Resources

From CBO

Papers

• Useful because it defines naming conventions for OBO ontologies. Survey-based naming conventions for use in OBO Foundry ontology development. Daniel Schober, Barry Smith, Suzanna E Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F Taylor, Philippe Rocca-Serra and Susanna-Assunta Sansone, BMC Bioinformatics 2009, 10:125 doi:10.1186/1471-2105-10-125. view and download
• Useful because it discusses another potential pitfall of BFO: the function/role definitions. Lord, Phillip. An evolutionary approach to Function. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3228.1> (2009)
• Useful because it describes a method of decentralised ontology development that might be good for us. Garcia, Alexander , O’Neill, Kieran, Garcia, Leyla, Lord, Phillip, Stevens, Robert, Corcho, Oscar, and Gibson, Frank. Developing ontologies in decentralised settings. Available from Nature Precedings <http://hdl.handle.net/10101/npre.2009.3231.1> (2009)

• Anatomics: the intersection of anatomy and bioinformatics Journal of Anatomy. 206(1):1-16, January 2005. Bard, Jonathan B. L. Full Text
• The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Nature Biotechnology 25, 1251 - 1255 (2007)Full Text
• The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience Neuroinformatics. 2008 Sep;6(3):175-94. Epub 2008 Oct 31Full Text

Software

• Protégé: is a free, open source ontology editor and knowledge-base framework. We will be using Protégé as our primary tool to develop the CBO.

Websites

• Open Biomedical Ontologies : The OBO provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development

• Bioportal: BioPortal allows users to browse, upload, download, search, comment on, and create mappings for ontologies.

Ontologies

• GO: The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.

• Cellular Process Ontology: A Gene Ontology slice describing cellular processes.

• OPB: Ontology of Physics for Biology

Google Spreadsheet LINK

James's List

• Cell Division
• Cell Growth
• Cell Death
• Cell Shape
• Cell Adhesion
• Cell Motility
• Cell Movement
• Cell Force Generation
• Cell Mechanics
• Cell Polarization
• Cell Modifications of Environment
  • Cell Secretion
  • Cell Absorption
  • Cell Remodeling of Environment
  • Cell Electrical Behaviors

Group List

• Divide
• Fragment
• Move
• Change Shape
• Exert Force/Pull
• Change Volume
• Delaminate
• Interact
• Secrete/excrete export
• Absorb/adsorb import
• Change neighbors
• Disappear
• Fusion
• Give off heat
• Change electrical field
• Interact w/ ECM
• Alter subcellular distribution
• Alter extracellular distribution
• Alter mechanical properties