format-version: 1.0 date: 03:02:2011 12:06 saved-by: sakainoriko2 auto-generated-by: OBO-Edit 1.002 default-namespace: location remark: version: 1.02 [Term] id: ILC:0000001 name: Location [Term] id: ILC:0000002 name: extracellular def: "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." [GO:0005576] exact_synonym: "extracellular region" [GO:0005576] xref_analog: GO:0005576 relationship: part_of ILC:0000001 ! Location [Term] id: ILC:0000003 name: plasma membrane def: "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." [GO:0005886] exact_synonym: "cell membrane" [] exact_synonym: "cytoplasmic membrane" [GO:0005586] exact_synonym: "plasmalemma" [GO:0005586] narrow_synonym: "bacterial inner membrane" [GO:0005586] broad_synonym: "juxtamembrane" [GO:0005586] xref_analog: GO:0005886 relationship: part_of ILC:0000032 ! cell [Term] id: ILC:0000004 name: plasma membrane (extrinsic to external side of plasma membrane) def: "Loosely bound to the surface of the plasma membrane that faces away from the cytoplasm,but not integrated into the hydrophobic region." [GO:0031232] xref_analog: GO:0031232 is_a: ILC:0000049 ! plasma membrane (external side of plasma membrane) [Term] id: ILC:0000005 name: membrane raft (extrinsic to external side of membrane ) xref_analog: GO:0045121 relationship: part_of ILC:0000004 ! plasma membrane (extrinsic to external side of plasma membrane) relationship: part_of ILC:0000013 ! membrane raft [Term] id: ILC:0000006 name: caveola (extrinsic to external side of membrane ) xref_analog: GO:0016599 relationship: part_of ILC:0000004 ! plasma membrane (extrinsic to external side of plasma membrane) relationship: part_of ILC:0000014 ! caveola [Term] id: ILC:0000007 name: plasma membrane (extrinsic to internal side of plasma membrane) def: "Loosely bound to the surface of the plasma membrane that faces the cytoplasm, but not integrated into the hydrophobic region." [GO:0031234] xref_analog: GO:0031234 is_a: ILC:0000048 ! plasma membrane (internal side of plasma membrane) [Term] id: ILC:0000008 name: membrane raft (extrinsic to internal side of membrane) xref_analog: GO:0045121 relationship: part_of ILC:0000007 ! plasma membrane (extrinsic to internal side of plasma membrane) relationship: part_of ILC:0000013 ! membrane raft [Term] id: ILC:0000009 name: caveola (extrinsic to internal side of membrane) xref_analog: GO:0016599 relationship: part_of ILC:0000007 ! plasma membrane (extrinsic to internal side of plasma membrane) relationship: part_of ILC:0000014 ! caveola [Term] id: ILC:0000010 name: plasma membrane (integral to plasma membrane) def: "Penetrating at least one phospholipid bilayer of a plasma membrane. Also refers to the state of being buried in the bilayer with no exposure outside the bilayer." [GO:0005887] xref_analog: GO:0005887 relationship: part_of ILC:0000003 ! plasma membrane [Term] id: ILC:0000011 name: membrane raft (integral to membrane) xref_analog: GO:0045121 relationship: part_of ILC:0000010 ! plasma membrane (integral to plasma membrane) relationship: part_of ILC:0000013 ! membrane raft [Term] id: ILC:0000012 name: caveola (integral to membrane) xref_analog: GO:0016599 relationship: part_of ILC:0000010 ! plasma membrane (integral to plasma membrane) relationship: part_of ILC:0000014 ! caveola [Term] id: ILC:0000013 name: membrane raft def: "Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.\n\n\n" [GO:0045121] exact_synonym: "lipid raft" [GO:0045121] xref_analog: GO:0045121 relationship: part_of ILC:0000032 ! cell [Term] id: ILC:0000014 name: caveola def: "A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include any of the minute pits or incuppings of the cell membrane formed during pinocytosis. Such caveolae may be pinched off to form free vesicles within the cytoplasm." [GO:0005901] exact_synonym: "caveolae" [GO:0005901] xref_analog: GO:0005901 is_a: ILC:0000013 ! membrane raft relationship: part_of ILC:0000003 ! plasma membrane [Term] id: ILC:0000015 name: cytosol def: "That part of the cytoplasm that does not contain membranous or particulate subcellular components." [GO:0005829] xref_analog: GO:0005829 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000016 name: Golgi apparatus def: "A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions." [GO:0005794] comment: Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon. exact_synonym: "Golgi complex" [GO:0005794] narrow_synonym: "Golgi ribbon" [GO:0005794] xref_analog: GO:0005794 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000017 name: Golgi trans face def: "The concave side of the Golgi apparatus, from which secretory vesicles emerge." [GO:0005802] related_synonym: "maturing face" [GO:0005802] exact_synonym: "TGN" [] exact_synonym: "trans-Golgi network" [GO:0005802] xref_analog: GO:0005802 relationship: part_of ILC:0000016 ! Golgi apparatus [Term] id: ILC:0000018 name: mitochondria def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [GO:0005739] xref_analog: GO:0005739 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000019 name: nucleus def: "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." [GO:0005634] xref_analog: GO:0005634 relationship: part_of ILC:0000032 ! cell [Term] id: ILC:0000020 name: chromatin def: "The ordered and organized complex of DNA and protein that forms the chromosome." [GO:0000785] xref_analog: GO:0000785 relationship: part_of ILC:0000019 ! nucleus [Term] id: ILC:0000021 name: nucleoplasm def: "That part of the nuclear content other than the chromosomes or the nucleolus." [GO:0005654] xref_analog: GO:0005654 relationship: part_of ILC:0000019 ! nucleus [Term] id: ILC:0000022 name: nuclear membrane def: "Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space." [GO:0031965] xref_analog: GO:0031965 relationship: part_of ILC:0000019 ! nucleus [Term] id: ILC:0000023 name: nuclear pore def: "Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined." [GO:0005643] exact_synonym: "NPC" [GO:0005643] exact_synonym: "nuclear pore complex" [GO:0005643] narrow_synonym: "nuclear pore membrane protein " [GO:0005643] xref_analog: GO:0005643 relationship: part_of ILC:0000022 ! nuclear membrane [Term] id: ILC:0000024 name: endoplasmic reticulum def: "The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached)." [GO:0005783] exact_synonym: "ER" [GO:0005783] xref_analog: GO:0005783 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000025 name: endoplasmic reticulum ( extrinsic to external side of membrane ) def: "Loosely bound to one surface of the endoplasmic reticulum membrane, but not integrated into the hydrophobic region." [GO:0042406] exact_synonym: "extrinsic to ER membrane" [GO:0042406] xref_analog: GO:0042406 relationship: part_of ILC:0000015 ! cytosol relationship: part_of ILC:0000041 ! endoplasmic reticulum(membrane) [Term] id: ILC:0000026 name: endoplasmic reticulum ( extrinsic to internal side of membrane ) def: "Loosely bound to one surface of the endoplasmic reticulum membrane, but not integrated into the hydrophobic region." [GO:0042406] exact_synonym: "extrinsic to ER membrane" [GO:0042406] xref_analog: GO:0042406 relationship: part_of ILC:0000041 ! endoplasmic reticulum(membrane) [Term] id: ILC:0000027 name: endoplasmic reticulum ( integral to membrane ) def: "Penetrating at least one phospholipid bilayer of an endoplasmic reticulum membrane. Also refers to the state of being buried in the bilayer with no exposure outside the bilayer." [GO:0030176] exact_synonym: "ER integral membrane protein" [GO:0030176] exact_synonym: "integral to ER membrane" [GO:0030176] xref_analog: GO:0030176 relationship: part_of ILC:0000041 ! endoplasmic reticulum(membrane) [Term] id: ILC:0000028 name: endoplasmic reticulum ( inner space ) def: "The volume enclosed by the membranes of the endoplasmic reticulum." [GO:0005788] exact_synonym: "cisternal lumen" [GO:0005788] exact_synonym: "endoplasmic reticulum cisterna" [] exact_synonym: "ER cisterna" [] exact_synonym: "ER lumen" [GO:0005788] xref_analog: GO:0005788 relationship: part_of ILC:0000024 ! endoplasmic reticulum [Term] id: ILC:0000029 name: neighbour cell surface def: "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." [GO:0043230] xref_analog: GO:0043230 is_obsolete: true [Term] id: ILC:0000030 name: extracellular matrix(in animals) def: "A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as in plants)." [GO:0031012] exact_synonym: "ECM" [] exact_synonym: "ecm" [] xref_analog: GO:0031012 relationship: part_of ILC:0000002 ! extracellular [Term] id: ILC:0000031 name: cytoskeleton def: "Any of the various filamentous elements within the cytoplasm of eukaryotic cells that remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, and the microtrabecular lattice. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.\n\n\n" [GO:0005856] xref_analog: GO:0005856 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000032 name: cell def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GO:0005623] xref_analog: GO:0005623 relationship: part_of ILC:0000001 ! Location [Term] id: ILC:0000033 name: endosome def: "A membrane-bound organelle that carries materials newly ingested by endocytosis. It passes many of the materials to lysosomes for degradation." [GO:0005768] xref_analog: GO:0005768 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000034 name: endosome membrane def: "The lipid bilayer surrounding an endosome." [GO:0010008] xref_analog: GO:0010008 relationship: part_of ILC:0000033 ! endosome [Term] id: ILC:0000035 name: neighbour cell endoplasmic reticulum def: "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." [GO:0043230] xref_analog: GO:0043230 is_obsolete: true [Term] id: ILC:0000036 name: cytoplasm def: "All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." [GO:0005737] xref_analog: GO:0005737 relationship: part_of ILC:0000032 ! cell [Term] id: ILC:0000037 name: mitochondrial intermembrane space def: "The space between the mitochondrial outer membrane and inner membrane." [GO:0005758] xref_analog: GO:0005758 relationship: part_of ILC:0000018 ! mitochondria [Term] id: ILC:0000038 name: mitochondrial outer membrane def: "The membrane on the outer surface of the mitochondrion, interfacing with the cell cytoplasm." [GO:0005741] xref_analog: GO:0005741 relationship: part_of ILC:0000018 ! mitochondria [Term] id: ILC:0000039 name: plasma membrane (intrinsic to external side of plasma membrane) def: "Located in the plasma membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane, with the bulk of the gene product located on the side opposite to the side that faces the cytoplasm." [GO:0031233] xref_analog: GO:0031233 is_a: ILC:0000049 ! plasma membrane (external side of plasma membrane) [Term] id: ILC:0000040 name: plasma membrane (intrinsic to internal side of plasmamembrane) def: "Located in the plasma membrane such that some covalently attached portion of the gene product spans or is embedded in one or both leaflets of the membrane, with the bulk of the gene product located on the side that faces the cytoplasm." [GO:0031235] xref_analog: GO:0031235 is_a: ILC:0000048 ! plasma membrane (internal side of plasma membrane) [Term] id: ILC:0000041 name: endoplasmic reticulum(membrane) def: "The lipid bilayer surrounding the endoplasmic reticulum." [GO:0005789] exact_synonym: " ER membrane" [GO:0005789] relationship: part_of ILC:0000024 ! endoplasmic reticulum [Term] id: ILC:0000042 name: nucleolus def: "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." [GO:0005730] xref_analog: GO:0005730 relationship: part_of ILC:0000019 ! nucleus [Term] id: ILC:0000043 name: peroxisome def: "A small, membrane-bounded organelle that uses dioxygen (O2) to oxidize organic molecules; contains some enzymes that produce and others that degrade hydrogen peroxide (H2O2)." [GO:0005777] broad_synonym: "peroxisome vesicle" [GO:0005777] xref_analog: GO:0005777 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000044 name: glycogen granule def: "Cytoplasmic bead-like structures of animal cells, visible by electron microscope. Each granule is a functional unit with the biosynthesis and catabolism of glycogen being catalyzed by enzymes bound to the granule surface." [GO:0042587] exact_synonym: "glycogen particle" [GO:0042587] xref_analog: GO:0042587 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000045 name: lipid particle def: "Any particle of coalesced lipids in the cytoplasm of a cell. May include associated proteins." [GO:0005811] comment: Note that this term does not refer to vesicle, but instead to structures in which lipids do not necessarily form bilayers. exact_synonym: "adiposome" [] exact_synonym: "lipid body" [] exact_synonym: "lipid droplet" [GO:0005811] xref_analog: GO:0005811 relationship: part_of ILC:0000036 ! cytoplasm [Term] id: ILC:0000046 name: extracellular matrix(in plants) def: "A structure lying external to one or more cells, which provides structural support for cells or tissues; may be completely external to the cell (as in animals) or be part of the cell (as in plants)." [GO:0031012] exact_synonym: "ECM" [] exact_synonym: "ecm" [] xref_analog: GO:0031012 relationship: part_of ILC:0000032 ! cell [Term] id: ILC:0000047 name: cell wall def: "The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan." [GO:0005618] xref_analog: GO:0005618 relationship: part_of ILC:0000046 ! extracellular matrix(in plants) [Term] id: ILC:0000048 name: plasma membrane (internal side of plasma membrane) def: "The side of the plasma membrane that faces the cytoplasm." [GO:0009898] broad_synonym: "juxtamembrane" [GO:0009898] xref_analog: GO:0009898 relationship: part_of ILC:0000003 ! plasma membrane relationship: part_of ILC:0000015 ! cytosol [Term] id: ILC:0000049 name: plasma membrane (external side of plasma membrane) def: "The side of the plasma membrane that is opposite to the side that faces the cytoplasm." [GO:0009897] exact_synonym: "outer surface of cytoplasmic membrane" [GO:0009897] broad_synonym: "juxtamembrane" [GO:0009897] xref_analog: GO:0009897 relationship: part_of ILC:0000002 ! extracellular relationship: part_of ILC:0000003 ! plasma membrane [Term] id: ILC:0000050 name: cilium def: "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." [GO:0005929] xref_analog: GO:0005929 relationship: part_of ILC:0000032 ! cell [Term] id: ILC:0000051 name: cilium membrane def: "The portion of the plasma membrane surrounding a cilium." [GO:0060170] xref_analog: GO:0060170 relationship: part_of ILC:0000003 ! plasma membrane relationship: part_of ILC:0000050 ! cilium [Term] id: ILC:0000052 name: cilium membrane (integral to membrane) relationship: part_of ILC:0000010 ! plasma membrane (integral to plasma membrane) relationship: part_of ILC:0000051 ! cilium membrane [Typedef] id: part_of name: part of is_transitive: true