ontology: go/extensions/x-cc-self

!default-namespace: cellular_component_xp_self
! 2008-12-21: CJM - fixed some of the problematic lumen_of relations
! 2009-10-05

! TODO: See https://sourceforge.net/tracker/?func=detail&atid=440764&aid=2039153&group_id=36855
! not really a vacuole
![Term]
!id: GO:0020003 ! parasitophorous vacuole
!intersection_of: GO:0005773 ! vacuole
!intersection_of: part_of obol:parasite ! parasite

! TODO: define this such that it does not include plasma membrane, cell wall etc
![Term]
!id: GO:0005576 ! extracellular region [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."]
!intersection_of: GO:0005575 ! cellular_component
!intersection_of: bounds GO:0005623 ! cell

! This needs fixing - it's a receptor *for* SRP, not part_of SRP.
![Term]
!id: GO:0005785 ! signal recognition particle receptor complex
!intersection_of: GO:0043235 ! receptor complex
!intersection_of: part_of GO:0048500 ! signal recognition particle

! awaiting overhaul of viral terms
![Term]
!id: GO:0055036 ! virion membrane
!intersection_of: GO:0016020 ! membrane
!intersection_of: boundary_part_of GO:0019012 ! virion

! http://sourceforge.net/tracker/index.php?func=detail&aid=2097130&group_id=36855&atid=440764
! I've left this out of the checked set because there's no way to currently describe it uniquely with xp. Need to be able to indicate it's made of membranous material, no other proteins which are also po membrane.
![Term]
!id: GO:0009925 ! basal plasma membrane [DEF: "Part of the plasma membrane at the basal end of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis."]
!intersection_of: GO:0044459 ! plasma membrane part
!intersection_of: part_of GO:0045178 ! basal part of cell

! http://sourceforge.net/tracker/index.php?func=detail&aid=2097130&group_id=36855&atid=440764
! I've left this out of the checked set because there's no way to currently describe it uniquely with xp. Need to be able to indicate it's made of membranous material, no other proteins which are also po membrane.
![Term]
!id: GO:0016324 ! apical plasma membrane [DEF: "Part of the plasma membrane at the apical end of the cell."]
!intersection_of: GO:0044459 ! plasma membrane part
!intersection_of: part_of GO:0045177 ! apical part of cell

! intra?
![Term]
!id: GO:0005780 ! extrinsic to intraperoxisomal membrane
!intersection_of: GO:0005575 ! cellular_component
!intersection_of: extrinsic_to GO:0005789 ! endoplasmic reticulum membrane

! todo
![Term]
!id: GO:0005938 ! cell cortex [DEF: "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins."]
!intersection_of: GO:0044444 ! cytoplasmic part
!intersection_of: adjacent_to GO:0005886 ! plasma membrane

! too permissive?
![Term]
!id: GO:0005801 ! cis-Golgi network
!intersection_of: GO:0044431 ! Golgi apparatus part
!intersection_of: adjacent_to GO:0005783 ! endoplasmic reticulum

!! ??? membrane or envelope or something else..?
!! http://sourceforge.net/tracker/index.php?func=detail&aid=2019054&group_id=36855&atid=440764
!!That is actually the case -- it's got lots of lipids, like a membrane, but
!!isn't a lipid bilayer and therefore doesn't fit GO's definition of
!!membrane. It also doesn't quite fit the definition of 'envelope', so I'm
!!willing to consider renaming it if we can come up with something sensible.
![Term]
!id: GO:0033105 ! chlorosome envelope
!intersection_of: GO:0031975 ! envelope
!intersection_of: boundary_part_of GO:0046858 ! chlorosome

!Bit tricky this one (see def) - attaches_to Golgi complex?
!!Def: Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
![Term]
!id: GO:0005798 ! Golgi-associated vesicle
!intersection_of: GO:0031988 ! membrane-bounded vesicle
!intersection_of: part_of GO:0005794 ! Golgi apparatus

!Not N&S - also true of other filopodium parts e.g. filopodium membrane. I think we'd need a 'cell projection tip' term.
![Term]
!id: GO:0032433 ! filopodium tip
!intersection_of: GO:0044463 ! cell projection part
!intersection_of: part_of GO:0030175 ! filopodium

!This is necessary but not sufficient - there are other pore complexes in the mitochondrial envelope.
![Term]
!id: GO:0005757 ! mitochondrial permeability transition pore complex
!intersection_of: GO:0046930 ! pore complex
!intersection_of: part_of GO:0005740 ! mitochondrial envelope

![Term]
!id: GO:0005615 ! extracellular space
!intersection_of: GO:0005575 ! cellular_component
!intersection_of: bounds GO:0005886 ! plasma membrane

![Term]
!id: GO:0005618 ! cell wall
!intersection_of: GO:0030312 ! external encapsulating structure
!intersection_of: boundary_part_of GO:0005623 ! cell
!intersection_of: bounds GO:0005886 ! plasma membrane

![Term]
!id: GO:0005930 ! axoneme [DEF: "The bundle of microtubules and associated proteins that forms the core of cilia and flagella in eukaryotic cells and is responsible for their movements."]
!intersection_of: part_of
!intersection_of: has_part GO:0005874 ! microtubule

![Term]
!id: GO:0009898 ! internal side of plasma membrane [DEF: "The side of the plasma membrane that faces the cytoplasm."]
!relationship: adjacent_to GO:0005737 ! cytoplasm

![Term]
!id: GO:0043204 ! perikaryon
!intersection_of: GO:0005575 ! cellular_component
!intersection_of: part_of GO:0043025 ! cell soma
!intersection_of: shares_outer_boundary_with GO:0043025 ! cell soma
!intersection_of: boundary_part_of ! GO:0005634 nucleus

![Term]
!id: GO:0043228 ! non-membrane-bounded organelle
!intersection_of: GO:0043226 ! organelle
!intersection_of: not_bounded_by GO:0016020 ! membrane

![Term]
!id: GO:0043657 ! host cell
!intersection_of: GO:0044421 ! extracellular region part
!intersection_of: part_of GO:0018995 ! host

[Term]
id: GO:0000137 ! Golgi cis cisterna [DEF: "The Golgi cisterna closest to the endoplasmic reticulum; the first processing compartment through which proteins pass after export from the ER."]
intersection_of: GO:0031985 ! Golgi cisterna
intersection_of: adjacent_to GO:0005783 ! endoplasmic reticulum

[Term]
id: GO:0000138 ! Golgi trans cisterna [DEF: "The Golgi cisterna farthest from the endoplasmic reticulum; the final processing compartment through which proteins pass before exiting the Golgi apparatus; the compartment in which N-linked protein glycosylation is completed."]
intersection_of: GO:0031985 ! Golgi cisterna
intersection_of: outwards_of GO:0005797 ! Golgi medial cisterna

[Term]
id: GO:0000139 ! Golgi membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005794 ! Golgi apparatus

[Term]
id: GO:0000306 ! extrinsic to vacuolar membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005774 ! vacuolar membrane

[Term]
id: GO:0000328 ! fungal-type vacuole lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: part_of GO:0000324 ! fungal-type vacuole
intersection_of: bounded_by GO:0000329 ! fungal-type vacuole membrane

[Term]
id: GO:0000329 ! fungal-type vacuole membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0000324 ! fungal-type vacuole

[Term]
id: GO:0000330 ! plant-type vacuole lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: part_of GO:0000325 ! plant-type vacuole
intersection_of: bounded_by GO:0009705 ! plant-type vacuole membrane

[Term]
id: GO:0000345 ! cytosolic DNA-directed RNA polymerase complex
intersection_of: GO:0000428 ! DNA-directed RNA polymerase complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0000421 ! autophagic vacuole membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005776 ! autophagic vacuole

[Term]
id: GO:0001536 ! radial spoke stalk
intersection_of: GO:0043234 ! protein complex
intersection_of: part_of GO:0001534 ! radial spoke
intersection_of: attaches_to GO:0005879 ! axonemal microtubule

[Term]
id: GO:0002079 ! inner acrosomal membrane
intersection_of: GO:0044464 ! cell part
intersection_of: inner_part_of GO:0002080 ! acrosomal membrane

[Term]
id: GO:0002080 ! acrosomal membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0001669 ! acrosome

[Term]
id: GO:0002081 ! outer acrosomal membrane
intersection_of: GO:0044464 ! cell part
intersection_of: outer_part_of GO:0002080 ! acrosomal membrane

[Term]
id: GO:0005622 ! intracellular
intersection_of: GO:0005575 ! cellular_component
intersection_of: completely_bounded_by GO:0005886 ! plasma membrane

[Term]
id: GO:0005628 ! prospore membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042764 ! ascospore-type prospore

[Term]
id: GO:0005634 ! nucleus
intersection_of: GO:0043227 ! membrane-bounded organelle
intersection_of: adjacent_to GO:0005783 ! endoplasmic reticulum
intersection_of: has_part GO:0005694 ! chromosome

[Term]
id: GO:0005635 ! nuclear envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0005634 ! nucleus

[Term]
id: GO:0005637 ! nuclear inner membrane
intersection_of: GO:0019866 ! organelle inner membrane
intersection_of: adjacent_to GO:0031981 ! nuclear lumen
intersection_of: boundary_part_of GO:0005634 ! nucleus

[Term]
id: GO:0005639 ! integral to nuclear inner membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005637 ! nuclear inner membrane

[Term]
id: GO:0005640 ! nuclear outer membrane
intersection_of: GO:0031968 ! organelle outer membrane
intersection_of: boundary_part_of GO:0005634 ! nucleus

[Term]
id: GO:0005641 ! nuclear envelope lumen
intersection_of: GO:0031970 ! organelle envelope lumen
intersection_of: bounded_by GO:0005640 ! nuclear outer membrane
intersection_of: bounds GO:0005637 ! nuclear inner membrane

[Term]
id: GO:0005643 ! nuclear pore
intersection_of: GO:0046930 ! pore complex
intersection_of: perforates GO:0005635 ! nuclear envelope
intersection_of: adjacent_to GO:0005637 ! nuclear inner membrane
intersection_of: adjacent_to GO:0005640 ! nuclear outer membrane

[Term]
id: GO:0005654 ! nucleoplasm
intersection_of: GO:0044428 ! nuclear part
intersection_of: part_of GO:0031981 ! nuclear lumen
intersection_of: bounds GO:0005694 ! chromosome
intersection_of: bounds GO:0005730 ! nucleolus

[Term]
id: GO:0005664 ! nuclear origin of replication recognition complex
intersection_of: GO:0000808 ! origin recognition complex
intersection_of: part_of GO:0000228 ! nuclear chromosome

[Term]
id: GO:0005737 ! cytoplasm
intersection_of: GO:0005575 ! cellular_component
intersection_of: bounded_by GO:0005886 ! plasma membrane
intersection_of: bounds GO:0005634 ! nucleus

[Term]
id: GO:0005740 ! mitochondrial envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0005739 ! mitochondrion

[Term]
id: GO:0005741 ! mitochondrial outer membrane
intersection_of: GO:0031968 ! organelle outer membrane
intersection_of: boundary_part_of GO:0005739 ! mitochondrion

[Term]
id: GO:0005743 ! mitochondrial inner membrane
intersection_of: GO:0019866 ! organelle inner membrane
intersection_of: boundary_part_of GO:0005739 ! mitochondrion

[Term]
id: GO:0005758 ! mitochondrial intermembrane space
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounded_by GO:0005741 ! mitochondrial outer membrane
intersection_of: bounds GO:0005743 ! mitochondrial inner membrane

[Term]
id: GO:0005765 ! lysosomal membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005764 ! lysosome

[Term]
id: GO:0005774 ! vacuolar membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005773 ! vacuole

[Term]
id: GO:0005778 ! peroxisomal membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005777 ! peroxisome

[Term]
id: GO:0005779 ! integral to peroxisomal membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005778 ! peroxisomal membrane

[Term]
id: GO:0005782  ! peroxisomal matrix
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0005778  ! peroxisomal membrane

[Term]
id: GO:0005788  ! endoplasmic reticulum lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0005789  ! endoplasmic reticulum membrane

[Term]
id: GO:0005789 ! endoplasmic reticulum membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005783 ! endoplasmic reticulum

[Term]
id: GO:0005796  ! Golgi lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0000139  ! Golgi membrane

[Term]
id: GO:0005797 ! Golgi medial cisterna [DEF: "The middle Golgi cisterna (or cisternae)."]
intersection_of: GO:0031985 ! Golgi cisterna
intersection_of: outwards_of GO:0000137 ! Golgi cis cisterna
intersection_of: inwards_of GO:0000138 ! Golgi trans cisterna

[Term]
id: GO:0005826 ! actomyosin contractile ring
intersection_of: GO:0070938 ! contractile ring
intersection_of: part_of GO:0015629 ! actin cytoskeleton

[Term]
id: GO:0005828 ! kinetochore microtubule
intersection_of: GO:0005874 ! microtubule
intersection_of: attaches_to GO:0000776 ! kinetochore

! not quite right: we want to say maximal cytoplasmic part
[Term]
id: GO:0005829 ! cytosol
intersection_of: GO:0044444 ! cytoplasmic part
intersection_of: lacks_part GO:0043226 ! organelle

[Term]
id: GO:0005844 ! polysome
intersection_of: GO:0030529 ! ribonucleoprotein complex
intersection_of: complex_of GO:0005840 ! ribosome

[Term]
id: GO:0005863 ! striated muscle thick filament
intersection_of: GO:0032982 ! myosin filament
intersection_of: part_of GO:0030017 ! sarcomere
!!!??intersection_of: subclass GO:0005859 ! muscle myosin complex

[Term]
id: GO:0005865 ! striated muscle thin filament
intersection_of: GO:0044449 ! contractile fiber part
intersection_of: part_of GO:0015629 ! actin cytoskeleton
intersection_of: attaches_to GO:0030018 ! Z disc

[Term]
id: GO:0005886 ! plasma membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005623 ! cell

[Term]
id: GO:0005887 ! integral to plasma membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005886 ! plasma membrane

[Term]
id: GO:0005902 ! microvillus
intersection_of: GO:0042995 ! cell projection
intersection_of: has_part GO:0005884 ! actin filament

[Term]
id: GO:0005913 ! cell-cell adherens junction
intersection_of: GO:0005912 ! adherens junction
intersection_of: attaches_to GO:0005886 ! plasma membrane [implicitly of another cell - it is part_of the PM of the cell it belongs to]

[Term]
id: GO:0005916 ! fascia adherens
intersection_of: GO:0005913 ! cell-cell adherens junction
intersection_of: part_of GO:0014704 ! intercalated disc
intersection_of: attaches_to GO:0030017 ! sarcomere

[Term]
id: GO:0005924 ! cell-substrate adherens junction
intersection_of: GO:0005912 ! adherens junction
intersection_of: attaches_to GO:0031012 ! extracellular matrix
intersection_of: part_of GO:0016323 ! basolateral plasma membrane

[Term]
id: GO:0008002 ! lamina lucida [DEF: "The electron-lucent layer of the basal lamina adjacent to the basal plasma membrane of the cells that rest on the lamina."]
intersection_of: GO:0044421 ! extracellular region part
intersection_of: part_of GO:0005605 ! basal lamina
intersection_of: adjacent_to GO:0009925 ! basal plasma membrane

[Term]
id: GO:0008043 ! intracellular ferritin complex
intersection_of: GO:0070288 ! ferritin complex
intersection_of: part_of GO:0005622 ! intracellular

[Term]
id: GO:0009506 ! plasmodesma
intersection_of: GO:0005911 ! intercellular junction
intersection_of: adjacent_to GO:0005737 ! cytoplasm
intersection_of: part_of GO:0055044 ! symplast

[Term]
id: GO:0009526 ! plastid envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0009536 ! plastid

[Term]
id: GO:0009527 ! plastid outer membrane
intersection_of: GO:0031968 ! organelle outer membrane
intersection_of: boundary_part_of GO:0009536 ! plastid

[Term]
id: GO:0009528 ! plastid inner membrane
intersection_of: GO:0019866 ! organelle inner membrane
intersection_of: boundary_part_of GO:0009536 ! plastid

[Term]
id: GO:0009529 ! plastid intermembrane space
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounded_by GO:0009527 ! plastid outer membrane
intersection_of: bounds GO:0009528 ! plastid inner membrane

[Term]
id: GO:0009535 ! chloroplast thylakoid membrane
intersection_of: GO:0042651 ! thylakoid membrane
intersection_of: boundary_part_of GO:0009534 ! chloroplast thylakoid

[Term]
id: GO:0009543 ! chloroplast thylakoid lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounded_by GO:0009535 ! chloroplast thylakoid membrane

!todo: check
[Term]
id: GO:0009546 ! plasmodesmatal cytoplasmic sleeve
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: adjacent_to GO:0009510 ! plasmodesmatal desmotubule

[Term]
id: GO:0009548 ! plasmodesmatal plasma membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0009506 ! plasmodesma

[Term]
id: GO:0009570 ! chloroplast stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009507 ! chloroplast

[Term]
id: GO:0009571 ! proplastid stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009537 ! proplastid

[Term]
id: GO:0009575 ! chromoplast stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009509 ! chromoplast

[Term]
id: GO:0009576 ! leucoplast stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009516 ! leucoplast

[Term]
id: GO:0009577 ! elaioplast stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009545 ! elaioplast

[Term]
id: GO:0009578 ! etioplast stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009513 ! etioplast

[Term]
id: GO:0009705 ! plant-type vacuole membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0000325 ! plant-type vacuole

[Term]
id: GO:0009706 ! chloroplast inner membrane
intersection_of: GO:0019866 ! organelle inner membrane
intersection_of: boundary_part_of GO:0009507 ! chloroplast

[Term]
id: GO:0009707 ! chloroplast outer membrane
intersection_of: GO:0031968 ! organelle outer membrane
intersection_of: boundary_part_of GO:0009507 ! chloroplast

[Term]
id: GO:0009897 ! external side of plasma membrane [DEF: "The side of the plasma membrane that is opposite to the side that faces the cytoplasm."]
relationship: adjacent_to GO:0005615 ! extracellular space

[Term]
id: GO:0009898 ! internal side of plasma membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: bounded_by GO:0005886 ! plasma membrane
intersection_of: bounds GO:0005737 ! cytoplasm

[Term]
id: GO:0009941 ! chloroplast envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0009507 ! chloroplast

[Term]
id: GO:0010008 ! endosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005768 ! endosome

! we need a term 'face' or 'side'
[Term]
id: GO:0010009 ! external side of endosome membrane [DEF: "The external (cytoplasmic face) of an endosome membrane."]
intersection_of: GO:0044425 ! membrane part
intersection_of: part_of GO:0010008 ! endosome membrane
intersection_of: adjacent_to GO:0005737 ! cytoplasm

[Term]
id: GO:0010339 ! external side of cell wall [DEF: "The side of the cell wall that is opposite to the side that faces the cell and its contents."]
relationship: adjacent_to GO:0005615 ! extracellular space

[Term]
id: GO:0010370 ! perinucleolar chromocenter [DEF: "A chromocenter adjacent to the nucleolus."]
intersection_of: GO:0010369 ! chromocenter
intersection_of: adjacent_to GO:0005730 ! nucleolus

[Term]
id: GO:0012506 ! vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031982 ! vesicle

[Term]
id: GO:0012507 ! ER to Golgi transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030134 ! ER to Golgi transport vesicle

[Term]
id: GO:0012508 ! Golgi to ER transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030142 ! Golgi to ER transport vesicle

[Term]
id: GO:0012509 ! inter-Golgi transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030143 ! inter-Golgi transport vesicle

[Term]
id: GO:0012510 ! trans-Golgi network transport vesicle membrane
intersection_of: GO:0030658 ! transport vesicle membrane
intersection_of: boundary_part_of GO:0030140 ! trans-Golgi network transport vesicle

[Term]
id: GO:0014731 ! spectrin-associated cytoskeleton
intersection_of: GO:0005856 ! cytoskeleton
intersection_of: has_part GO:0008091 ! spectrin
intersection_of: adjacent_to GO:0005886 ! plasma membrane

! TODO: request term?
[Term]
id: GO:0014803 ! longitudinal sarcoplasmic reticulum lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: part_of GO:0014801 ! longitudinal sarcoplasmic reticulum
intersection_of: bounded_by GO:0033017 ! sarcoplasmic reticulum membrane

[Term]
id: GO:0014804 ! terminal cisterna lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: lumen_of GO:0014802 ! terminal cisterna

[Term]
id: GO:0015630 ! microtubule cytoskeleton
intersection_of: GO:0005856 ! cytoskeleton
intersection_of: has_part GO:0005874 ! microtubule

[Term]
id: GO:0016529 ! sarcoplasmic reticulum
intersection_of: GO:0005783 ! endoplasmic reticulum
intersection_of: part_of GO:0016528 ! sarcoplasm
relationship: continuous_with GO:0005635 ! nuclear envelope

! TODO
![Term]
!id: GO:0019866 ! organelle inner membrane
!intersection_of: GO:0019866 ! organelle inner membrane
!intersection_of: boundary_part_of GO:0043226 ! organelle

[Term]
id: GO:0019897 ! extrinsic to plasma membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005886 ! plasma membrane

[Term]
id: GO:0019898 ! extrinsic to membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0016020 ! membrane

! TODO
![Term]
!id: GO:0020004 ! parasitophorous vacuolar space
!intersection_of: GO:0005775 ! vacuolar lumen
!intersection_of: ???lumen_of GO:0020003 ! parasitophorous vacuole
!intersection_of: boundary_part_of GO:0020005 ! parasitophorous vacuolar membrane

[Term]
id: GO:0020005 ! parasitophorous vacuolar membrane
intersection_of: GO:0005774 ! vacuolar membrane
intersection_of: boundary_part_of GO:0020003 ! parasitophorous vacuole

[Term]
id: GO:0020017 ! flagellar membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0019861 ! flagellum

[Term]
id: GO:0020018 ! flagellar pocket membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0020016 ! flagellar pocket

[Term]
id: GO:0030056 ! hemidesmosome
intersection_of: GO:0030055 ! cell-substrate junction
intersection_of: part_of GO:0009925 ! basal plasma membrane
intersection_of: adjacent_to GO:0005605 ! basal lamina
intersection_of: attaches_to GO:0005882 ! intermediate filament
intersection_of: attaches_to GO:0031012 ! extracellular matrix

! https://sourceforge.net/tracker/index.php?func=detail&aid=2028364&group_id=36855&atid=440764
[Term]
id: GO:0030057 ! desmosome [DEF: "A specialised type of cell junction into which intermediate filaments of adjacent cells are inserted. This type of cell junction is characteristic of epithelia. Desmosomes are particularly conspicuous in tissues such as skin that have to withstand mechanical stress."]
intersection_of: GO:0005911 ! intercellular junction
intersection_of: attaches_to GO:0045095 ! keratin filament

[Term]
id: GO:0030075 ! plasma membrane-derived thylakoid
intersection_of: GO:0009579 ! thylakoid
intersection_of: derived_from GO:0005886 ! plasma membrane

[Term]
id: GO:0030117 ! membrane coat
intersection_of: GO:0043234 ! protein complex
intersection_of: boundary_part_of GO:0048475 ! coated membrane

[Term]
id: GO:0030120 ! vesicle coat
intersection_of: GO:0030117 ! membrane coat
intersection_of: boundary_part_of GO:0031982 ! vesicle

[Term]
id: GO:0030125 ! clathrin vesicle coat
intersection_of: GO:0030118 ! clathrin coat
intersection_of: boundary_part_of GO:0012506 ! vesicle membrane

[Term]
id: GO:0030130 ! clathrin coat of trans-Golgi network vesicle
intersection_of: GO:0030125 ! clathrin vesicle coat
intersection_of: boundary_part_of GO:0012510 ! trans-Golgi network transport vesicle membrane

[Term]
id: GO:0030139 ! endocytic vesicle
intersection_of: GO:0031982 ! vesicle
intersection_of: derives_from GO:0005886 ! plasma membrane

[Term]
id: GO:0030173 ! integral to Golgi membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0000139 ! Golgi membrane

[Term]
id: GO:0030176 ! integral to endoplasmic reticulum membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005789 ! endoplasmic reticulum membrane

[Term]
id: GO:0030285 ! integral to synaptic vesicle membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0030672 ! synaptic vesicle membrane

[Term]
id: GO:0030287 ! cell wall-bounded periplasmic space
intersection_of: GO:0042597 ! periplasmic space
intersection_of: bounded_by GO:0005618 ! cell wall
intersection_of: bounds GO:0005886 ! plasma membrane

[Term]
id: GO:0030288 ! outer membrane-bounded periplasmic space
intersection_of: GO:0042597 ! periplasmic space
intersection_of: bounded_by GO:0019867 ! outer membrane
intersection_of: bounds GO:0005886 ! plasma membrane

[Term]
id: GO:0030312 ! external encapsulating structure
intersection_of: GO:0005575 ! cellular_component
intersection_of: boundary_part_of GO:0005623 ! cell
intersection_of: bounds GO:0005886 ! plasma membrane

[Term]
id: GO:0030313 ! cell envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0005623 ! cell
intersection_of: has_part GO:0005886 ! plasma membrane

[Term]
id: GO:0030314 ! junctional membrane complex
intersection_of: GO:0043234 ! protein complex
intersection_of: adjacent_to GO:0016529 ! sarcoplasmic reticulum
intersection_of: adjacent_to GO:0030315 ! T-tubule


! def: "Invagination of the plasma membrane of a muscle cell that extends inward from the cell surface around each myofibril. The ends of T-tubules make contact with the sarcoplasmic reticulum membrane."
! is the T-tubule the (extracellular) space partially bounded by the PM, or the PM portion? GO says the latter
[Term]
id: GO:0030315 ! T-tubule
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: partially_enclosed_by GO:0005737 ! cytoplasm
intersection_of: adjacent_to GO:0014802 ! terminal cisterna

[Term]
id: GO:0030658 ! transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030133 ! transport vesicle

[Term]
id: GO:0030659 ! cytoplasmic vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031410 ! cytoplasmic vesicle

[Term]
id: GO:0030660 ! Golgi-associated vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005798 ! Golgi-associated vesicle

[Term]
id: GO:0030661 ! chitosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0045009 ! chitosome

[Term]
id: GO:0030662 ! coated vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030135 ! coated vesicle

[Term]
id: GO:0030663 ! COPI coated vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030137 ! COPI-coated vesicle

[Term]
id: GO:0030665 ! clathrin coated vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030136 ! clathrin-coated vesicle

[Term]
id: GO:0030666 ! endocytic vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030139 ! endocytic vesicle

[Term]
id: GO:0030667 ! secretory granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030141 ! secretory granule

[Term]
id: GO:0030668 ! merozoite dense granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0020026 ! merozoite dense granule

[Term]
id: GO:0030669 ! clathrin-coated endocytic vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0045334 ! clathrin-coated endocytic vesicle

[Term]
id: GO:0030670 ! phagocytic vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0045335 ! phagocytic vesicle

[Term]
id: GO:0030671 ! clathrin-coated phagocytic vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0045336 ! clathrin-coated phagocytic vesicle

[Term]
id: GO:0030672 ! synaptic vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0008021 ! synaptic vesicle

[Term]
id: GO:0030673 ! axolemma
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0033267 ! axon part

[Term]
id: GO:0030867 ! rough endoplasmic reticulum membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005791 ! rough endoplasmic reticulum

[Term]
id: GO:0030868 ! smooth endoplasmic reticulum membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005790 ! smooth endoplasmic reticulum

[Term]
id: GO:0030936 ! transmembrane collagen
intersection_of: GO:0005581 ! collagen
intersection_of: spans GO:0016020 ! membrane

[Term]
id: GO:0030981 ! cortical microtubule cytoskeleton
intersection_of: GO:0030863 ! cortical cytoskeleton
intersection_of: part_of GO:0015630 ! microtubule cytoskeleton
intersection_of: adjacent_to GO:0005886 ! plasma membrane

[Term]
id: GO:0031088 ! platelet dense granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042827 ! platelet dense granule

[Term]
id: GO:0031089  ! platelet dense granule lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031088  ! platelet dense granule membrane

[Term]
id: GO:0031090 ! organelle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0043226 ! organelle

[Term]
id: GO:0031092 ! platelet alpha granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031091 ! platelet alpha granule

[Term]
id: GO:0031093  ! platelet alpha granule lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031092  ! platelet alpha granule membrane

[Term]
id: GO:0031095 ! platelet dense tubular network membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031094 ! platelet dense tubular network

[Term]
id: GO:0031096  ! platelet dense tubular network lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031095  ! platelet dense tubular network membrane

[Term]
id: GO:0031164 ! contractile vacuolar membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0000331 ! contractile vacuole

[Term]
id: GO:0031165 ! integral to contractile vacuolar membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0031164 ! contractile vacuolar membrane

[Term]
id: GO:0031166 ! integral to vacuolar membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005774 ! vacuolar membrane

[Term]
id: GO:0031226 ! intrinsic to plasma membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005886 ! plasma membrane

[Term]
id: GO:0031227 ! intrinsic to endoplasmic reticulum membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005789 ! endoplasmic reticulum membrane

[Term]
id: GO:0031228 ! intrinsic to Golgi membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0000139 ! Golgi membrane

[Term]
id: GO:0031229 ! intrinsic to nuclear inner membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005637 ! nuclear inner membrane

[Term]
id: GO:0031230 ! intrinsic to cell outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009279 ! cell outer membrane

[Term]
id: GO:0031231 ! intrinsic to peroxisomal membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005778 ! peroxisomal membrane

[Term]
id: GO:0031232 ! extrinsic to external side of plasma membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0009897 ! external side of plasma membrane

[Term]
id: GO:0031233 ! intrinsic to external side of plasma membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009897 ! external side of plasma membrane

[Term]
id: GO:0031234 ! extrinsic to internal side of plasma membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0009898 ! internal side of plasma membrane

[Term]
id: GO:0031235 ! intrinsic to internal side of plasma membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009898 ! internal side of plasma membrane

[Term]
id: GO:0031240 ! external side of cell outer membrane
intersection_of: GO:0044462 ! external encapsulating structure part
intersection_of: bounds GO:0009279 ! cell outer membrane
intersection_of: bounded_by GO:0005615 ! extracellular space

[Term]
id: GO:0031241 ! internal side of cell outer membrane
intersection_of: GO:0044462 ! external encapsulating structure part
intersection_of: bounded_by GO:0009279 ! cell outer membrane
intersection_of: bounds GO:0042597 ! periplasmic space

[Term]
id: GO:0031242 ! extrinsic to external side of cell outer membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0031240 ! external side of cell outer membrane

[Term]
id: GO:0031243 ! intrinsic to external side of cell outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0031240 ! external side of cell outer membrane

[Term]
id: GO:0031244 ! extrinsic to cell outer membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0009279 ! cell outer membrane

[Term]
id: GO:0031245 ! extrinsic to internal side of cell outer membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0031241 ! internal side of cell outer membrane

[Term]
id: GO:0031246 ! intrinsic to internal side of cell outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0031241 ! internal side of cell outer membrane

[Term]
id: GO:0031253 ! cell projection membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: part_of GO:0005886 ! plasma membrane
intersection_of: boundary_part_of GO:0042995 ! cell projection

[Term]
id: GO:0031256 ! leading edge membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0031252 ! leading edge

[Term]
id: GO:0031257 ! trailing edge membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0031254 ! trailing edge

[Term]
id: GO:0031258 ! lamellipodium membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0030027 ! lamellipodium

[Term]
id: GO:0031259 ! uropod membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0001931 ! uropod

[Term]
id: GO:0031260 ! pseudopodium membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0031143 ! pseudopodium

[Term]
id: GO:0031300 ! intrinsic to organelle membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0031090 ! organelle membrane

[Term]
id: GO:0031301 ! integral to organelle membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0031090 ! organelle membrane

[Term]
id: GO:0031302 ! intrinsic to endosome membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0010008 ! endosome membrane

[Term]
id: GO:0031303 ! integral to endosome membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0010008 ! endosome membrane

[Term]
id: GO:0031304 ! intrinsic to mitochondrial inner membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005743 ! mitochondrial inner membrane

[Term]
id: GO:0031305 ! integral to mitochondrial inner membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005743 ! mitochondrial inner membrane

[Term]
id: GO:0031306 ! intrinsic to mitochondrial outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005741 ! mitochondrial outer membrane

[Term]
id: GO:0031307 ! integral to mitochondrial outer membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005741 ! mitochondrial outer membrane

[Term]
id: GO:0031308 ! intrinsic to nuclear outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005640 ! nuclear outer membrane

[Term]
id: GO:0031309 ! integral to nuclear outer membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0005640 ! nuclear outer membrane

[Term]
id: GO:0031310 ! intrinsic to vacuolar membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0005774 ! vacuolar membrane

[Term]
id: GO:0031311 ! intrinsic to contractile vacuolar membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0031164 ! contractile vacuolar membrane

[Term]
id: GO:0031312 ! extrinsic to organelle membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0031090 ! organelle membrane

[Term]
id: GO:0031313 ! extrinsic to endosome membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0010008 ! endosome membrane

[Term]
id: GO:0031314 ! extrinsic to mitochondrial inner membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005743 ! mitochondrial inner membrane

[Term]
id: GO:0031315 ! extrinsic to mitochondrial outer membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005741 ! mitochondrial outer membrane

[Term]
id: GO:0031316 ! extrinsic to nuclear outer membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005640 ! nuclear outer membrane

[Term]
id: GO:0031350 ! intrinsic to plastid membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0042170 ! plastid membrane

[Term]
id: GO:0031351 ! integral to plastid membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0042170 ! plastid membrane

[Term]
id: GO:0031352 ! intrinsic to plastid inner membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009528 ! plastid inner membrane

[Term]
id: GO:0031353 ! integral to plastid inner membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0009528 ! plastid inner membrane

[Term]
id: GO:0031354 ! intrinsic to plastid outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009527 ! plastid outer membrane

[Term]
id: GO:0031355 ! integral to plastid outer membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0009527 ! plastid outer membrane

[Term]
id: GO:0031356 ! intrinsic to chloroplast inner membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009706 ! chloroplast inner membrane

[Term]
id: GO:0031357 ! integral to chloroplast inner membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0009706 ! chloroplast inner membrane

[Term]
id: GO:0031358 ! intrinsic to chloroplast outer membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0009707 ! chloroplast outer membrane

[Term]
id: GO:0031359 ! integral to chloroplast outer membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0009707 ! chloroplast outer membrane

[Term]
id: GO:0031360 ! intrinsic to thylakoid membrane
intersection_of: GO:0031224 ! intrinsic to membrane
intersection_of: located_in GO:0042651 ! thylakoid membrane

[Term]
id: GO:0031361 ! integral to thylakoid membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0042651 ! thylakoid membrane

[Term]
id: GO:0031373 ! cytosolic fatty acid synthase complex
intersection_of: GO:0005835 ! fatty acid synthase complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031376 ! cytosolic type II fatty acid synthase complex
intersection_of: GO:0031375 ! type II fatty acid synthase complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031520 ! plasma membrane of cell tip
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0051286 ! cell tip

[Term]
id: GO:0031526 ! brush border membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0005903 ! brush border

[Term]
id: GO:0031527 ! filopodium membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0030175 ! filopodium

[Term]
id: GO:0031528 ! microvillus membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0005902 ! microvillus


[Term]
id: GO:0031597 ! cytosolic proteasome complex
intersection_of: GO:0000502 ! proteasome complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031600 ! cytosolic proteasome regulatory particle
intersection_of: GO:0005838 ! proteasome regulatory particle
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031603 ! cytosolic proteasome core complex
intersection_of: GO:0005839 ! proteasome core complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031606 ! cytosolic proteasome core complex, alpha-subunit complex
intersection_of: GO:0019773 ! proteasome core complex, alpha-subunit complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031609 ! cytosolic proteasome core complex, beta-subunit complex
intersection_of: GO:0019774 ! proteasome core complex, beta-subunit complex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031612 ! cytosolic proteasome regulatory particle, base subcomplex
intersection_of: GO:0008540 ! proteasome regulatory particle, base subcomplex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031615 ! cytosolic proteasome regulatory particle, lid subcomplex
intersection_of: GO:0008541 ! proteasome regulatory particle, lid subcomplex
intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0031676 ! plasma membrane-derived thylakoid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0030075 ! plasma membrane-derived thylakoid
!!!! intersection_of: boundary_part_of GO:0034357 ! photosynthetic membrane - see email thread Re: thylakoid membrane question

[Term]
id: GO:0031898 ! chromoplast envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0009509 ! chromoplast

[Term]
id: GO:0031899 ! chromoplast inner membrane
intersection_of: GO:0019866 ! organelle inner membrane
intersection_of: boundary_part_of GO:0009509 ! chromoplast

[Term]
id: GO:0031900 ! chromoplast outer membrane
intersection_of: GO:0031968 ! organelle outer membrane
intersection_of: boundary_part_of GO:0009509 ! chromoplast

[Term]
id: GO:0031901 ! early endosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005769 ! early endosome

[Term]
id: GO:0031902 ! late endosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005770 ! late endosome

[Term]
id: GO:0031903 ! microbody membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042579 ! microbody

[Term]
id: GO:0031904  ! endosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0010008  ! endosome membrane

[Term]
id: GO:0031905  ! early endosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031901  ! early endosome membrane

[Term]
id: GO:0031906  ! late endosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031902  ! late endosome membrane

[Term]
id: GO:0031907  ! microbody lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031903  ! microbody membrane

[Term]
id: GO:0031908  ! glyoxysomal lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0046861  ! glyoxysomal membrane

[Term]
id: GO:0031913 ! contractile vacuole pore
intersection_of: GO:0043234 ! protein complex
intersection_of: perforates GO:0031164 ! contractile vacuolar membrane
intersection_of: adjacent_to GO:0005829 ! cytosol

[Term]
id: GO:0031965 ! nuclear membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005634 ! nucleus
intersection_of: continuous_with GO:0005789 ! endoplasmic reticulum membrane

[Term]
id: GO:0031966 ! mitochondrial membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005739 ! mitochondrion

[Term]
id: GO:0031967 ! organelle envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0043226 ! organelle

[Term]
id: GO:0031968 ! organelle outer membrane
intersection_of: GO:0019867 ! outer membrane
intersection_of: boundary_part_of GO:0043226 ! organelle
intersection_of: adjacent_to GO:0005829 ! cytosol

[Term]
id: GO:0031969 ! chloroplast membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009507 ! chloroplast

[Term]
id: GO:0031970 ! organelle envelope lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounds GO:0019866 ! organelle inner membrane
intersection_of: bounded_by GO:0031968 ! organelle outer membrane

[Term]
id: GO:0031972 ! chloroplast intermembrane space
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounds GO:0009706 ! chloroplast inner membrane
intersection_of: bounded_by GO:0009707 ! chloroplast outer membrane

[Term]
id: GO:0070115 ! organellar chromatophore intermembrane space
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounds GO:0070113 ! organellar chromatophore inner membrane
intersection_of: bounded_by GO:0070114 ! organellar chromatophore outer membrane
 
[Term]
id: GO:0031973 ! chromoplast intermembrane space
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounds GO:0031899 ! chromoplast inner membrane
intersection_of: bounded_by GO:0031900 ! chromoplast outer membrane
 
[Term]
id: GO:0031977  ! thylakoid lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0042651  ! thylakoid membrane

[Term]
id: GO:0031978  ! plastid thylakoid lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0055035  ! plastid thylakoid membrane

[Term]
id: GO:0031979  ! plasma membrane-derived thylakoid lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031676  ! plasma membrane-derived thylakoid membrane

[Term]
id: GO:0031980  ! mitochondrial lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0005743 ! mitochondrial inner membrane

! the nuclear lumen is the space inside the inner nuclear membrane
[Term]
id: GO:0031981 ! nuclear lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: bounded_by GO:0005637 ! nuclear inner membrane

[Term]
id: GO:0031983  ! vesicle lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0012506  ! vesicle membrane

! remove
[Term]
id: GO:0031984 ! organelle subcompartment
intersection_of: GO:0044422 ! organelle part
intersection_of: bounded_by GO:0016020 ! membrane

[Term]
id: GO:0032127 ! dense core granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031045 ! dense core granule

[Term]
id: GO:0032419 ! extrinsic to lysosome membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005765 ! lysosomal membrane

!???
[Term]
id: GO:0032541 ! cortical endoplasmic reticulum
intersection_of: GO:0044432 ! endoplasmic reticulum part
intersection_of: adjacent_to GO:0005886 ! plasma membrane

[Term]
id: GO:0032578 ! aleurone grain membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0033095 ! aleurone grain

[Term]
id: GO:0032580 ! Golgi cisterna membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031985 ! Golgi cisterna

[Term]
id: GO:0032584 ! growth cone membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0030426 ! growth cone

[Term]
id: GO:0032585 ! multivesicular body membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005771 ! multivesicular body

[Term]
id: GO:0032586 ! protein storage vacuole membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0000326 ! protein storage vacuole

[Term]
id: GO:0032587 ! ruffle membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0001726 ! ruffle

[Term]
id: GO:0032588 ! trans-Golgi network membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005802 ! trans-Golgi network

[Term]
id: GO:0032589 ! neuron projection membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0043005 ! neuron projection

[Term]
id: GO:0032590 ! dendrite membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0030425 ! dendrite

[Term]
id: GO:0032591 ! dendritic spine membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0043197 ! dendritic spine

[Term]
id: GO:0032592 ! integral to mitochondrial membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0031966 ! mitochondrial membrane

! "The plasma membrane of a cell that bears surface projections such as axons, dendrites, cilia, or flagella, excluding the plasma membrane on cell projections."
[Term]
id: GO:0032809 ! cell soma membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: adjacent_to GO:0043025 ! cell soma

[Term]
id: GO:0032838 ! cell projection cytoplasm
intersection_of: GO:0044444 ! cytoplasmic part
intersection_of: part_of GO:0042995 ! cell projection
intersection_of: adjacent_to GO:0005886 ! plasma membrane

[Term]
id: GO:0032839 ! dendrite cytoplasm
intersection_of: GO:0044444 ! cytoplasmic part
intersection_of: part_of GO:0030425 ! dendrite
intersection_of: adjacent_to GO:0005886 ! plasma membrane

[Term]
id: GO:0033011 ! perinuclear theca
intersection_of: GO:0005856 ! cytoskeleton
intersection_of: part_of GO:0048471 ! perinuclear region of cytoplasm
intersection_of: adjacent_to GO:0001673 ! male germ cell nucleus

[Term]
id: GO:0033016 ! rhoptry membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0020008 ! rhoptry

[Term]
id: GO:0033017 ! sarcoplasmic reticulum membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0016529 ! sarcoplasmic reticulum

[Term]
id: GO:0033018  ! sarcoplasmic reticulum lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033017  ! sarcoplasmic reticulum membrane

[Term]
id: GO:0033096 ! amyloplast envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0009501 ! amyloplast

[Term]
id: GO:0033097 ! amyloplast membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009501 ! amyloplast

[Term]
id: GO:0033098 ! amyloplast inner membrane
intersection_of: GO:0019866 ! organelle inner membrane
intersection_of: boundary_part_of GO:0009501 ! amyloplast

[Term]
id: GO:0033101 ! cellular bud membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0005933 ! cellular bud

[Term]
id: GO:0033102 ! acidocalcisome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0020022 ! acidocalcisome

[Term]
id: GO:0033106 ! cis-Golgi network membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005801 ! cis-Golgi network

[Term]
id: GO:0033110 ! CVT vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0033107 ! CVT vesicle

[Term]
id: GO:0033111 ! attachment organelle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0033099 ! attachment organelle

[Term]
id: GO:0033112 ! cyanelle envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0009842 ! cyanelle

[Term]
id: GO:0033113 ! cyanelle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009842 ! cyanelle

[Term]
id: GO:0033114  ! cyanelle thylakoid lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033115  ! cyanelle thylakoid membrane

[Term]
id: GO:0033115 ! cyanelle thylakoid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009843 ! cyanelle thylakoid

[Term]
id: GO:0033116 ! ER-Golgi intermediate compartment membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0005793 ! ER-Golgi intermediate compartment

[Term]
id: GO:0033118 ! esterosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0033117 ! esterosome

[Term]
id: GO:0033162 ! melanosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042470 ! melanosome

[Term]
id: GO:0033163 ! microneme membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0020009 ! microneme

[Term]
id: GO:0033172 ! gas vesicle shell
intersection_of: GO:0044433 ! cytoplasmic vesicle part
intersection_of: boundary_part_of GO:0031411 ! gas vesicle

[Term]
id: GO:0033269 ! internode region of axon
intersection_of: GO:0033267 ! axon part
intersection_of: partially_bounded_by GO:0033268 ! node of Ranvier
intersection_of: bounded_by GO:0043218 ! compact myelin

[Term]
id: GO:0033270 ! paranode region of axon
intersection_of: GO:0033267 ! axon part
intersection_of: adjacent_to GO:0033268 ! node of Ranvier
intersection_of: bounded_by GO:0043219 ! lateral loop

[Term]
id: GO:0033289 ! intraconoid microtubule
intersection_of: GO:0005874 ! microtubule
intersection_of: partially_enclosed_by GO:0020010 ! conoid
intersection_of: partially_enclosed_by GO:0020031 ! polar ring of apical complex

[Term]
id: GO:0033583 ! rhabdomere membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: part_of GO:0005886 ! plasma membrane
intersection_of: boundary_part_of GO:0016028 ! rhabdomere

[Term]
id: GO:0033985  ! acidocalcisome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033102  ! acidocalcisome membrane

[Term]
id: GO:0034045 ! pre-autophagosomal structure membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0000407 ! pre-autophagosomal structure

[Term]
id: GO:0034060 ! cyanelle stroma
intersection_of: GO:0009532 ! plastid stroma
intersection_of: boundary_part_of GO:0009842 ! cyanelle

[Term]
id: GO:0034399 ! nuclear periphery
intersection_of: GO:0044428 ! nuclear part
intersection_of: part_of GO:0031981 ! nuclear lumen
intersection_of: adjacent_to GO:0005635 ! nuclear envelope

[Term]
id: GO:0034422  ! aleurone grain lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0032578  ! aleurone grain membrane

[Term]
id: GO:0034423  ! autophagic vacuole lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0000421  ! autophagic vacuole membrane

[Term]
id: GO:0034425 ! etioplast envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0009513 ! etioplast

[Term]
id: GO:0034426 ! etioplast membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009513 ! etioplast

[Term]
id: GO:0034430 ! monolayer-surrounded lipid storage body outer lipid monolayer
intersection_of: GO:0034646 ! organelle-enclosing lipid monolayer
intersection_of: boundary_part_of GO:0012511 ! monolayer-surrounded lipid storage body

[Term]
id: GO:0034466  ! chromaffin granule lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0042584  ! chromaffin granule membrane

[Term]
id: GO:0034467  ! esterosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033118  ! esterosome membrane

[Term]
id: GO:0034468  ! glycosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0046860  ! glycosome membrane

[Term]
id: GO:0034469 ! Golgi stack lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: lumen_of GO:0005795 ! Golgi stack

[Term]
id: GO:0034492  ! hydrogenosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0046859  ! hydrogenosomal membrane

[Term]
id: GO:0034493  ! melanosome lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033162  ! melanosome membrane

[Term]
id: GO:0034494  ! microneme lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033163  ! microneme membrane

[Term]
id: GO:0034495  ! protein storage vacuole lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0032586  ! protein storage vacuole membrane

[Term]
id: GO:0034519 ! cytoplasmic RNA cap binding complex
intersection_of: GO:0034518 ! RNA cap binding complex
intersection_of: part_of GO:0005737 ! cytoplasm

[Term]
id: GO:0034591  ! rhoptry lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0033016  ! rhoptry membrane

[Term]
id: GO:0034592  ! synaptic vesicle lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0030672  ! synaptic vesicle membrane

[Term]
id: GO:0034992 ! microtubule organizing center attachment site
intersection_of: GO:0044428 ! nuclear part
intersection_of: part_of GO:0005635 ! nuclear envelope
intersection_of: attaches_to GO:0005815 ! microtubule organizing center

! should be defined by its parts, but consider adding normal relationships for these
![Term]
!id: GO:0034993 ! SUN-KASH complex
!intersection_of: GO:0043234 ! protein complex
!intersection_of: part_of GO:0034992 ! microtubule organizing center attachment site
!intersection_of: spans GO:0005637 ! nuclear inner membrane
!intersection_of: spans GO:0005640 ! nuclear outer membrane

[Term]
id: GO:0042170 ! plastid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009536 ! plastid

! def: "The continuous network of membranes encompassing the outer nuclear membrane and the endoplasmic reticulum."
[Term]
id: GO:0042175 ! nuclear envelope-endoplasmic reticulum network
intersection_of: GO:0016020 ! membrane
intersection_of: part_of GO:0012505 ! endomembrane system
intersection_of: has_part GO:0005640 ! nuclear outer membrane
intersection_of: has_part GO:0005783 ! endoplasmic reticulum

[Term]
id: GO:0042406 ! extrinsic to endoplasmic reticulum membrane
intersection_of: GO:0005575 ! cellular_component
intersection_of: extrinsic_to GO:0005789 ! endoplasmic reticulum membrane

[Term]
id: GO:0042584 ! chromaffin granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042583 ! chromaffin granule

[Term]
id: GO:0042589 ! zymogen granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042588 ! zymogen granule

[Term]
id: GO:0042622 ! photoreceptor outer segment membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0001750 ! photoreceptor outer segment

[Term]
id: GO:0042650 ! prothylakoid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042649 ! prothylakoid

[Term]
id: GO:0042651 ! thylakoid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009579 ! thylakoid

[Term]
id: GO:0042717 ! chromatophore membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042716 ! chromatophore

[Term]
id: GO:0043083 ! synaptic cleft
intersection_of: GO:0044420 ! extracellular matrix part
intersection_of: part_of GO:0045202 ! synapse
intersection_of: adjacent_to GO:0042734 ! presynaptic membrane
intersection_of: adjacent_to GO:0045211 ! postsynaptic membrane

[Term]
id: GO:0043160  ! acrosomal lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0002080  ! acrosomal membrane

[Term]
id: GO:0043202  ! lysosomal lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0005765  ! lysosomal membrane

[Term]
id: GO:0043227 ! membrane-bounded organelle
intersection_of: GO:0043226 ! organelle
intersection_of: bounded_by GO:0016020 ! membrane

[Term]
id: GO:0043229 ! intracellular organelle
intersection_of: GO:0043226 ! organelle
intersection_of: contained_by GO:0005623 ! cell

[Term]
id: GO:0043231 ! intracellular membrane-bounded organelle
intersection_of: GO:0043227 ! membrane-bounded organelle
intersection_of: contained_by GO:0005623 ! cell

[Term]
id: GO:0043232 ! intracellular non-membrane-bounded organelle
intersection_of: GO:0043228 ! non-membrane-bounded organelle
intersection_of: contained_by GO:0005623 ! cell

[Term]
id: GO:0043233  ! organelle lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0031090  ! organelle membrane

[Term]
id: GO:0043264 ! extracellular non-membrane-bounded organelle
intersection_of: GO:0043228 ! non-membrane-bounded organelle
intersection_of: boundary_part_of GO:0005576 ! extracellular region

[Term]
id: GO:0044446 ! intracellular organelle part
intersection_of: GO:0044422 ! organelle part
intersection_of: contained_by GO:0005623 ! cell

[Term]
id: GO:0045203 ! integral to cell outer membrane
intersection_of: GO:0016021 ! integral to membrane
intersection_of: located_in GO:0009279 ! cell outer membrane

![Term]
!id: GO:0045241 ! cytosolic alpha-ketoglutarate dehydrogenase complex
!intersection_of: GO:0045240 ! alpha-ketoglutarate dehydrogenase complex
!intersection_of: part_of GO:0005829 ! cytosol

![Term]
!id: GO:0045243 ! cytosolic isocitrate dehydrogenase complex (NAD+)
!intersection_of: GO:0045242 ! isocitrate dehydrogenase complex (NAD+)
!intersection_of: part_of GO:0005829 ! cytosol

![Term]
!id: GO:0045246 ! cytosolic tricarboxylic acid cycle enzyme complex
!intersection_of: GO:0045239 ! tricarboxylic acid cycle enzyme complex
!intersection_of: part_of GO:0005829 ! cytosol

![Term]
!id: GO:0045247 ! cytosolic electron transfer flavoprotein complex
!intersection_of: GO:0045251 ! electron transfer flavoprotein complex
!intersection_of: part_of GO:0005829 ! cytosol

![Term]
!id: GO:0045248 ! cytosolic oxoglutarate dehydrogenase complex
!intersection_of: GO:0045252 ! oxoglutarate dehydrogenase complex
!intersection_of: part_of GO:0005829 ! cytosol

![Term]
!id: GO:0045249 ! cytosol pyruvate dehydrogenase (lipoamide) phosphatase complex
!intersection_of: GO:0045253 ! pyruvate dehydrogenase (lipoamide) phosphatase complex
!intersection_of: part_of GO:0005829 ! cytosol

![Term]
!id: GO:0045250 ! cytosolic pyruvate dehydrogenase complex
!intersection_of: GO:0045254 ! pyruvate dehydrogenase complex
!intersection_of: part_of GO:0005829 ! cytosol

[Term]
id: GO:0045334 ! clathrin-coated endocytic vesicle
intersection_of: GO:0030139 ! endocytic vesicle
intersection_of: has_part GO:0030118 ! clathrin coat

[Term]
id: GO:0045336 ! clathrin-coated phagocytic vesicle
intersection_of: GO:0045335 ! phagocytic vesicle
intersection_of: has_part GO:0030118 ! clathrin coat

[Term]
id: GO:0046658 ! anchored to plasma membrane
intersection_of: GO:0031225 ! anchored to membrane
intersection_of: subclass GO:0031226 ! intrinsic to plasma membrane

[Term]
id: GO:0046859 ! hydrogenosomal membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0042566 ! hydrogenosome

[Term]
id: GO:0046860 ! glycosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0020015 ! glycosome

[Term]
id: GO:0046861 ! glyoxysomal membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009514 ! glyoxysome

[Term]
id: GO:0046862 ! chromoplast membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0009509 ! chromoplast

[Term]
id: GO:0048196 ! middle lamella-containing extracellular matrix
intersection_of: GO:0031012 ! extracellular matrix
intersection_of: has_part GO:0009519 ! middle lamella
intersection_of: has_part GO:0005618 ! cell wall

[Term]
id: GO:0048237  ! rough endoplasmic reticulum lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0030867  ! rough endoplasmic reticulum membrane

[Term]
id: GO:0048238  ! smooth endoplasmic reticulum lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0030868  ! smooth endoplasmic reticulum membrane

[Term]
id: GO:0048471 ! perinuclear region of cytoplasm
intersection_of: GO:0044444 ! cytoplasmic part
intersection_of: adjacent_to GO:0005634 ! nucleus

[Term]
id: GO:0048475 ! coated membrane
intersection_of: GO:0016020 ! membrane
intersection_of: has_part GO:0030117 ! membrane coat

[Term]
id: GO:0048787 ! presynaptic active zone membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0048786 ! presynaptic active zone

[Term]
id: GO:0055028 ! cortical microtubule
intersection_of: GO:0005874 ! microtubule
intersection_of: attached_to GO:0005886 ! plasma membrane
intersection_of: part_of GO:0030863 ! cortical cytoskeleton

[Term]
id: GO:0055035 ! plastid thylakoid membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0031976 ! plastid thylakoid

[Term]
id: GO:0055038 ! recycling endosome membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0055037 ! recycling endosome

[Term]
id: GO:0055040 ! periplasmic flagellum
intersection_of: GO:0009288 ! bacterial-type flagellum
intersection_of: part_of GO:0042597 ! periplasmic space

[Term]
id: GO:0060053 ! neurofilament cytoskeleton
intersection_of: GO:0005856 ! cytoskeleton
intersection_of: has_part GO:0005883 ! neurofilament

! TODO: check
[Term]
id: GO:0060091 ! kinocilium
intersection_of: GO:0031513 ! nonmotile primary cilium
intersection_of: part_of GO:0032421 ! stereocilium bundle
intersection_of: part_of GO:0045177 ! apical part of cell

[Term]
id: GO:0060170 ! cilium membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0005929 ! cilium

[Term]
id: GO:0060171 ! stereocilium membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0032420 ! stereocilium

[Term]
id: GO:0060201 ! clathrin sculpted acetylcholine transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0060200 ! clathrin sculpted acetylcholine transport vesicle

[Term]
id: GO:0060202  ! clathrin sculpted acetylcholine transport vesicle lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0060201  ! clathrin sculpted acetylcholine transport vesicle membrane

[Term]
id: GO:0060203 ! clathrin sculpted glutamate transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0060199 ! clathrin sculpted glutamate transport vesicle

[Term]
id: GO:0060204  ! clathrin sculpted glutamate transport vesicle lumen
intersection_of: GO:0031974  ! membrane-enclosed lumen
intersection_of: bounded_by GO:0060203  ! clathrin sculpted glutamate transport vesicle membrane

[Term]
id: GO:0060205 ! cytoplasmic membrane-bounded vesicle lumen
intersection_of: GO:0031974 ! membrane-enclosed lumen
intersection_of: lumen_of GO:0016023 ! cytoplasmic membrane-bounded vesicle

[Term]
id: GO:0060342 ! photoreceptor inner segment membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0001917 ! photoreceptor inner segment

[Term]
id: GO:0065010 ! extracellular membrane-bounded organelle
intersection_of: GO:0043227 ! membrane-bounded organelle
intersection_of: boundary_part_of GO:0005576 ! extracellular region

[Term]
id: GO:0070083 ! clathrin sculpted monoamine transport vesicle membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0070081 ! clathrin sculpted monoamine transport vesicle

[Term]
id: GO:0070112 ! organellar chromatophore membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0070111 ! organellar chromatophore

! TODO
![Term]
!id: GO:0070114 ! organellar chromatophore outer membrane
!intersection_of: GO:0019867 ! outer membrane
!intersection_of: boundary_part_of GO:0070111 ! organellar chromatophore

[Term]
id: GO:0070116 ! organellar chromatophore thylakoid
intersection_of: GO:0009579 ! thylakoid
intersection_of: part_of GO:0070111 ! organellar chromatophore

[Term]
id: GO:0070118 ! organellar chromatophore thylakoid membrane
intersection_of: GO:0042651 ! thylakoid membrane
intersection_of: boundary_part_of GO:0070111 ! organellar chromatophore

[Term]
id: GO:0070250 ! mating projection membrane
intersection_of: GO:0031253 ! cell projection membrane
intersection_of: boundary_part_of GO:0005937 ! mating projection

[Term]
id: GO:0070289 ! extracellular ferritin complex
intersection_of: GO:0070288 ! ferritin complex
intersection_of: part_of GO:0005576 ! extracellular region

[Term]
id: GO:0070470 ! plasma membrane respiratory chain
intersection_of: GO:0070469 ! respiratory chain
intersection_of: boundary_part_of GO:0005886 ! plasma membrane

[Term]
id: GO:0070686 ! macropinocytic cup membrane
intersection_of: GO:0031253 ! cell projection membrane
intersection_of: boundary_part_of GO:0070685 ! macropinocytic cup

[Term]
id: GO:0070687 ! macropinocytic cup cytoskeleton
intersection_of: GO:0044463  ! cell projection part
intersection_of: part_of GO:0030864 ! cortical actin cytoskeleton
intersection_of: part_of GO:0070685 ! macropinocytic cup

[Term]
id: GO:0070732 ! spindle envelope
intersection_of: GO:0031975 ! envelope
intersection_of: boundary_part_of GO:0005819 ! spindle

[Term]
id: GO:0070821 ! tertiary granule membrane
intersection_of: GO:0016020 ! membrane
intersection_of: boundary_part_of GO:0070820 ! tertiary granule

[Term]
id: GO:0070867 ! mating projection tip membrane
intersection_of: GO:0044459 ! plasma membrane part
intersection_of: boundary_part_of GO:0043332 ! mating projection tip

[Term]
id: GO:0031988 ! membrane-bounded vesicle
intersection_of: GO:0031982 ! vesicle
intersection_of: has_part GO:0016020 ! membrane

[Typedef]
id: reachable_over_adjacent_to
name: reachable_over_adjacent_to
is_transitive: true

[Typedef]
id: adjacent_to
name: adjacent_to
def: "in spatial proximity to, but not overlapping" [RO:overlaps]
is_a: reachable_over_adjacent_to

[Typedef]
id: attaches_to
name: attaches_to

[Typedef]
id: bounded_by
name: bounded_by
comment: does NOT imply part of (a boundary is ny necessity between two things). E.g. GO:0030287 cell wall-bounded periplasmic space. x and y are externally connected and the whole of the external boundary of x is in contact with y. (ie holes don't count)
is_a: adjacent_to

[Typedef]
id: bounds
name: bounds
is_a: adjacent_to
inverse_of_on_instance_level: bounded_by

[Typedef]
id: completely_bounded_by
name: completely_bounded_by
comment: TODO - change many of the existing bounded_by relations to this
is_a: bounded_by
comment: x and y are externally connected and the whole boundary of x is in contact with y.

[Typedef]
id: complex_of
name: complex_of
def: "X complex_of Y all instance of X has_part y1 and has_part y2 where y1 and y2 are distinct instances of Y" []
comment: Example: polysome complex_of ribosome

[Typedef]
id: continuous_with
name: continuous_with
def: "shares fiat boundary with" []
is_transitive: true

[Typedef]
id: extrinsic_to
name: extrinsic_to

[Typedef]
id: has_part
name: has_part
is_transitive: true

[Typedef]
id: inner_part_of
name: inner_part_of
is_a: part_of

[Typedef]
id: lacks_part
name: lacks_part

[Typedef]
id: outer_part_of
name: outer_part_of
is_a: part_of

[Typedef]
id: overlaps
name: overlaps
def: "x overlaps y if there is some region that is part of both x and y" []
holds_over_chain: spans adjacent_to

[Typedef]
id: partially_enclosed_by
name: partially_enclosed_by
comment: a cross-section of x is lumen_of y. i.e. x is an invagination within y

[Typedef]
id: perforates
name: perforates
comment: x perforates y if x is part of y and x surrounds a space that is adjacent_to the inside and outside of y
is_a: part_of

[Typedef]
id: spans
name: spans
is_a: overlaps
def: "A spans B iff A overlaps B and A overlaps the two regions on either side of B" []

[Typedef]
id: lumen_of
name: lumen_of
is_a: part_of
comment: placeholder relation until the relevant membrane term has been declared. X lumen_of Y if X is a lumen and there exists some membrane Z such that X bounded_by Z and Z boundary_part_of Y.

[Typedef]
id: enclosed_by
name: enclosed_by
comment: similar to bounded_by but not necessarily adjacent.
holds_over_chain: bounded_by part_of

[Typedef]
id: boundary_part_of
name: boundary_part_of
comment: X boundary_part_of Y if (1) X part_of Y and (2) all parts of Y that are adjacent_to the exterior are parts of X. For example, between a membrane and the organelle it is part of
is_a: part_of
!is_a: bounds
!intersection_of: part_of
!intersection_of: bounds

!! think this xp is probably wrong - the vesicle shuttles between trans-Golgi and other places so not really part_of trans-Golgi network
[Term]
id: GO:0030140 ! trans-Golgi network transport vesicle
intersection_of: GO:0030133 ! transport vesicle
intersection_of: part_of GO:0005802 ! trans-Golgi network

[Term]
id: GO:0045111 ! intermediate filament cytoskeleton
intersection_of: GO:0005856 ! cytoskeleton
intersection_of: has_part GO:0005882 ! intermediate filament


[Term]
id: GO:0009511 ! plasmodesmatal endoplasmic reticulum
intersection_of: GO:0005783 ! endoplasmic reticulum
intersection_of: part_of GO:0009506 ! plasmodesma