# Spatial compartment model for GO-CAM location QC. # # Used by ai_gene_review.gocam_compartments to check that the `occurs_in` # locations of GO-CAM activities can be placed in a cell, and that causally # connected activities sit in the same or adjacent compartments. # # compartments: a pairwise-disjoint set of spatial regions. Together they are # intended to cover a cell (eukaryote, Gram-negative bacterium, plant) and its # surroundings. Each compartment has one or more GO `anchors`. A cellular # component term resolves to a compartment when the anchor is the term itself # or one of its is_a / part_of ancestors. Where several anchors match, the most # specific wins (an anchor that is an ancestor of another matching anchor is # dropped), so lysosomal lumen resolves to LYSOSOME_LUMEN, not VACUOLE_LUMEN. # `kind` is membrane (a bilayer or envelope) or space (an aqueous or bulk # region). Two membranes that border the same space are BRIDGED rather than # NONADJACENT: their proteins can meet across it at a contact site or when a # vesicle docks, so such edges are reported separately and at lower priority. # # unions: GO terms that span several compartments (cytoplasm = cytosol plus the # organelles in it). A term that reaches one of these, but no compartment # anchor, is COARSE: it narrows the location to the listed compartments without # choosing one. # # adjacency: undirected pairs of compartments that share a boundary, so that an # activity in one can act directly on a molecule in the other (a membrane and # the aqueous space on either side of it). Two lumens are never adjacent to # each other, and the cytosol is not adjacent to the nucleoplasm: material # crosses the nuclear envelope only by transport through the pore. # # context_hints: terms that GO does not place in any compartment (chromatin, # cytoskeleton) but whose usual location is obvious to a biologist. These are # reported as hints next to an UNRESOLVED finding. They are never used to # resolve the term, because the point of the check is that the model does not # say where the activity is. A hint applies to the term and its descendants; # the most specific matching hint wins. Cell-type terms (CL:) used as # occurs_in get a fixed hint in code. compartments: EXTRACELLULAR: kind: space label: extracellular region anchors: [GO:0005576] PLASMA_MEMBRANE: kind: membrane label: plasma membrane anchors: [GO:0005886] CYTOSOL: kind: space label: cytosol anchors: [GO:0005829] NUCLEAR_ENVELOPE: kind: membrane label: nuclear envelope anchors: [GO:0005635] NUCLEAR_LUMEN: kind: space label: nuclear lumen anchors: [GO:0031981] MITOCHONDRIAL_OUTER_MEMBRANE: kind: membrane label: mitochondrial outer membrane anchors: [GO:0005741] MITOCHONDRIAL_INTERMEMBRANE_SPACE: kind: space label: mitochondrial intermembrane space anchors: [GO:0005758] MITOCHONDRIAL_INNER_MEMBRANE: kind: membrane label: mitochondrial inner membrane anchors: [GO:0005743] MITOCHONDRIAL_MATRIX: kind: space label: mitochondrial matrix anchors: [GO:0005759] ER_MEMBRANE: kind: membrane label: endoplasmic reticulum membrane anchors: [GO:0005789] ER_LUMEN: kind: space label: endoplasmic reticulum lumen anchors: [GO:0005788] GOLGI_MEMBRANE: kind: membrane label: Golgi membrane anchors: [GO:0000139] GOLGI_LUMEN: kind: space label: Golgi lumen anchors: [GO:0005796] ENDOSOME_MEMBRANE: kind: membrane label: endosome membrane anchors: [GO:0010008] ENDOSOME_LUMEN: kind: space label: endosome lumen anchors: [GO:0031904] LYSOSOME_MEMBRANE: kind: membrane label: lysosomal membrane anchors: [GO:0005765] LYSOSOME_LUMEN: kind: space label: lysosomal lumen anchors: [GO:0043202] VACUOLE_MEMBRANE: kind: membrane label: vacuolar membrane anchors: [GO:0005774] VACUOLE_LUMEN: kind: space label: vacuolar lumen anchors: [GO:0005775] PEROXISOME_MEMBRANE: kind: membrane label: peroxisomal membrane anchors: [GO:0005778] PEROXISOME_MATRIX: kind: space label: peroxisomal matrix anchors: [GO:0005782] VESICLE_MEMBRANE: kind: membrane label: cytoplasmic vesicle membrane anchors: [GO:0030659] VESICLE_LUMEN: kind: space label: cytoplasmic vesicle lumen anchors: [GO:0060205] CHLOROPLAST_ENVELOPE: kind: membrane label: chloroplast envelope anchors: [GO:0009941] CHLOROPLAST_STROMA: kind: space label: chloroplast stroma anchors: [GO:0009570] THYLAKOID_MEMBRANE: kind: membrane label: thylakoid membrane anchors: [GO:0042651] THYLAKOID_LUMEN: kind: space label: thylakoid lumen anchors: [GO:0031977] PERIPLASM: kind: space label: periplasmic space anchors: [GO:0042597] CELL_OUTER_MEMBRANE: kind: membrane label: cell outer membrane anchors: [GO:0009279] LIPID_DROPLET: kind: space label: lipid droplet anchors: [GO:0005811] unions: GO:0005737: label: cytoplasm members: [CYTOSOL, MITOCHONDRIAL_OUTER_MEMBRANE, MITOCHONDRIAL_INTERMEMBRANE_SPACE, MITOCHONDRIAL_INNER_MEMBRANE, MITOCHONDRIAL_MATRIX, ER_MEMBRANE, ER_LUMEN, GOLGI_MEMBRANE, GOLGI_LUMEN, ENDOSOME_MEMBRANE, ENDOSOME_LUMEN, LYSOSOME_MEMBRANE, LYSOSOME_LUMEN, VACUOLE_MEMBRANE, VACUOLE_LUMEN, PEROXISOME_MEMBRANE, PEROXISOME_MATRIX, VESICLE_MEMBRANE, VESICLE_LUMEN, CHLOROPLAST_ENVELOPE, CHLOROPLAST_STROMA, THYLAKOID_MEMBRANE, THYLAKOID_LUMEN, LIPID_DROPLET] GO:0005634: label: nucleus members: [NUCLEAR_ENVELOPE, NUCLEAR_LUMEN] GO:0005739: label: mitochondrion members: [MITOCHONDRIAL_OUTER_MEMBRANE, MITOCHONDRIAL_INTERMEMBRANE_SPACE, MITOCHONDRIAL_INNER_MEMBRANE, MITOCHONDRIAL_MATRIX] GO:0005783: label: endoplasmic reticulum members: [ER_MEMBRANE, ER_LUMEN] GO:0005794: label: Golgi apparatus members: [GOLGI_MEMBRANE, GOLGI_LUMEN] GO:0005768: label: endosome members: [ENDOSOME_MEMBRANE, ENDOSOME_LUMEN] GO:0005764: label: lysosome members: [LYSOSOME_MEMBRANE, LYSOSOME_LUMEN] GO:0005773: label: vacuole members: [VACUOLE_MEMBRANE, VACUOLE_LUMEN, LYSOSOME_MEMBRANE, LYSOSOME_LUMEN] GO:0005777: label: peroxisome members: [PEROXISOME_MEMBRANE, PEROXISOME_MATRIX] GO:0031410: label: cytoplasmic vesicle members: [VESICLE_MEMBRANE, VESICLE_LUMEN, ENDOSOME_MEMBRANE, ENDOSOME_LUMEN] GO:0009507: label: chloroplast members: [CHLOROPLAST_ENVELOPE, CHLOROPLAST_STROMA, THYLAKOID_MEMBRANE, THYLAKOID_LUMEN] GO:0009986: label: cell surface members: [PLASMA_MEMBRANE, EXTRACELLULAR, CELL_OUTER_MEMBRANE] GO:0016020: label: membrane members: [PLASMA_MEMBRANE, NUCLEAR_ENVELOPE, MITOCHONDRIAL_OUTER_MEMBRANE, MITOCHONDRIAL_INNER_MEMBRANE, ER_MEMBRANE, GOLGI_MEMBRANE, ENDOSOME_MEMBRANE, LYSOSOME_MEMBRANE, VACUOLE_MEMBRANE, PEROXISOME_MEMBRANE, VESICLE_MEMBRANE, CHLOROPLAST_ENVELOPE, THYLAKOID_MEMBRANE, CELL_OUTER_MEMBRANE] GO:0071944: label: cell periphery members: [PLASMA_MEMBRANE, CYTOSOL, EXTRACELLULAR, PERIPLASM, CELL_OUTER_MEMBRANE] adjacency: - [EXTRACELLULAR, PLASMA_MEMBRANE] - [PLASMA_MEMBRANE, CYTOSOL] - [CYTOSOL, NUCLEAR_ENVELOPE] - [NUCLEAR_ENVELOPE, NUCLEAR_LUMEN] - [CYTOSOL, MITOCHONDRIAL_OUTER_MEMBRANE] - [MITOCHONDRIAL_OUTER_MEMBRANE, MITOCHONDRIAL_INTERMEMBRANE_SPACE] - [MITOCHONDRIAL_INTERMEMBRANE_SPACE, MITOCHONDRIAL_INNER_MEMBRANE] - [MITOCHONDRIAL_INNER_MEMBRANE, MITOCHONDRIAL_MATRIX] - [CYTOSOL, ER_MEMBRANE] - [ER_MEMBRANE, ER_LUMEN] # the outer nuclear membrane is continuous with the ER membrane, and the # perinuclear space with the ER lumen - [NUCLEAR_ENVELOPE, ER_MEMBRANE] - [NUCLEAR_ENVELOPE, ER_LUMEN] - [CYTOSOL, GOLGI_MEMBRANE] - [GOLGI_MEMBRANE, GOLGI_LUMEN] - [CYTOSOL, ENDOSOME_MEMBRANE] - [ENDOSOME_MEMBRANE, ENDOSOME_LUMEN] - [CYTOSOL, LYSOSOME_MEMBRANE] - [LYSOSOME_MEMBRANE, LYSOSOME_LUMEN] - [CYTOSOL, VACUOLE_MEMBRANE] - [VACUOLE_MEMBRANE, VACUOLE_LUMEN] - [CYTOSOL, PEROXISOME_MEMBRANE] - [PEROXISOME_MEMBRANE, PEROXISOME_MATRIX] - [CYTOSOL, VESICLE_MEMBRANE] - [VESICLE_MEMBRANE, VESICLE_LUMEN] - [CYTOSOL, CHLOROPLAST_ENVELOPE] - [CHLOROPLAST_ENVELOPE, CHLOROPLAST_STROMA] - [CHLOROPLAST_STROMA, THYLAKOID_MEMBRANE] - [THYLAKOID_MEMBRANE, THYLAKOID_LUMEN] # Gram-negative envelope - [PLASMA_MEMBRANE, PERIPLASM] - [PERIPLASM, CELL_OUTER_MEMBRANE] - [CELL_OUTER_MEMBRANE, EXTRACELLULAR] # lipid droplets bud from the ER membrane and face the cytosol - [CYTOSOL, LIPID_DROPLET] - [ER_MEMBRANE, LIPID_DROPLET] context_hints: GO:0000785: label: chromatin usual: NUCLEAR_LUMEN better_term: {id: GO:0000228, label: nuclear chromosome} note: GO places chromatin under chromosome, which is not part of the nucleus because prokaryotic chromosomes exist. GO:0005694: label: chromosome usual: NUCLEAR_LUMEN better_term: {id: GO:0000228, label: nuclear chromosome} GO:0005856: label: cytoskeleton usual: CYTOSOL GO:0005874: label: microtubule usual: CYTOSOL GO:0015629: label: actin cytoskeleton usual: CYTOSOL GO:0005813: label: centrosome usual: CYTOSOL GO:0032991: label: protein-containing complex note: a complex term says nothing about where the complex is. GO:0005816: label: spindle pole body usual: NUCLEAR_ENVELOPE note: the fungal spindle pole body is embedded in the nuclear envelope. GO:0098857: label: membrane microdomain usual: PLASMA_MEMBRANE GO:0044232: label: organelle membrane contact site note: a contact site joins two membranes across the cytosol; name the membrane the activity is in. GO:0030054: label: cell junction note: a junction spans plasma membrane, cytosol and extracellular region; name the side the activity is on. GO:0032153: label: cell division site note: a region of the cell periphery, not a compartment. GO:0044217: label: other organism part note: a location in another organism (host or symbiont); the compartment model covers one cell, so edges into it cross organisms. GO:0005575: label: cellular_component note: the root term carries no location.