The Cell

The cell is defined in GO as all components within and including the plasma membrane and any external encapsulating structures, such as the cell wall and the cell envelope. intracellular ; GO:0005622 is defined as the contents of the cell excluding the plasma membrane and any structures outside the plasma membrane. For this reason, cell projection ; GO:0042995 is a direct child of cell ; GO:0005623; cell projection membrane ; GO:0031253 is part of cell projection ; GO:0042995 and plasma membrane ; GO:0005886.

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Protein Complexes

A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains.

All complexes in the component ontology should be given parentage under the general term protein complex ; GO:0043234.

To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term pyruvate dehydrogenase activity ; GO:0004738 describes the enzyme activity whereas the cellular component term pyruvate dehydrogenase complex ; GO:0045254 describes the multi-subunit structure in which the enzyme activity resides.

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Membranes and Envelopes

Terms and structure

GO distinguishes single and double membranes surrounding organelles: an organelle envelope is defined as two lipid bilayers plus the space, or lumen, between them, whereas an organelle membrane is defined as a single bilayer. For double-membrane organelles, the membrane term refers to either of the lipid bilayers, but excludes the intermembrane space. The envelope is part of the organelle and is a organelle envelope ; GO:0031967; the membrane is part of the envelope, and inner membrane and outer membrane terms can be included:

History

Prior to December 2005, GO:0005635 was named nuclear membrane, with nuclear envelope as a synonym; this reflected a usage fairly common in the literature. For consistency with other organelle envelope and membrane terms, GO:0005635 is now named nuclear envelope, consistent with its definition, and a separate term, nuclear membrane ; GO:0031965, has been added.

Standard Definitions

organelle envelope

The double lipid bilayer enclosing the organelle and separating its contents from the rest of the cytoplasm; includes the intermembrane space.

organelle membrane, organelle with a single membrane

The lipid bilayer surrounding a(n) organelle.

organelle membrane, organelle with a double membrane

Either of the lipid bilayers that enclose the organelle and form the organelle envelope.

organelle inner membrane

The inner, i.e. lumen-facing, lipid bilayer of the organelle envelope.

organelle outer membrane

The outer, i.e. cytoplasm-facing, lipid bilayer of the organelle envelope.

organelle membrane lumen

The region between the inner and outer lipid bilayers of the organelle envelope.

Standard synonyms

The following synonym can be added to terms as long as the synonym string makes sense and does not have alternative meanings. Note that the term name and synonym can be switched depending on typical usage.

organelle membrane lumen

exact_synonym: organelle intermembrane space

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Membrane Proteins

As GO cellular component terms describe locations where a gene product may act, rather than physical features of proteins or RNAs, the terms integral membrane protein and peripheral membrane protein are present only as non-exact synonyms.

GO distinguishes classes of membrane-related location:

extrinsic to membrane ; GO:0019898 refers to gene products that are associated with membranes, but are neither directly embedded in the membrane nor anchored by covalent bonds to any moiety embedded in the membrane.

intrinsic to membrane ; GO:0031224 refers to gene products that have some covalently attached moiety embedded in the membrane, and is further split into integral to membrane ; GO:0016021 and anchored to membrane ; GO:0031225. The former refers to proteins in which some part of the peptide sequence spans all or part of the membrane (in theory, it could also be used for RNAs embedded in a membrane, if any such exist); the latter refers to gene products tethered to a membrane by a covalently attached anchor, such as a lipid moiety, which is embedded in the membrane.

Each of these terms can have child terms referring to specific membranes, for example integral to plasma membrane ; GO:0031226 or extrinsic to vacuolar membrane ; GO:0000306.

Note that even these terms actually describe spatial relationships between a membrane and a gene product, and therefore do not fit the strictest interpretation of a 'location'. They are retained nevertheless because of their considerable utility.

The cellular component ontology does not include terms for type I, II, etc., membrane proteins, because these classifications are not locations, but instead describe a different feature of the proteins, namely topological orientation with respect to the membrane and other cellular components. Furthermore, the wording type I integral membrane protein describes a class of gene products.

The DAG structure is as follows:

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Hosts, Symbionts and Viruses

The cellular component ontology provides terms to complement those in the biological process ontology representing multi-organism processes. There are two main locations for these terms: the first set, for the representation of the larger organism in the interaction, can be found under host in extraorganismal space; the second set are to capture virus components, and are under the term virion.

Viruses should be annotated like any other organism involved in a multi-organism process, using cellular component terms such as host cell cytoplasm or host cell nucleus. Locations in the virus itself are found under the term virion.

The GO annotation conventions have a guide to annotating with these terms and how to represent the other organism in the interaction.

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Maintaining complete is a and part of trees in cellular component

The cellular component ontology is is a complete, meaning that every term has a path to the root node which passes solely through is a relationships. This should be preserved; the following guidelines should help maintain this structure.

• Make sure the term has an is a path to the root, i.e. there are is a parent terms by at least one path all the way to cellular component.
• Make sure the term has at least one part of relation in its ancestry, to ensure that there are no part of orphans. It does not need to be an immediate part of parent, but every term has to be part of something. So, for complex Y, this would be okay for example:

  cell
  [p] complex X
  ---[i] complex Y

  because complex Y is transitively part of cell.
• Ensure that all logical is a parents are added. So, for example, if your term is a protein complex, make sure it has the parent protein complex. Or if your term, or one of its parents, is part of cell, it will need to be is a cell part, or have cell part in its ancestry.
• Check none of the relations you create are redundant. You can check for this in OBO-Edit by using the reasoner, and then using the link filter [self] [self] [is redundant].

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