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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
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Include Cell Behavior Ontology in OLS #501

Open jpsluka opened 3 years ago

jpsluka commented 3 years ago

I would like to deposit our Cell Behavior Ontology (CBO) in OLS (https://www.ebi.ac.uk/ols/ontologies). CBO has been available in BioPortal since 2012 with the most recent version dated January 2020 -- https://bioportal.bioontology.org/ontologies/CBO

The original publication describing the CBO is: 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 Aug 15;30(16):2367-74. doi: 10.1093/bioinformatics/btu210. Epub 2014 Apr 22. PMID: 24755304; PMCID: PMC4133580. The article full text is available at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4133580/

A brief description of the CBO: The Cell Behavior Ontology (CBO) describes multi-cell computational models. CBO is designed to describe both the existential behaviors of cells (spatiality, growth, movement, adhesion, death, ...) and computational models of those behaviors.

Some additional information is available at https://cbo.biocomplexity.indiana.edu/ Including a step-by-step example of using the CBO to describe a model: CBO_step_by_step.pdf (PDF)

The permanent link to the most recent version of the CBO is: http://cbo.biocomplexity.indiana.edu/svn/cbo/trunk/CBO.owl

If there is any other information needed to include the CBO in OLS please let me know.

Thank you.

James P. Sluka, PhD Biocomplexity Institute Intelligent Systems Engineering School of Informatics, Computing and Engineering Indiana University Bloomington, IN USA Office: 812-855-2441 Cell: 317-331-7465 JSluka@IU.edu

henrietteharmse commented 3 years ago

Sure! Please fillout the spreadsheet as detailed in (2) decribed here.

Once you have uploaded the speadsheet, we will test the ontology in our dev environment and if all goes well, we will add it to production OLS.

jpsluka commented 3 years ago

The page at https://github.com/EBISPOT/OLS/wiki/How-are-ontologies-added-to-OLS%3F has a hyperlink to the spreadsheet of https://github.com/EBISPOT/OLS/raw/master/documentation/uptake/New%20OLS%20ontology%20request.xlsx that gives a 404 error.

henrietteharmse commented 3 years ago

@jpsluka Appologies for the 404 error. This has been fixed.