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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
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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 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 SeungRhee and first described in 2005, Genome Biology, 6:R21. • Available as the files cl.obo or cl.owlat http://obofoundry.org or http://cellontology.org. • The CL currently has ~2100 cell type terms.
CL ontology development via logical definitions based on cross-products
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 [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 serosaldendritic cell [Term] id: CL:0002466 name: small intestine serosaldendritic 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 alpha-X intersection_of: has_plasma_membrane_part GO:0042613 ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR:000001006 ! receptor-type tyrosine-protein 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