1. Cell Ontology 2.0 Elimination of multiple is_a inheritance through instantiation of relationships to terms in outside ontologies, such as the GO cellular component, GO biological process, and the PATO phenotype ontologies. Outcome should be more ontologically correct, and more useful for data analysis. Process is likely to be slow, due to lack of personnel and funding to organize the work.

2. Goals for this Workshop (per Alex) Pragmatic Goal Extend the ontology in its current form to include additional immune cell types. Ideal Outcome Lay the groundwork for CL 2.0 in the area of immune cell types.

3. Use Cases for Cell Ontology 1.Annotation (ongoing for GO). 2.Cross product term formation with GO, MP, and other ontologies (ongoing). 3.Representation of Flow Cytometry Results. 4.Immune System Modeling. 5.IEDB annotation needs. 6.Other?

4. How do we describe Cells? Morphology Surface markers Transcription factors Location Role or process involvement Lineage

5. How do we describe Cells? Morphology Surface markers Transcription factors Location Role or process involvement Lineage Protein Ontology Anatomy Ontology GO Biological Process Link to external ontology

6. How do we describe Cells? Morphology Surface markers Transcription factors Location Role or process involvement Lineage expresses_protein located_in participates_in Link via specific relationships

7. Issues to Discuss 1.Distinction between ontology, knowledgebase, and vocabulary. 2.How much information is needed to describe a cell uniquely — to create a formal definition? 3.How to deal with species differences.