nucleus/nuclear-membrane

[alexg...@gmail.com]

According to GO:

acrosomal lumen GO:0043160
Ontology
cellular component
Synonyms
None
Definition
The volume enclosed within the acrosome membrane. [source:
GOC:go_curators]
Comment
None

and,

endosome lumen
Accession
GO:0031904
Ontology
cellular component
Synonyms
None
Definition
The volume enclosed by the membranes of an endosome. [source:
GOC:mah]
Comment
None

are cellular components. For instance, 1-2nm peptidoglycan-based cell
wall ; GO:0009276 is a cellular component, by the same vein that:

extrinsic to nuclear outer membrane ; GO:0031316
integral to nuclear inner membrane ; GO:0005639
integral to nuclear outer membrane ; GO:0031309
intrinsic to nuclear inner membrane ; GO:0031229

are all cellular components. There is not distinction between a
sub_cellular_component and those components of the
sub_cellular_components. For instance the nucleus has a membrane as
well as the vacuoles have membranes (nuclear, and vacuolar). Probably
this is a granularity problem. If we wanted to model "protein A enters
the nucleus via a nuclear-pore". Both, nucleus and nuclear-pore, are
cellular components. But they should not be positioned under the same
level of granularity. Shouldn't the nuclear-pore be classified as a
sub_cellular_component?


In BFOTOP:

PolyMolecularCompound
-CellularComponent
-CellMembrane
-Cytoplasm

Again, in BFOTOP, from my understanding, CellMembrane is at the same
level of granularity as the nucleus; it may be necessary to include
one more level of granularity so that the components of the components
are differentiated. As for the Cytoplasm, shouldn't it be
Cytoplasm_fluid, as the Cytoplasm it self is just the fluid?