Taxon constraints, numerous descendants of cytoplasm

[ValWood]

only in metazoa? ~GO:0060417 yolk~ see #22279 ~GO:0005883 neurofilament~ #22279

~only in protists? (although single EXP is from rat?) GO:0043265 ectoplasm~ see https://github.com/geneontology/go-ontology/issues/24424

only in bacteria ~GO:0019812 type I site-specific deoxyribonuclease complex~ see #22279 ~GO:0009359 type II site-specific deoxyribonuclease complex~  see #22279 ~GO:0019813 type III site-specific deoxyribonuclease complex~  see #22279 ~GO:00320 type IV site-specific deoxyribonuclease complex~ see #22279

only in plants

• [x] GO:0009574 preprophase band ->A dense band of microtubules, 1-3 pm wide, that appears just beneath the cell membrane before the start of cell division in the cells of higher plants.
• [x] GO:00095 phragmoplast see https://github.com/geneontology/go-ontology/issues/24426
• [x] GO:0009525 see phragmosome https://github.com/geneontology/go-ontology/issues/24427

~GO:0120293 dynein axonemal particle~ see #22279

only in metazoa? or never in yeast ~GO:0120098 procentriole~  https://github.com/geneontology/go-ontology/issues/22279

• [x] GO:0005814 centriole ~GO:0120099 procentriole replication complex~  https://github.com/geneontology/go-ontology/issues/22279
• [x] GO:0098534 centriole assembly (any term with centriole/procentriole)

[ValWood]

only in metazoa ~GO:0045169 fusome~ https://github.com/geneontology/go-ontology/issues/22279 ~GO:0036457 keratohyalin granule (organisms with keratin?)~ https://github.com/geneontology/go-ontology/issues/22279

• [x] GO:0042587 glycogen granule -> Cytoplasmic bead-like structures of animal cells, (adding only in metazoa or will need redefinign)

only in bacteria ~GO:0044227 methane-oxidizing organelle~ https://github.com/geneontology/go-ontology/issues/22279

only on protozoa ~GO:0042566 hydrogenosome~ GO:0042566

[ValWood]

Only in metazoa (IGNORING THIS ONE FOR NOW) GO:0071142 homomeric SMAD protein complex A protein complex composed of a single type of SMAD family proteins. In the absence of Smad4, phosphorylation of R-SMADs results in their homotrimerization. However, these complexes do not appear to import into the nucleus and are assumed to be transcriptionally inactive. PMID:11779505 PMID:16322555 PMID:9670020

Probably obsolete this one as it isn't used, and doesn't seem to represent a functional complex?

[ValWood]

• [x] GO:0020022 acidocalcisome Definition | An electron-dense acidic membrane-bounded organelle which contains a matrix of pyrophosphate and polyphosphates with bound calcium and other cations. Although this may be broader: https://en.wikipedia.org/wiki/Acidocalcisome perhaps this one is OK as is. Acidocalcisomes were originally discovered in Trypanosomes (the causing agents of sleeping sickness and Chagas disease) but have since been found in Toxoplasma gondii (causes toxoplasmosis), Plasmodium (malaria), Chlamydomonas reinhardtii (a green alga), Dictyostelium discoideum (a slime mould), bacteria and human platelets.

~GO:007008 Term name | PHA granule An inclusion body located in the cytoplasm that consists of polyhydroxyalkanoate (PHA) molecules and associated proteins, surrounded by a phospholipid monolayer; the proteins include PHA synthase, PHA depolymerase and 3HB-oligomer hydroxylase, phasins (PhaPs), which are thought to be the major structural proteins of the membrane surrounding the inclusion, and the regulator of phasin expression PhaR~ https://github.com/geneontology/go-ontology/issues/24423

only in plant

• [x] GO:0042735 protein body Definition A membrane-bounded plant organelle found in the developing endosperm, contains storage proteins. -> rename to endosperm protein body?

• [x] only in bacteria | GO:0044222 | anammoxosome Definition | An intracytoplasmic membrane-bounded compartment in anaerobic ammonium oxidation (anammox) bacteria, is the site of anammox catabolism.

[ValWood]

This is primarily to make it easier for our community curators to find the correct descendant terms under cytoplasm (once a taxon restriction is applied we do not see the irrelevant ones), but good for QC anyway...

[ValWood]

HI @krchristie is this on your radar? I think I have some overlap with other tickets, so if you can let me know when this one is done I can pick up the remaining.

[krchristie]

@ValWood - You should just take this one as I am no longer doing a significant amount of ontology work. I'll assign it to you and remove myself.

[ValWood]

only in plants GO:0009574 preprophase band GO:0042735 protein body

only in prokaryotes GO:0044222 anammoxosome

only in metazoa GO:0005814 centriole GO:0098534 centriole assembly GO:0042587 glycogen granule

never in yeast (won't do all fungi for now) GO:0020022 acidocalcisome

[ValWood]

@pgaudet could you check this one. Will add tomorrow if it looks OK

[ValWood]

still to do "never in"