Single Cell Atlas

The Single Cell Atlas Ontology (SCAO) provides a systematic description of many experimental variables available in single cell atlas databases (Expression Atlas http://www.ebi.ac.uk/gxa), and for projects datas such data sets from ArrayExpress , NCBI’s Gene Expression Omnibus (GEO), European Nucleotide Archive (ENA) as well as other sources. Increasingly, mass spectrometry proteomics data coming from the PRoteomics IDEntification (PRIDE) database are included. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, Cell Ontology, NCBITaxon, NCIT, BTO, FBDV, RS, WBLS ,PECO (EO), EFO, Orphanet, PATO, PO, GO, and others. The scope of SCAO is to support the annotation, analysis and visualization of data handled by the Expression Atlas group at the EBI and as the core ontology for Single Cell Atlas project (https://www.ebi.ac.uk/gxa/sc/home). SCAO is developed by the EMBL-EBI Samples, Phenotypes and Ontologies Team (SPOT). We for the maintainance of the ontology.

Release versions

Stable release versions

The latest version of the ontology can always be found attached to each scatlas release, found here:

https://github.com/EBISPOT/scatlas_ontology/releases

This is the asserted ontology and requires an OWL-DL reasoner to view the inferred classification.

Since Jan 2024, releases are scheduled the first day of the month.

Editors' version

Editors of this ontology should use the edit version, scatlas_ontology/src/ontology/scatlas-edit.owl

Term requests and contact

Submit new terms or report bugs using our issue tracker, or join SCATLAS mailing list for announcement and monthly update.

Acknowledgements

This ontology repository was created using the ontology starter kit