the cell ontology an ontology of cell types built by biologists for the needs of data annotation and...

The Cell Ontology• An ontology of cell types built by biologists for the needs of data

annotation and analysis.

• The main branch organizes and enumerates in vivo cell types.

• The Cell Ontology covers cell types from all of biology.

• The Cell Ontology is not– A list of specific cell lines, immortal or otherwise, although the Cell

Ontology may be used to describe such cells if they correspond to an in vivo cell type.

– A list of in vitro methods for preparing cell cultures, although the Cell Ontology may be used to describe the resulting cells if they correspond to an in vivo cell type.

The Cell Ontology

• Initially developed in 2003 by Jonathan Bard, David States, Michael Ashburner, and Seung Rhee.

• First described in 2005, Genome Biology, 6:R21.

• Current version is available at http://obofoundry.org in the file cell.obo.

• Oliver Hoffman of SANBI is nominally “official” curator, although the position of editor for the ontology has been unfilled for 9 months.

• A Cell Ontology Working Group is currently considering ways to improve the ontology from an ontological perspective.

Hematopoietic Cells in CL• Hematopoietic cell types were extensively revised in 2006 as

part of the GO immunology revision to allow for consistency between the two ontologies.

• 80 new cell types introduced (well over 100 cell types in total).

• Is_a parentage provided for all hematopoietically derived cells.

• Develops_from parentage provided for all major hematopoietic lineages.

• The B and T cell lineages were completely revised and greatly expanded.

• Nomenclature now reflects literature better.

Hematopoietic Cells in CL

Dendritic Cells Too!

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

End of Intro

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

Ontology Basics

• [Term]• id: CL:0000084• name: T cell• def: "A type of lymphocyte whose defining

characteristic is the expression of a T cell receptor complex." [GOC:add, ISBN:0781735149]

• exact_synonym: "T lymphocyte" []• exact_synonym: "T-cell" []• exact_synonym: "T-lymphocyte" []• is_a: CL:0000542 ! lymphocyte• relationship: develops_from CL:0000827 ! pro-T

cell

Ontology Basics

Hematopoietic Cells in CL

Upcoming Changes to theCell Ontology

• 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.

• This a work in progress, and we can add terms to the existing ontology as necessary.