ArticleBioinformatics (Oxford, England)2014
The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
- Foundations of a Compositional Systems Biology.ArXiv · 2024Article
- Digitize your Biology! Modeling multicellular systems through interpretable cell behavior.bioRxiv : the preprint server for biology · 2023Article
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- Sharing biological data: why, when, and how.FEBS letters · 2021Article
- Key challenges facing data-driven multicellular systems biology.GigaScience · 2019Review
- The 2019 mathematical oncology roadmap.Physical biology · 2019Review
- High-throughput cancer hypothesis testing with an integrated PhysiCell-EMEWS workflow.BMC bioinformatics · 2018Article
- Sharing and reusing cell image data.Molecular biology of the cell · 2018Article
- Creating a Structured AOP Knowledgebase via Ontology-Based Annotations.Applied in vitro toxicology · 2017Article
- TOWARDS A MULTI-SCALE AGENT-BASED PROGRAMMING LANGUAGE METHODOLOGY.Proceedings of the ... Winter Simulation Conference. Winter Simulation Conference · 2016Article
- Formalizing Knowledge in Multi-Scale Agent-Based Simulations.Model driven engineering languages and systems : ... International Conference, MoDELS ... : proceedings. MODELS (Conference) · 2016Article
- Article
- Progress Towards Computational 3-D Multicellular Systems Biology.Advances in experimental medicine and biology · 2016Review
- Agent-Based Modeling of Cancer Stem Cell Driven Solid Tumor Growth.Methods in molecular biology (Clifton, N.J.) · 2016Article
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Authors and funding
6 authors.
Funding
Abstract
motivationCurrently, 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.
resultsWe 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).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.