phagocytosis, engulfment children

[gocentral]

In doing a clustering analysis we noticed some genes annotated to 'cytoskeletal organization and biogenesis' that didn't make sense. This is because the parent term is defined as being comprised of both cytoskeletal processes and membrane processes. 'phagocytosis, engulfment' has two is_a parents, membrane organization and cytoskeletal organization. This leads to true path violations if a gene product is only involved in one or the other. I propose 2 new part_of children of phagocytosis, engulfment children (GO:0006911) described below. I would also move GO:0006911 to be an is_a 'membrane invagination'.

id: GO:0006911 name:phagocytosis, engulfment def:The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis. [] exact_synonym:same as in current term is_a: membrane invagination ; GO:GO:0010324 part_of:phagocytosis ; GO:GO:0006909

id:GO:new name: cytoskeletal rearrangement involved in phagocytosis, engulfment def: The assembly and arrangement of cytoskeletal structures that is involved in the internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis.[GOC:dph] exact_synonym: is_a:cytoskeletal organization and biogenesis ; GO:0007010 part_of: phagocytosis, engulfment ; GO:0006911

id:GO:new2 name: membrane reorganization involved in phagocytosis, engulfment def:The assembly and arrangement of the plasma membrane that is involved in the internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis.[GOC:dph] exact_synonym: is_a:plasma membrane organization and biogenesis ; GO:0007009 part_of: phagocytosis, engulfment ; GO:0006911

id: GO:new3 name: regulation of phagocytosis, engulfment def: Any process that modulates the frequency, rate or extent of the internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis.[GOC:dph] exact_synonym: is_a:regulation of phagocytosis ; GO:0050764 part_of: phagocytosis, engulfment ; GO:0006911

Reported by: ukemi

Original Ticket: "geneontology/ontology-requests/4042":https://sourceforge.net/p/geneontology/ontology-requests/4042

[gocentral]

Logged In: YES user_id=865072 Originator: NO

Are you planning on making positive and negative regulation terms as well (I would recommend them)?

Thanks,

Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=631592 Originator: YES

Yes, when I make a regulation term, I make the positive and negative terms unless I have a good reason not to.

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=631592 Originator: YES

Created these terms and made parentage as is discussed in this request.

cytoskeletal rearrangement involved in phagocytosis, engulfment ; GO:0060097 membrane reorganization involved in phagocytosis, engulfment ; GO:0060098 regulation of phagocytosis, engulfment ; GO:0060099 positive regulation of phagocytosis, engulfment ; GO:0060100 negative regulation of phagocytosis, engulfment ; GO:0060101

Original comment by: ukemi

[gocentral]

• status: open --> closed

Original comment by: ukemi