Download Diehl - Buffalo Ontology Site

PRO-PO-GO
Alexander Diehl
5-15-13
The Gene Ontology
• Cellular Component
– Subcellular structures, locations, and macromolecular complexes
including protein complexes; examples include nucleus, telomere, and
RNA polymerase II holoenzyme
• Molecular Function
– The tasks performed by individual gene products, such as catalytic or
binding activities, that occur at the molecular level; examples are
carbohydrate binding and ATPase activity.
• Biological Process
– A biological process is series of events accomplished by one or more
ordered assemblies of molecular functions such as mitosis or purine
metabolism.
Cellular Component
Cellular Component
proteasome complex (GO:0000502)
GO:0009506
GO:0009507
GO:0042651
GO:0043036
GO:0000325
GO:0009705
GO:0005777
Numbers of GO Terms
38137 terms
23928 biological_process
3050 cellular_component
9467 molecular_function
1692 obsolete terms
(9/19/12)
The Cell Ontology
• An ontology of cell types built by biologists for the needs of data
annotation and analysis.
• Developed by Jonathan Bard, David States, Michael Ashburner,
and Seung Rhee and first described in 2005, Genome Biology,
6:R21.
• Available as the files cl.obo or cl.owl at http://obofoundry.org or
http://cellontology.org.
• The CL currently has ~2100 cell type terms.
14
CL ontology development
via logical definitions based on cross-products
15
Induced T-regulatory cell
[Term]
id: CL:0000902
name: induced T-regulatory cell
namespace: cell
def: "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with
regulatory function." [GO_REF:0000031, GOC:add, GOC:pam, GOC:tfm, PMID:19464985]
synonym: "adaptive Treg" RELATED []
synonym: "aTreg" RELATED []
synonym: "induced regulatory T cell" EXACT []
synonym: "induced regulatory T lymphocyte" EXACT []
synonym: "induced regulatory T-cell" EXACT []
synonym: "induced regulatory T-lymphocyte" EXACT []
synonym: "induced Treg" EXACT []
synonym: "iTreg" EXACT []
is_a: CL:0000792 {is_inferred="true"} ! CD4-positive, CD25-positive, alpha-beta regulatory T cell
intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell
intersection_of: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell
intersection_of: has_part PR:000001350 ! forkhead box protein P3
intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4
CD56-bright cytokine secreting natural killer cell
cell
is_a
protein
is_a
hematopoietic
cell
biological_process
is_a
is_a
is_a
immunoglobulin gamma Fc
receptor II/III/IV
neural cell adhesion
molecule
leukocyte
is_a
multicellular
organismal
process
lymphocyte
is_a
is_a
cytokine
production
is_a
is_a
neural cell adhesion
molecule
NCAM
is_a
is_a
natural killer
cell
is_a
low affinity
immunoglobulin
gamma Fc region
receptor III
lacks_plasma_membrane_part
SLAM family
member 5
has_plasma_membrane_part
neural cell adhesion
molecule
1
has_high_plasma_membrane_amount
mature natural
killer cell
is_a
is_a
interferon-gamma
production
capable_of
CD56-bright cytokine
secreting
natural killer cell
17
CD56-bright cytokine secreting natural killer cell
[Term]
id: CL:0000938
name: CD56-bright cytokine secreting natural killer cell
namespace: cell
def: "NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function
to secrete interferon-gamma but is not cytotoxic." [GO_REF:0000031, GOC:add, GOC:pam,
GOC:tfm, PMID:19796267]
comment: Markers are associated with human cell types.
synonym: "CD56-bright cytokine secreting NK cell" EXACT []
is_a: CL:0000824 {is_inferred="true"} ! mature natural killer cell
intersection_of: CL:0000824 ! mature natural killer cell
intersection_of: has_high_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1
intersection_of: has_plasma_membrane_part PR:000001319 ! SLAM family member 5
intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc
region receptor III
intersection_of: RO:0002215 GO:0032609 ! capable_of interferon-gamma production
disjoint_from: CL:0000939 ! cytotoxic CD56-dim natural killer cell
small intestine serosal dendritic cell
[Term]
id: CL:0002466
name: small intestine serosal dendritic cell
namespace: cell
def: "A CD11b-positive dendritic cell located in the serosal portion of the small
intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low,
CD103-negative." [GOC:tfm, http://www.immgen.org/index_content.html]
synonym: "DC.11cloSer.SI" EXACT []
is_a: CL:0002465 {is_inferred="true"} ! CD11b-positive dendritic cell
intersection_of: CL:0002465 ! CD11b-positive dendritic cell
intersection_of: has_low_plasma_membrane_amount PR:000001013 ! integrin alphaX
intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein
complex
intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosineprotein phosphatase C
intersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E
No Plant Cells in CL
[Term]
id: CL:0000610
name: plant cell
namespace: cell
comment: This term was obsoleted as it is redundant with PO:0009002 in the Plant Ontology (PO)
is_obsolete: true
consider: PO:0009002
[Term]
id: CL:0002392
name: plant spore
namespace: cell
def: "Obsolete. Use PO:0025017 from Plant Ontology instead. A plant cell that arises through meiosis
and develops into a gametophyte." [GOC:tfm, PO:0025017]
comment: replaced_by: PO:0025017
is_obsolete: true