Transcript A_Diehl_Cell_Ontology_Workshop_Introduction

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
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[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
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[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
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[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
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[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
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[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
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[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
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[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 the
Cell 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.