Cell ontology in an age of data-driven cell classification

David Osumi-Sutherland
2017 BMC Bioinformatics  
Data-driven cell classification is becoming common and is now being implemented on a massive scale by projects such as the Human Cell Atlas. The scale of these efforts poses a challenge. How can the results be made searchable and accessible to biologists in general? How can they be related back to the rich classical knowledge of cell-types, anatomy and development? How will data from the various types of single cell analysis be made cross-searchable? Structured annotation with ontology terms
more » ... vides a potential solution to these problems. In turn, there is great potential for using the outputs of data-driven cell classification to structure ontologies and integrate them with data-driven cell query systems. Results: Focusing on examples from the mouse retina and Drosophila olfactory system, I present worked examples illustrating how formalization of cell ontologies can enhance querying of data-driven cell-classifications and how ontologies can be extended by integrating the outputs of data-driven cell classifications. Conclusions: Annotation with ontology terms can play an important role in making data driven classifications searchable and query-able, but fulfilling this potential requires standardized formal patterns for structuring ontologies and annotations and for linking ontologies to the outputs of data-driven classification.
doi:10.1186/s12859-017-1980-6 pmid:29322914 pmcid:PMC5763290 fatcat:joye47nfkbezdnnt62frjivjdu