Dataset Information

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.

ABSTRACT:

Motivation

Currently, there are no ontologies capable of describing both the spatial organization of groups of cells and the behaviors of those cells. The lack of a formalized method for describing the spatiality and intrinsic biological behaviors of cells makes it difficult to adequately describe cells, tissues and organs as spatial objects in living tissues, in vitro assays and in computational models of tissues.

Results

We have developed an OWL-2 ontology to describe the intrinsic physical and biological characteristics of cells and tissues. The Cell Behavior Ontology (CBO) provides a basis for describing the spatial and observable behaviors of cells and extracellular components suitable for describing in vivo, in vitro and in silico multicell systems. Using the CBO, a modeler can create a meta-model of a simulation of a biological model and link that meta-model to experiment or simulation results. Annotation of a multicell model and its computational representation, using the CBO, makes the statement of the underlying biology explicit. The formal representation of such biological abstraction facilitates the validation, falsification, discovery, sharing and reuse of both models and experimental data.

Availability and implementation

The CBO, developed using Protégé 4, is available at http://cbo.biocomplexity.indiana.edu/cbo/ and at BioPortal (http://bioportal.bioontology.org/ontologies/CBO).

SUBMITTER: Sluka JP

PROVIDER: S-EPMC4133580 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature

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Publications

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.

Sluka James P JP Shirinifard Abbas A Swat Maciej M Cosmanescu Alin A Heiland Randy W RW Glazier James A JA

Bioinformatics (Oxford, England) 20140422 16

<h4>Motivation</h4>Currently, there are no ontologies capable of describing both the spatial organization of groups of cells and the behaviors of those cells. The lack of a formalized method for describing the spatiality and intrinsic biological behaviors of cells makes it difficult to adequately describe cells, tissues and organs as spatial objects in living tissues, in vitro assays and in computational models of tissues.<h4>Results</h4>We have developed an OWL-2 ontology to describe the intrin ...[more]

PMID: 24755304

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Project description:BackgroundExpressive writing and motivational interviewing are well-known approaches to help patients cope with stressful life events. Although these methods are often applied by human counselors, it is less well understood if an automated artificial intelligence approach can benefit patients. Providing an automated method would help expose a wider range of people to the possible benefits of motivational interviewing, with lower cost and more adaptability to sudden events like the COVID-19 pandemic.ObjectiveThis study presents an automated writing system and evaluates possible outcomes among participants with respect to behavior related to the COVID-19 pandemic.MethodsWe developed a rule-based dialogue system for "Expressive Interviewing" to elicit writing from participants on the subject of how COVID-19 has impacted their lives. The system prompts participants to describe their life experiences and emotions and provides topic-specific prompts in response to participants' use of topical keywords. In May 2021 and June 2021, we recruited participants (N=151) via Prolific to complete either the Expressive Interviewing task or a control task. We surveyed participants immediately before the intervention, immediately after the intervention, and again 2 weeks after the intervention. We measured participants' self-reported stress, general mental health, COVID-19-related health behavior, and social behavior.ResultsParticipants generally wrote long responses during the task (53.3 words per response). In aggregate, task participants experienced a significant decrease in stress in the short term (~23% decrease, P<.001) and a slight difference in social activity compared with the control group (P=.03). No significant differences in short-term or long-term outcomes were detected between participant subgroups (eg, male versus female participants) except for some within-condition differences by ethnicity (eg, higher social activity among African American people participating in Expressive Interviewing vs participants of other ethnicities). For short-term effects, participants showed different outcomes based on their writing. Using more anxiety-related words was correlated with a greater short-term decrease in stress (r=-0.264, P<.001), and using more positive emotion words was correlated with a more meaningful experience (r=0.243, P=.001). As for long-term effects, writing with more lexical diversity was correlated with an increase in social activity (r=0.266, P<.001).ConclusionsExpressive Interviewing participants exhibited short-term, but not long-term, positive changes in mental health, and some linguistic metrics of writing style were correlated with positive change in behavior. Although there were no significant long-term effects observed, the positive short-term effects suggest that the Expressive Interviewing intervention could be used in cases in which a patient lacks access to traditional therapy and needs a short-term solution.Trial registrationClincaltrials.gov NCT05949840; https://www.clinicaltrials.gov/study/NCT05949840.

Dataset Information

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.

Motivation

Results

Availability and implementation

Publications

The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.

Similar Datasets

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