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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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NTR: CC terms referred to in BP #5483

Closed gocentral closed 9 years ago

gocentral commented 15 years ago

I didn't make any attempt to filter this list; e.g. the first may be OK as a qualifier indicating the process is located in the spliceosome.

GO:0000387 ! spliceosomal snRNP biogenesis GO:0000456 ! dimethylation during SSU-rRNA biogenesis GO:0006323 ! DNA packaging GO:0007008 ! outer mitochondrial membrane organization GO:0008057 ! eye pigment granule organization and biogenesis GO:0008058 ! ocellus pigment granule organization and biogenesis GO:0009297 ! pilus biogenesis GO:0009833 ! plant-type primary cell wall biogenesis GO:0009834 ! plant-type secondary cell wall biogenesis GO:0009933 ! meristem organization GO:0010256 ! endomembrane organization GO:0010344 ! seed oilbody biogenesis GO:0010358 ! leaf shaping GO:0016043 ! cellular component organization GO:0017004 ! cytochrome complex assembly GO:0030723 ! ovarian fusome organization GO:0030724 ! testicular fusome organization GO:0031032 ! actomyosin structure organization GO:0031121 ! equatorial microtubule organization and biogenesis GO:0032118 ! horsetail-astral microtubule organization and biogenesis GO:0032200 ! telomere organization GO:0032528 ! microvillus organization and biogenesis GO:0032581 ! ER-dependent peroxisome biogenesis GO:0034724 ! DNA replication-independent nucleosome organization GO:0035058 ! sensory cilium biogenesis GO:0035316 ! non-sensory hair organization and biogenesis GO:0035317 ! imaginal disc-derived wing hair organization and biogenesis GO:0042254 ! ribosome biogenesis GO:0042273 ! ribosomal large subunit biogenesis GO:0042274 ! ribosomal small subunit biogenesis GO:0043062 ! extracellular structure organization GO:0043165 ! cell outer membrane biogenesis GO:0043683 ! type IV pilus biogenesis GO:0043711 ! pilus organization and biogenesis GO:0045470 ! R8 cell-mediated photoreceptor organization GO:0048532 ! anatomical structure organization GO:0051216 ! cartilage development GO:0060122 ! inner ear receptor stereocilium organization and biogenesis

Reported by: cmungall

Original Ticket: "geneontology/ontology-requests/5501":https://sourceforge.net/p/geneontology/ontology-requests/5501

gocentral commented 15 years ago

Ignore the first list. Corrected:

(obviously some of these are new synonym requests rather than NTRs...)

GO:0006323 ! DNA packaging GO:0007008 ! outer mitochondrial membrane organization GO:0008057 ! eye pigment granule organization and biogenesis GO:0008058 ! ocellus pigment granule organization and biogenesis GO:0009297 ! pilus biogenesis GO:0009833 ! plant-type primary cell wall biogenesis GO:0009834 ! plant-type secondary cell wall biogenesis GO:0009933 ! meristem organization GO:0010256 ! endomembrane organization GO:0010344 ! seed oilbody biogenesis GO:0016043 ! cellular component organization GO:0017004 ! cytochrome complex assembly GO:0030723 ! ovarian fusome organization GO:0030724 ! testicular fusome organization GO:0031032 ! actomyosin structure organization GO:0031121 ! equatorial microtubule organization and biogenesis GO:0032118 ! horsetail-astral microtubule organization and biogenesis GO:0032200 ! telomere organization GO:0032528 ! microvillus organization and biogenesis GO:0034724 ! DNA replication-independent nucleosome organization GO:0035058 ! sensory cilium biogenesis GO:0035316 ! non-sensory hair organization and biogenesis GO:0035317 ! imaginal disc-derived wing hair organization and biogenesis GO:0043062 ! extracellular structure organization GO:0043683 ! type IV pilus biogenesis GO:0043711 ! pilus organization and biogenesis GO:0048532 ! anatomical structure organization GO:0051216 ! cartilage development GO:0060122 ! inner ear receptor stereocilium organization and biogenesis

Original comment by: cmungall

gocentral commented 15 years ago

Mostly dealt with or commented upon ... just a few that still need work. Only one new term so far, but quite a few synonyms.

> GO:0006323 ! DNA packaging

DNA is a type of macromolecule, and we have no precedent for including macromolecules in CC (no term for proteis, tho there are lots of protein complexes, and lots of BP terms where protein is a target/substrate/participant/etc.).

> GO:0007008 ! outer mitochondrial membrane organization

added synonyms for both BP and CC terms (and inner mito membrane terms)

> GO:0008057 ! eye pigment granule organization and biogenesis > GO:0008058 ! ocellus pigment granule organization and biogenesis

The differentia for these is that the pigment granule is in the specified organ (i.e., not a CC).

> GO:0009833 ! plant-type primary cell wall biogenesis > GO:0009834 ! plant-type secondary cell wall biogenesis

renamed these terms; moved the 'plant-type' to synonyms, since only plants have primary and secondary cell walls anyway

> GO:0009933 ! meristem organization

The meristem is a supracellular plant anatomical structure, if I understand correctly.

> GO:0010256 ! endomembrane organization

added synonym

> GO:0010344 ! seed oilbody biogenesis

added synonym to CC term GO:0012511; otherwise, differentia is that the oilbody is in a seed, which isn't a CC

> GO:0016043 ! cellular component organization

could add a synonym with the underscore; is it worth it?

> GO:0017004 ! cytochrome complex assembly

cytochrome complex GO:0070069

> GO:0030723 ! ovarian fusome organization > GO:0030724 ! testicular fusome organization

For these the differentia is which organ the fusome is in ... does that call for separate CC terms? Indeed, should we keep the BP terms or merge them with the parent?

> GO:0031032 ! actomyosin structure organization

added synonyms to GO:0031032 and GO:0042641 (actomyosin)

> GO:0031121 ! equatorial microtubule organization and biogenesis

This is microtubule organization that takes place at the equatorial part (i.e. middle) of the cell. Should we have a term for the equatorial part, aka midzone, of a cell?

> GO:0032118 ! horsetail-astral microtubule organization and biogenesis

added synonym

> GO:0032200 ! telomere organization

The existing CC term 'chromosome, telomeric region' (GO:0000781) has 'telomere' as a related synonym. Added synonym to GO:0032200.

> GO:0032528 ! microvillus organization and biogenesis

microvillus is GO:0005902 (i.e. we've had it for ages)

> GO:0034724 ! DNA replication-independent nucleosome organization

The CC is nucleosome; it's the organization process that's independent of DNA replication. Is there a synonym that would help here?

> GO:0035316 ! non-sensory hair organization and biogenesis > GO:0035317 ! imaginal disc-derived wing hair organization and biogenesis

Not sure what to do for these, tho it seems that we need at least one new CC term. I'll ask around for help.

> GO:0043062 ! extracellular structure organization

I think extracellular structures aren't all at the cellular level.

> GO:0009297 ! pilus biogenesis > GO:0043683 ! type IV pilus biogenesis > GO:0043711 ! pilus organization and biogenesis

In BP, the term uses 'pilus' and there are narrow synonyms using 'fimbrium', whereas in CC it's the other way around -- 'fimbrium' (GO:0009289) has 'pilus' as a broad synonym. This came up on the pamgo wiki ages ago, but I don't think it was ever resolved. I'll see if they'll look at it again.

> GO:0048532 ! anatomical structure organization

Anatomical structure includes all those multicellular organismal structures at bigger-than-cellular levels (tissues, organs, etc.).

> GO:0051216 ! cartilage development

Cartilage is a supra-cellular anatomical structure.

> GO:0035058 ! sensory cilium biogenesis > GO:0060122 ! inner ear receptor stereocilium organization and biogenesis

I'll ask David about these ... he's done some work on the cilium terms.

m

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11

gocentral commented 15 years ago

The reasoning some come up is because of exact syns: GO:0006323 ! DNA packaging *** [SYNONYM: "DNA organisation" (exact)] [SYNONYM: "DNA organization" (exact)]

The assumption was that "organization" is only used sans qualifier for CCs. "structural organization" for gross anatomy.

It seems this is still a false positive, like many of the others below.

> GO:0030723 ! ovarian fusome organization > GO:0030724 ! testicular fusome organization

For these the differentia is which organ the fusome is in ... does that call for separate CC terms? Indeed, should we keep the BP terms or merge them with the parent?

I presume the BPs are discriminated for a biological reason so I'd be hesitant to merge them. They don't need to be defined in CC. If the difference is purely one of the mechanism of organization but not structure then having more depth in BP is fine.

I can't think why microvillus showed up, sorry about that.

You know, it probably wouldn't do any harm to add an underscore free synonym for cellular_component. I dunno.

I'm happy for this to be closed.

Original comment by: cmungall

gocentral commented 15 years ago

added underscore-free synonyms for all three root terms; closing (tho David might revisit it sometime for the cilium terms)

Original comment by: mah11

gocentral commented 15 years ago

Original comment by: mah11