a cue move.' In other words, inductive reasoning infers probable antecedents as a result of observing multiple consequents - i.e., inferring some 'b' from multiple instantiations of 'a' when 'b' entails 'a'.. (Wikipedia - BB:2007-03-05). 2007-03-06 2007-03-06 Bill Bug Inductive_reasoning_activity Bill Bug 2007-03-06 Verbal_writing Verbal_writing 2007-03-06 uncurated uncurated Interpretive_verbal_activity 2007-03-06 Bill Bug Interpretive_verbal_activity 2007-03-06 Bill Bug 2007-03-06 Interpretive_braille_reading Interpretive_braille_reading 2007-03-06 uncurated uncurated C0015726 Jessica Turner C0015726 UMLS Fear The affective response to an actual current external danger which subsides with the elimination of the threatening condition. (MeSH) 2007-03-05 Fear 2006-06-01 Unpleasant but normal emotional response to genuine external danger or threats; compare with ANXIETY and CLINICAL ANXIETY. (CSP) 2007-03-06 Behavioral_activity Bill Bug Behavioral_activity 2007-03-06 uncurated Overt activity inhering in the action of instantiating a behavioral function. In other words, the expressed activity resulting from the action of the behavioral process which makes up a given behavioral function (BB: 2007-03-05). This seems a bit contrived but appears to be an appropriate way to classify the sub-classes of behavioral activity derived from this class. These certainly are dispositions inhering in the entity performing the activity. There are also many behavioral activities where it really is a non-sequetor to call them behavioral functions - e.g., 'smoking' is certainly a behavior, but it really makes little sense to represent a 'smoking function' and underlying 'smoking process.' Describing behavior as an activity to which an entity is disposed makes it possible to represent very complex behaviors for which the corresponding behavioral function(s) and underlying process(es) are not yet characterized. Note also that one can describe the activity without proscribing the associated function and underlying process - e.g., ants and humans can both be said to be disposed toward expressing 'locomotive behavior', and, yet, the associated 'locomotor function' and underlying 'locomotor process' in each organism is very different. Note also that behavior in general is not restricted to organic 'living' entities but can also be expressed by 'non-living' entities such as the old 'bobbing bird' toy or an automatic loom. Specific entities may have specific dispositions for expressing certain sets of behavioral activities (BB:2007-03-05). uncurated 2007-03-06 2007-03-06 Reasoning_activity Reasoning_activity Bill Bug 2007-03-06 2007-03-06 uncurated Heat_stimulus_triggered_activity Bill Bug Heat_stimulus_triggered_activity Deductive_reasoning_activity Bill Bug Deductive_reasoning_activity Wikipedia 2007-03-06 Deductive reasoning is a type of reasoning in which the conclusion is necessitated by, or reached from, previously known facts (the premises). If the premises are true, the conclusion must be true. In deductive reasoning, the conclusion is dependent on its premises. That is, a false premise can possibly lead to a false conclusion, and inconclusive premises will also yield an inconclusive conclusion (Wikipedia - BB:2007-03-05). 2007-03-06 uncurated 2007-03-06 2007-03-06 Bill Bug uncurated chewing A behavioral activity expressed while ingesting food. Appetitive_activity masticating Appetitive_activity swallowing Locomotor_function uncurated 2007-03-06 Bill Bug 2007-03-06 Locomotor_function A behavioral function enabling an entity to alter its location under the power of its own motive force (BB:2007-03-05). Jessica Turner C0013987 A mental state that arises spontaneously rather than through conscious effort and is often accompanied by physiological changes; a feeling. Emotion 2007-03-05 C0013987 uncurated Emotion UMLS 2006-06-01 Free_recall_function Free_recall_function 2006-10-11 2006-06-01 uncurated Bill Bug 2007-03-06 Appetitive_function Bill Bug 2007-03-06 A behavioral function supporting the process of ingesting food. uncurated Appetitive_function 2007-03-06 Bill Bug 2007-03-06 uncurated Gustatory_stimulus_triggered_activity Gustatory_stimulus_triggered_activity Jessica Turner 2006-05-15 BF_T0000218 2007-03-05 Working_memory Memory that involves the conscious encoding, storing and retrieving information encountered recently Working_memory uncurated 2007-03-06 Bill Bug 2007-03-06 Item_recognition_activity Item_recognition_activity uncurated 2007-03-06 Locomotor_activity 2007-03-06 uncurated Locomotor_activity Bill Bug 2006-05-15 C0524637 MeSH-UMLS 2007-03-05 Christine Fennema-Notestine Recognition_memory uncurated Recognition_memory The memory that someone or something present has been previously encountered. (MeSH) The cognitive process of remembering/recollecting previously learned material without aid of any external cues. Free_recall 2007-03-05 2006-05-15 Free_recall pending final vetting Christine Fennema-Notestine BF_T0000231 Skeletomotor_reflex_activity Skeletomotor_reflex_activity 2007-03-06 2007-03-06 A behavioral activity expressing immediate sensory-motor integration through activation of muscular-driven process (BB:2007-03-05). Bill Bug uncurated memory function Cognitive_function introspective function 2007-03-05 Cognitive functions are a type of behavioral function giving rise to actions only percieved internally by the individual in which the function inheres, though this internal perception may ultimately give rise to an externalized action (BB). Bill Bug creative function belief function imaginative function reasoning function uncurated emotional function conceptual function perceptual function The examples are derived from the Wikipedia page on 'Mental function.' Perhaps a more narrow set of examples that specifically fit to our requirements in BIRN would be more appropriate. A more authoritative neuropsychological source should also be used, as some of these examples may be considered by neuropsychologists to be degenerate - e.g., 'belief function' is_a 'imaginative function' (BB:2007-03-05). A specific instance of engaging a cognitive function leads to the creation of a mental event distinct from the cognitive functional process itself. The event of perceiving something, for instance, is different from the perceptual process in its entirety — the overall ability to perceive things. In other words, an instance of perceiving is different from the cognitive function that makes it possible (BB:2007-03-05 - derived from Wikipedia). 2007-03-05 volitional function Cognitive_function 2007-03-06 Bill Bug Touch_stimulus_triggered_activity 2007-03-06 uncurated Touch_stimulus_triggered_activity