PRO-PO-GO Alexander Diehl

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: )

GO: GO: GO: GO: GO: GO: GO:

Numbers of GO Terms terms biological_process 3050 cellular_component 9467 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 or 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: 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: , GOC:add, GOC:pam, GOC:tfm, PMID: ] 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: {is_inferred="true"} ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: CL: ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: develops_from CL: ! activated CD4-positive, alpha-beta T cell intersection_of: has_part PR: ! forkhead box protein P3 intersection_of: has_plasma_membrane_part PR: ! cytotoxic T-lymphocyte protein 4

17 CD56-bright cytokine secreting natural killer cell

[Term] id: CL: 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: , GOC:add, GOC:pam, GOC:tfm, PMID: ] comment: Markers are associated with human cell types. synonym: "CD56-bright cytokine secreting NK cell" EXACT [] is_a: CL: {is_inferred="true"} ! mature natural killer cell intersection_of: CL: ! mature natural killer cell intersection_of: has_high_plasma_membrane_amount PR: ! neural cell adhesion molecule 1 intersection_of: has_plasma_membrane_part PR: ! SLAM family member 5 intersection_of: lacks_plasma_membrane_part PR: ! low affinity immunoglobulin gamma Fc region receptor III intersection_of: RO: GO: ! capable_of interferon-gamma production disjoint_from: CL: ! cytotoxic CD56-dim natural killer cell

small intestine serosal dendritic cell [Term] id: CL: 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, synonym: "DC.11cloSer.SI" EXACT [] is_a: CL: {is_inferred="true"} ! CD11b-positive dendritic cell intersection_of: CL: ! CD11b-positive dendritic cell intersection_of: has_low_plasma_membrane_amount PR: ! integrin alpha- X intersection_of: has_plasma_membrane_part GO: ! MHC class II protein complex intersection_of: has_plasma_membrane_part PR: ! receptor-type tyrosine- protein phosphatase C intersection_of: lacks_plasma_membrane_part PR: ! integrin alpha-E

No Plant Cells in CL [Term] id: CL: name: plant cell namespace: cell comment: This term was obsoleted as it is redundant with PO: in the Plant Ontology (PO) is_obsolete: true consider: PO: [Term] id: CL: name: plant spore namespace: cell def: "Obsolete. Use PO: from Plant Ontology instead. A plant cell that arises through meiosis and develops into a gametophyte." [GOC:tfm, PO: ] comment: replaced_by: PO: is_obsolete: true