On the Future of the NeuroBehavior Ontology and Its Relation to the Mental Functioning Ontology Barry Smith

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) The Open Biological and Biomedical Ontologies (OBO) Foundry (draft, with Gene Ontology marked in yellow)

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) orthogonal modules to ensure consistent, additive annotation

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Behavior Ontology (NBO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) NBO homesteads a portion of the biological process domain

OBO Foundry principles always annotate to the lowest term – if you don’t know whether a movement is voluntary or involuntary, just annotate to ‘movement’ every term in an ontology should be a singular noun (traffic law) exploit the strategy of downward population (feeding behavior …) build orthogonal modules build modules in collaboration with the authors of neighboring modules work very hard to have clear definitions of the top-level terms, including – work very hard to have a clearly defined scope

with thanks to George Gkoutos and Robert Hoehndorf

gait = a type of walking behavior amimia = impairment of the power of communicating thought by gestures intellectual disability = IQ < 70 hyperactivity = body is too active aggression = engaging in actions that can harm epilepsy = a disease

Mental Functioning vs Behavior The first person experiences which form the object of MF are not observable Behavior is something physical and thus observable Study of behavior is analogous to study of physiology

Mental Functioning vs Behavior The first person experiences which form the object of MF are not observable Behavior is something physical and thus observable Study of behavior is analogous to study of physiology – where the latter pertains to internal bodily movements, behavior pertains to movements of the whole body and of external parts such as arms and legs (crying, sleep …) – both deal with patterns of movement that contribute to the life of the organism in question. Being squashed by a truck is not behavior. Being accidentally burned by a flame is not behavior But reacting thereto by withdrawing from the flame is.

Behavior in NBO Behavior Process Definition: The action, reaction, or performance of an organism in response to external or internal stimuli.

What is a stimulus? An event that is of a type that can be detected by a receptor in the body of some organism A thing or event that evokes a specific functional reaction in an organ or tissue Something that can elicit or evoke a physiological response in a cell, a tissue, or an organism

One-person vs. multi-person behavior what does behavior inhere in? – mating dance – social behavior Compare GO treatment of one-organism and multi-organism biological processes

What should NBO be focused on NBO should not focus on descriptions NBO should not focus on assays NBO focus on what is observable (physical)

Mental Functioning Ontolog

sensory perception in GO GO: sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GO: visual perception The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. GO: sensory perception of salty taste The series of events required to receive a salty taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.

Rule for definitions If A is the child and B the parent (A is_a B), then the definition of A should read: A =def. a B which Cs where C tells us what it is about the Bs which makes them As

sensory perception in GO GO: sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GO: visual perception The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image. GO: sensory perception of salty taste The series of events required to receive a salty taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.

sensory perception in GO GO: sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GO: visual perception Sensory perception with visual stimulus. GO: sensory perception of salty taste The series of events required to receive a salty taste stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.

sensory perception in GO GO: sensory perception The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. GO: visual perception Sensory perception with visual stimulus. GO: sensory perception of salty taste Sensory perception with salty taste stimulus

relation between NBO and MF NBO termMF term sensation behaviorsensation attention behaviorattention spatial perception behaviorspatial perception

RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Behavior Ontology (NBO) Mental Functioning (MF) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) The Open Biological and Biomedical Ontologies (OBO) Foundry (draft, with Gene Ontology marked in yellow)

A problem with ‘Neuro Behavior Ontology’ Neuro Behavior Ontology Neurobehavior Ontology Neuro = behavior of organisms with neurons Not

NBO will be renamed (George agrees) Henceforth it will be called: Behavior Ontology but we will keep ‘NBO’ as namespace ID Behavior ontology means ‘behavior’ in the narrow sense = not covering physiological behavior

Mental Functioning vs Behavior N Study of behavior is analogous to but distinct from study of physiology – physiology pertains to internal bodily movements, – ‘behavior’ in the sense of NBO pertains to movements of the whole body and of external parts such as arms and legs (crying, sleep …) Being squashed by a truck is not behavior. Being accidentally burned by a flame is not behavior But reacting thereto by withdrawing from the flame is.

Proposals Explore consequences of using the Feeding Behavior Ontology as a module descending from NBO:feeding behavior Create a version of NBO in which behavior terms applying only in humans are marked Explore the possibility of unifying NBO with ABO by labeling terms according to which taxa they apply to

GOTAX identifies to which taxa GO terms apply