PRO-PO-GO

Alexander Diehl5-15-13

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:0009507

GO:0042651

GO:0009506

GO:0043036

GO:0000325GO:0009705

GO:0005777

Numbers of GO Terms

38137 terms23928 biological_process3050 cellular_component9467 molecular_function

1692 obsolete terms(9/19/12)

14

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.

15

CL ontology development via logical definitions based on cross-products

Induced T-regulatory cell[Term]id: CL:0000902name: induced T-regulatory cellnamespace: celldef: "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 cellintersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cellintersection_of: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cellintersection_of: has_part PR:000001350 ! forkhead box protein P3intersection_of: has_plasma_membrane_part PR:000001852 ! cytotoxic T-lymphocyte protein 4

17

CD56-bright cytokine secreting natural killer cell

CD56-bright cytokine secreting natural killer cell

[Term]id: CL:0000938name: CD56-bright cytokine secreting natural killer cellnamespace: celldef: "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 cellintersection_of: CL:0000824 ! mature natural killer cellintersection_of: has_high_plasma_membrane_amount PR:000001024 ! neural cell adhesion molecule 1intersection_of: has_plasma_membrane_part PR:000001319 ! SLAM family member 5intersection_of: lacks_plasma_membrane_part PR:000001483 ! low affinity immunoglobulin gamma Fc

region receptor IIIintersection_of: RO:0002215 GO:0032609 ! capable_of interferon-gamma productiondisjoint_from: CL:0000939 ! cytotoxic CD56-dim natural killer cell

small intestine serosal dendritic cell

[Term]id: CL:0002466name: small intestine serosal dendritic cellnamespace: celldef: "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 cellintersection_of: CL:0002465 ! CD11b-positive dendritic cellintersection_of: has_low_plasma_membrane_amount PR:000001013 ! integrin alpha-Xintersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complexintersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-

protein phosphatase Cintersection_of: lacks_plasma_membrane_part PR:000001010 ! integrin alpha-E

No Plant Cells in CL[Term]id: CL:0000610name: plant cellnamespace: cellcomment: This term was obsoleted as it is redundant with PO:0009002 in the Plant Ontology (PO)is_obsolete: trueconsider: PO:0009002

[Term]id: CL:0002392name: plant sporenamespace: celldef: "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:0025017is_obsolete: true