complex assembly/formation inconsistencies/suggestions

[gocentral]

I noticed that there are some inconsistencies on the tems and parentages which refer to complex assembly.

For instance GO:0006267 pre-replicative complex formation def 'the assembly' of the pre-replicative complex

The most usual syntax is 'x complex assembly' maybe these could have standard terms and defs?

I noticed complex assembly complex formation complex biogenesis formation of x complex.

The upshot of these inconsistencies is that not all 'complex formation/biogenesis/assembly terms have a 'protein complex assembly' parent.

I spotted: 'pore complex biogenesis' and 'transcriptional preinitiation complex formation' which do not have a protein conmplex assembly parent.

I also spotted signalosome assembly suggest term name change to signalosom complex assembly and moving to under 'cellualr protein complex assembly'

What do you think?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/4230":https://sourceforge.net/p/geneontology/ontology-requests/4230

[gocentral]

• labels: --> Other term-related request
• milestone: --> 224410
• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Mostly I'm for consistency, so I've started fixing most of these; as a general rule I've kept old names as synonyms in case people have got used to searching for them. I'll put a long boring list of details in next; for now, some comments.

> 'x complex assembly' > maybe these could have standard terms and defs?

Most of them do, and I've converted a few more defs to the standard wording (the standard def is a fairly recent development). There are a few exceptions, but they seem to be for good reason (e.g. protein catenane formation, synaptic vesicle priming). I've yet to do the protein-RNA complex assembly ones, but it looks like it would be a good idea to keep some of the non-standard wordings there to avoid confusion.

> 'pore complex biogenesis'

This is a weird one. The corresponding component term isn't defined as necessarily being a protein complex, so I think it's safest to leave it as is.

> transcriptional preinitiation complex formation'

This one goes under 'protein-DNA complex assembly' cos, well, it's got DNA as well as protein (relationship was missing but isn't any more).

Off on a tangent: def and parentage of 'transcription initiation look wrong ...

> signalosome assembly

Move sounds sensible; I won't rename it because the word complex isn't really necessary; the signalosome is by definition a complex (and I'll rename the component term from 'signalosome complex' to just 'signalosome' ... really ought to do the proteasome terms too, but I'm kinda scared to mess with those).

m

Original comment by: mah11

[gocentral]

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as promised, the long dull list of changes ... SF 1733770

added relationship transcriptional preinitiation complex formation GO:0051123 is_a protein-DNA complex assembly GO:0065004

moved signalosome assembly GO:0010387 to is_a cellular protein complex assembly GO:0043623

renamed GO:0006267 to 'pre-replicative complex assembly' renamed GO:0007172 to 'signal complex assembly' renamed GO:0006294 to 'nucleotide-excision repair, preincision complex assembly' renamed GO:0051123 to 'transcriptional preinitiation complex assembly' for all renamed terms, kept old names as exact synonyms

reworded defs to '... complex assembly' standard cytochrome bc(1) complex assembly GO:0017062 Golgi membrane coat protein complex assembly GO:0048197 Golgi membrane priming complex assembly GO:0048195 kinetochore assembly GO:0051382 mitochondrial respiratory chain complex assembly GO:0033108 mitochondrial respiratory chain complex I assembly GO:0032981 NAD(P)H dehydrogenase complex assembly GO:0010275 NADH dehydrogenase complex assembly GO:0010257 NADH dehydrogenase complex (plastoquinone) assembly GO:0010258 nuclear pore complex assembly GO:0051292 photosystem I assembly GO:0048564 photosystem II assembly GO:0010207 photosystem II oxygen evolving complex assembly GO:0010270 pre-replicative complex assembly GO:0006267 septin ring assembly GO:0000921 signal complex assembly GO:0007172 spindle assembly GO:0051225 anastral spindle assembly GO:0055048 anastral spindle assembly involved in male meiosis GO:0009971 astral spindle assembly GO:0055049 astral spindle assembly involved in male meiosis GO:0055050 spindle assembly involved in female meiosis GO:0007056 spindle assembly involved in female meiosis I GO:0007057 spindle assembly involved in female meiosis II GO:0007058 spindle assembly involved in male meiosis GO:0007053 spindle midzone assembly GO:0051255 meiotic DNA recombinase assembly GO:0000707 meiotic recombination nodule assembly GO:0007146 early meiotic recombination nodule assembly GO:0042139 late meiotic recombination nodule assembly GO:0042140 intercellular junction assembly GO:0007043 dosage compensation complex assembly GO:0042714 dosage compensation complex assembly during dosage compensation by hyperactivation of X chromosome GO:0016457 dosage compensation complex assembly during dosage compensation by hypoactivation of X chromosome GO:0042715 nucleotide-excision repair, preincision complex assembly GO:00062944 transcriptional preinitiation complex assembly GO:0051123

also renamed GO:0008180 to simply 'signalosome' a la ribosome, polarisome, etc.

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I tihnk these changes get it as close to consistent as is reasonable ...

terms renamed: GO:0045898 to 'regulation of transcriptional preinitiation complex assembly' GO:0017055 to 'negative regulation of transcriptional preinitiation complex assembly' GO:0045899 to 'positive regulation of transcriptional preinitiation complex assembly'

for several terms, used the 'complex assembly' wording in exact synonyms, in case current term name reflects community usage: GO:0000244 assembly of spliceosomal tri-snRNP GO:0000351 assembly of spliceosomal tri-snRNP U4/U6.U5 GO:0000355 assembly of spliceosomal tri-snRNP U4atac/U6atac.U5 GO:0001732 formation of translation initiation complex GO:0001677 formation of translation initiation ternary complex GO:0001731 formation of translation preinitiation complex

for GO:0000349 and GO:0000350 made 'assembly' synonym related

reworded defs GO:0042256 mature ribosome assembly GO:0042257 ribosomal subunit assembly GO:0000027 ribosomal large subunit assembly and maintenance GO:0000028 ribosomal small subunit assembly and maintenance

also corrected scope of 'biopolymerization' synonyms for GO:006413 (now broad)

m

(will close next week, after you have a chance to look at things)

Original comment by: mah11

[gocentral]

• status: open --> open-fixed

Original comment by: mah11

[gocentral]

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I promise obol will be able to help automate all this v soon; synonyms, even defs..

some things that will help:

(1) add a new synonym:

[Term] id: GO:0015934 ! large ribosomal subunit exact_synonym: "ribosomal large subunit" []

(don't both with synonyms for the corresponding processes yet - suggestions can be automated)

(2) create a term "ribosomal subunit" (or get rid of term "ribosomal subunit assembly")

(3) I'm a little confused by the difference here:

assembly assembly and maintenance biogenesis formation biosynthesis organization and biogenesis biogenesis and assembly

I have been trying to get together def templates for each of these, but failed. If I can get help here - perhaps a wiki page just for this - I can implement the rules in obol

Original comment by: cmungall

[gocentral]

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(1) Done; also did the equivalent for the small subunit, GO:0015935. I have not done the child terms; should I, or can that be automated? (Also, some are supposed to be renamed as part of the de-sensu-fication effort.)

(2) Added 'ribosomal subunit' GO:

(3) Hm, good point, they're not all consistently used or well distinguished. There are some standard definitions in the process ontology guidelines (http://www.geneontology.org/GO.process.guidelines.shtml), but there's not yet a complete set; one more respect in which the doc seriously needs an update. Some specifics, such as they are:

> assembly

We've come up with a standard def for complex assembly, but it hasn't been propagated upwards to the parent and sibling terms; I suppose it could be. It also isn't in the documentation yet ... (I'll fix that).

Anyway, the wording for complexes is based on 'macromolecular complex assembly' GO:0065003 [DEF: "The aggregation and bonding together of a set of macromolecules to form a complex."]

> assembly and maintenance

Again, needs to be added to docs, and we should review whether defs are consistent, but is essentially assembly plus keeping it that way once it's assembled.

> biogenesis

It appears from various definitions that this is used inconsistently; some (e.g. cell projection biogenesis) could become "assembly," whereas others (e.g. ribosome biogenesis) seem to be synthesis of constituents + assembly (and maybe also + transport).

I still don't know what to do about "pore complex biogenesis" (GO:0046931) ...

> formation

Has a standard def (this one's documented!) in the context of development, but not more generally. Part of the formation-a-la-development def seems generally applicable, but possibly vague: "The process that gives rise to x. This process pertains to the initial formation of a structure from unspecified parts." The second sentence is a gloss relevant to the developmental context. A few of the non-developmental "formation" terms could probably be renamed to "assembly."

> biosynthesis

Has a standard definition (which needs an update to say "biosynthetic process,") and (I think) should only be used in the context of metabolism. Of six exceptions that I just found, one is a highly suspicious function term that ought to become obsolete forthwith, and the others are probably missing relationships but I'd have to ask (four for the interactions-between-organisms curators, and one about insect cuticle synthesis).

organization and biogenesis

Standard definition is in docs ("A process that is carried out at the cellular level which results in the formation, arrangement of constituent parts, or disassembly of [cellular component]"); formation + arrangement of parts does seem at least to overlap with assembly.

The difference between biogenesis/assembly and o&b is that the latter also includes disassembly.

> biogenesis and assembly

I don't see any difference from just "biogenesis," so I think these could be renamed.

I'll try to get the rest of the ggg + david to look at this item and weigh in ... m

Original comment by: mah11

[gocentral]

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oops, forgot to put in the ID for ribosomal subunit; it's GO:0033279

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Hi Midori,

I think you sorted this one so can close.

Val

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423 Originator: NO

Well, I sorted the original question, but then Chris hijacked the item ;) He brought some inconsistencies to light, which in turn made me notice that the documentation needs serious work ... so I'll leave this open for the sake of that stuff.

I oughta get back to it soon ... <sigh> m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Ah yes, didn't re-read the full thread.

Just clearing out the SF attic :(

Original comment by: ValWood

[gocentral]

OK, enough of this has been done as part of the larger effort that I think this is closable. See

http://wiki.geneontology.org/index.php/Cellular\_component\_processes

Original comment by: mah11

[gocentral]

• status: open-fixed --> closed-fixed

Original comment by: mah11

[gocentral]

I guess if ribosome /ribosome subunit and ribosome assembly/ ribosome subunit assembly are equivalent, for more consistent annotation they should merge rather than stay.

v

Original comment by: ValWood

[gocentral]

I added this comment to the wrong item didn't I....moving

Original comment by: ValWood

[gocentral]

So, it seems that for annotation consistency we should merge the terms.

I am not so sure about changing the relationship to has_part. We need to be careful because ribosome small subunit and ribosome large subunit would no longer automatically propagate to ribosome if we removed the part_of. I am convinced we need to retain the part_of relationships where they ensure the correct propagation of annotation, although has_part may also be appropriate.

Val Val

Original comment by: ValWood

[gocentral]

I just did it again, ignore previous comment I will move it to the correct item

Original comment by: ValWood

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11