CBO
The Cell Behavior Ontology (CBO)
The Cell Behavior Ontology (CBO) is designed to describe multi-cell computational models. In particular to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.The CBO is an OWL-2 ontology developed in Protégé 4 (see here).
To cite the CBO please use: Sluka JP, Shirinifard A, Swat M, Cosmanescu A, Heiland RW, Glazier JA. "The cell behavior ontology: describing the intrinsic biological behaviors of real and model cells seen as active agents." Bioinformatics. 2014 Apr 22. pii: btu210. [Epub ahead of print] PubMed PMID: 24755304. Download here.
Funding: US National Institute of Health grant R01GM76692, US Environmental Protection Agency grant R835001, Indiana University, Bloomington (IUB) and the Biocomplexity Institute at IUB all provided support for this work.
This work used the Protege resource, supported by grant LM007885 from the US National Library of Medicine to Stanford University.
CBO Versions
Link to the most recent version of the CBO:
CBO.owl This link will always point to the most recent stable version of the CBO.
Links to explicit versions of the CBO:
Version 1.1.2 CBO_1_1_2.owl (updated the license info)
Version 1.1.1 CBO_1_1_1.owl (updated the acknowledgements)
Version 1.1.0 CBO_1_1_0.owl (added classes for OMERO-Tiff files similar to those for VTK files)
Version 1.0.3 CBO_1_0_3.owl (only minor changes from 1.0.2)
Version 1.0.2 CBO_1_0_2.owl (only minor changes from 1.0.1)
Version 1.0.1 CBO_1_0_1.owl (only minor changes from 1.0.0)
Version 1.0.0 CBO_1_0.owl
Version 0.9.0 CBO_0_9.owl
Supplemental Ontologies:
Links to ontologies that are often loaded into CBO projects (these are copies specific to CBO, which we maintain):
Step-by-Step Guide
The Step-by-step guide, an example model and CBO description and a Compucell3D script, along with sample Python scripts for parsing a CBO-OWL and VTK files are located here. The actual step-by-step document in PDF: CBO_step_by_step.pdf or in DOCX: CBO_step_by_step.docx.
*** Latest News ***
10 October 2017
Version is now 1.1.0 Added classes for OMERO-Tiff format image files. Tthis new version has been deposited in BioPortal:CBO.
*** Old News ***
4 August 2016
Version is now 1.0.3. Only minor changes and this new version has been deposited in BioPortal.
18 January 2013
Version 1.0 of CBO has been deposited in BioPortal (CBO in BioPortal). CBO contains 241 classes. This version incorporates Relation Ontology (RO) as a native part of the ontology. Basic Formal Ontology (BFO) is linked via seeAlso annotations.
5 December 2012
A new version of the CBO is available at CBO repository. The file is the first full release, CBO_1_0.owl and is the RDF version of the OWL ontology built in Protege 4. In addition to the owl file, you will need to download the folder Import_Ontologies and place that folder in the same folder as the owl file.
This release of the CBO imports the Basic Formal Ontology (BFO), Relation Ontology (RO) and Unit Ontology (UO) giving a total of 592 classes. The CBO only part has 241 classes.
4 April 2011
A new version of the CBO is available at CBO repository. The file is CBO_0_9.owl and is the RDF version of the OWL ontology built in Protege 4. In addition to the owl file, you will need to download the folder Import_Ontologies and place that folder in the same folder as the owl file.
The current CBO contains 196 classes (terms) is still pretty rough. The annotations are 95% complete.
CBO Workshop 4 was Friday Feburary 4th to Sunday Feburary 6th 2011.
CBO Version 0.1 alpha is now available from the CBO repository.
It has been instantiated underneath a Basic Formal Ontology (BFO) top layer in Protege 4.
- RO is used as the relation list.
- There are very few annotations.
- There are very few non isA links.
- BFO terms have the annotation “creator:BFO"
- CBO terms have the annotation “creator:CBO”