Closed gocentral closed 1 year ago
gocentral
commented
11 years ago For eukaryotes there are also components to go with these processes:
GO:0005656 pre-replicative complex, which is child_of GO:0031261 DNA replication preinitiation complex
which explains why there are 2 processes associated with this! However, I still think it would be nice to have parental terms that apply to the whole taxonomic range.
Original comment by: bmeldal
gocentral
commented
11 years ago Original comment by: rebeccafoulger
gocentral
commented
11 years ago The primosome is part of the preinitiation complex, but travels with the DNA polymerase holoenzyme during the elongation phase of replication. The primosome is a multi-protein complex needed to lay down primers for Okazaki fragments.
http://en.wikipedia.org/wiki/Primosome
Original comment by: jimhu
gocentral
commented
11 years ago Hi Jim, The primosome is formed before the DNA polymerase joins up with the oriC and its function is more wide-reaching than just making primers for the Okasaki fragments. It acts during both, replication initiation and restart of replication after a stalled replication fork. I have spent weeks trying to get to the bottom of the definition and the wikipedia entry gets the replication initiation and restart of replication processes mixed up. The core of the primosome is the helicase and primase but it also contains a bunch of accessory proteins. My question is, can we extend the definition of pre-replicative complex to include prokaryote complexes? If yes, I don't have to define a new parent term for all the complexes that are part of the replication initiation which I am currently curating (for the new Complex Portal in IntAct).
References (pmids): 21856207 (review) 16677308 17588514 17139333 8663105 18179598 (introduction)
Regards, Birgit
Original comment by: bmeldal
gocentral
commented
11 years ago Hi Becky - could you deal with this first tomorrow please? There's a pending term for 'primosome complex' in FF, I've asked Paola not to commit it until this ticket is sorted. Ta.
Original comment by: jl242
gocentral
commented
11 years ago I would say yes, this can be extended to prokaryotes.
Original comment by: jimhu
gocentral
commented
11 years ago Morning,
To summarise the existing Eukaryotic GO terms (see PMID:23075259, also):
pre-RI DNA replication preinitiation complex ; GO:0031261 DNA replication preinitiation complex assembly ; GO:0071163
pre-RC pre-replicative complex ; GO:0005656 pre-replicative complex assembly ; GO:0006267
The pre-RI complex is formed by the assembly of additional proteins onto an existing pre-RC complex: DNA replication preinitiation complex ; GO:0031261 HAS_PART pre-replicative complex ; GO:0005656
Both CC terms have Eukaryotic taxon constraints due to their nuclear_part parentage. If we were to widen the definitions to include Prokaryotes, we'd loose this nuclear information. So we'd probably end up creating separate Euk and Prok terms anyway, whatever we call them. Therefore I'm inclined to create a separate replisome term for Prokaryotes (as currently logged in TermGenie).
Should the TG replisome term be is_a: protein-DNA complex ; GO:0032993 (similar to the existing pre-RC term, rather than just is_a: protein complex)?
thanks, Becky
Original comment by: rebeccafoulger
gocentral
commented
11 years ago It seems to me that the current definitions of many of these terms are way too specific, not only in nuclear parentage but also in naming components and specification of timing (e.g. in GO:0005656 ! pre-replicative complex).
IMO, the basic terms should be agnostic as to taxonomy and organellar location, and the specification of nuclear etc. should be by intersection below the agnostic terms. This may be functionally equivalent to "creating separate Euk and Prok terms anyway" but how this is done matters. In other words, agnostic terms should be create between protein complex and the current terms discussed above, and all current terms with "eukarotic chromosome" in their definitions should be children of their taxon/location-agnostic equivalents.
My concern is more general, so I will try to compose something for discussion on GO-discuss.
Original comment by: jimhu
gocentral
commented
11 years ago Hi Jim and Becky,
Thank you for your responses. I will leave the issue in your hands for now. I agree that a more hierarchial parentage would be very helpful!
Just one note, the GO:0030894 replisome term is ok as it is agnostic, it's the primosome term that I was trying to define in TG free form.
Becky, I'm at our Hackathon at The Nucleus for the rest of the week and on a course on Tuesday so you might not find me next door (except for first thing in the morning) but I will try to keep an eye on my emails.
Regards, Birgit
It seems to me that the current definitions of many of these terms are way too specific, not only in nuclear parentage but also in naming components and specification of timing (e.g. in GO:0005656 ! pre-replicative complex).
IMO, the basic terms should be agnostic as to taxonomy and organellar location, and the specification of nuclear etc. should be by intersection below the agnostic terms. This may be functionally equivalent to "creating separate Euk and Prok terms anyway" but how this is done matters. In other words, agnostic terms should be create between protein complex and the current terms discussed above, and all current terms with "eukarotic chromosome" in their definitions should be children of their taxon/location-agnostic equivalents.
My concern is more general, so I will try to compose something for discussion on GO-discuss.
\ [ontology-requests:#10156] definition of primosome**
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Wed May 01, 2013 08:48 AM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
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Original comment by: bmeldal
gocentral
commented
11 years ago Okay, so the simplest action is to make a taxon-agnostic grouping term for a Prokaryotic primosome term, and the Eukaryotic pre-RC and pre-RI terms:
protein-DNA complex ; GO:0032993 --[isa]replication origin complex ; GO:NEW ----[isa]primosome ; GO:NEW (submitted to TG)) ----[isa]pre-replicative complex ; GO:0005656 (pre-RC) ------[HAS_PART]DNA replication preinitiation complex ; GO:0031261 (pre-RI)
replication origin complex ; GO:NEW A protein-DNA complex that forms at the origin of replication or at the sites of replication restart, and is required for replication initiation or replication re-initiation.
Any naming/wording suggestions gratefully received.
Becky
Original comment by: rebeccafoulger
gocentral
commented
11 years ago Hi Becky,
It's a good start but I think the higher order hierarchies need more revision. For starters the GO:0031261 DNA replication preinitiation complex is described as a protein-DNA complex but is child of protein complex. I also feel that you switched the pre-RC and pre-RI around, at least in comparison to the hierarchy view. On top of that the GO:0030894 replisome doesn't seem to be in the same hierarchy... I'm in a meeting again for most of the day and at a workshop on Tuesday. I will try and catch you whether this afternoon or on Wednesday. I think it will be easier to sit down together and sort out all the relationships :)
Thanks, Birgit
On 02/05/2013 12:28, RFoulger wrote:
Okay, so the simplest action is to make a taxon-agnostic grouping term for a Prokaryotic primosome term, and the Eukaryotic pre-RC and pre-RI terms:
protein-DNA complex ; GO:0032993 --[isa]replication origin complex ; GO:NEW ----[isa]primosome ; GO:NEW (submitted to TG)) ----[isa]pre-replicative complex ; GO:0005656 (pre-RC) ------[HAS_PART]DNA replication preinitiation complex ; GO:0031261 (pre-RI)
replication origin complex ; GO:NEW A protein-DNA complex that forms at the origin of replication or at the sites of replication restart, and is required for replication initiation or replication re-initiation.
Any naming/wording suggestions gratefully received.
Becky
[ontology-requests:#10156] http://sourceforge.net/p/geneontology/ontology-requests/10156/ definition of primosome
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Wed May 01, 2013 01:45 PM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
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Dr. Birgit Meldal IntAct Curator European Bioinformatics Insitute Welcome Trust Sanger Centre Hinxton Cambridgeshire CB10 1SD
+44 1223 494107 bmeldal@ebi.ac.uk http://www.ebi.ac.uk/intact/
Original comment by: bmeldal
gocentral
commented
11 years ago There are pre-RCs in Proks, Euks and Archaea. So (in line with how we've done it for the ORC in GO), I will rename the existing GO:0005656 pre-RC term and create Prokaryotic and taxon-generic terms:
protein-DNA complex ; GO:0032993 --[isa]pre-replication complex (pre-RC) ; GO:NEW1 (Taxon AGNOSTIC) ----[isa]nuclear pre-replication complex ; GO:0005656 (RENAMED, EUKARYOTIC) ----[isa]DnaA pre-replication complex ; GO:NEW (PROKARYOTIC)
pre-replication complex ; GO:NEW1 (Taxon AGNOSTIC) A protein complex that forms at the origin of replication during the initial step of DNA replication and allows the origin to become competent, or 'licensed', for replication. is_a: protein-DNA complex Wikipedia: Pre-replication_complex
DnaA pre-replication complex ; GO:NEW2 (PROKARYOTIC) A protein-DNA complex containing the initiator protein DnaA bound to high-affinity recognition sites in the origin of replication, oriC. synonym: prokaryotic pre-RC (Wikipedia: Pre-replication_complex) PMID:19833870
All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone.
Which brings us full-circle back to the question of how the primosome fits in with the pre-RC terms. From the literature, the primosome appears to be further downstream from the pre-RC. I will move 'primosome complex ; GO:1990077' to be is_a: protein-DNA complex, and for now leave it as a sibling term to the new generic pre-RC term.
I will update the process 'complex assembly' terms to match.
Will do edits on Thursday morning if there's no objections. I'm off tomorrow (Tues) but will be back in Wednesday. Thanks, Becky
Original comment by: rebeccafoulger
gocentral
commented
11 years ago All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone. should read: All the pre-IC literature I've found is Eukaryotic, so I shall leave that term alone.
Other parentage edits I've done: primosome complex ; GO:1990077
DNA replication preinitiation complex ; GO:0031261 (pre-IC)
Original comment by: rebeccafoulger
gocentral
commented
11 years ago My understanding is that the analogous complexes in bacteria and viruses use different names but are functionally equivalent. I will email one of my friends who is a replication expert to ask about this.
Jim
On May 13, 2013, at 11:30 AM, RFoulger wrote:
All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone. should read: All the pre-IC literature I've found is Eukaryotic, so I shall leave that term alone.
Other parentage edits I've done: primosome complex ; GO:1990077
- is_a: protein complex ; GO:0043234
- is_a: protein-DNA complex ; GO:0032993
DNA replication preinitiation complex ; GO:0031261 (pre-IC)
- is_a: protein complex ; GO:0043234
- is_a: protein-DNA complex ; GO:0032993
[ontology-requests:#10156] definition of primosome
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Mon May 13, 2013 03:46 PM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
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Jim Hu Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054
Original comment by: jimhu
gocentral
commented
11 years ago Thanks, Jim. That would be great! I am only curating the E. coli complexes at the moment (got to start somewhere...). Becky and I came to the conclusion that most people would intuitively regard the replication preinitiation complex and the primosome as functionally homologous complexes. Similarly, the pre-replicative complex would be the equivalent to the DnaA-oriC complex. Different structures, same function.
Birgit
On 13/05/2013 19:09, Jim Hu wrote:
My understanding is that the analogous complexes in bacteria and viruses use different names but are functionally equivalent. I will email one of my friends who is a replication expert to ask about this.
Jim
On May 13, 2013, at 11:30 AM, RFoulger wrote:
All the pre-RI literature I've found is Eukaryotic, so I shall leave that term alone. should read: All the pre-IC literature I've found is Eukaryotic, so I shall leave that term alone. Other parentage edits I've done: primosome complex ; GO:1990077 - is_a: protein complex ; GO:0043234 + is_a: protein-DNA complex ; GO:0032993 DNA replication preinitiation complex ; GO:0031261 (pre-IC) - is_a: protein complex ; GO:0043234 + is_a: protein-DNA complex ; GO:0032993 [ontology-requests:#10156] </p/geneontology/ontology-requests/10156/> definition of primosome Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Mon May 13, 2013 03:46 PM UTC Owner: RFoulger Hi, I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes: GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly. I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition. Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171) Thanks, Birgit Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10156/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/Jim Hu Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054
[ontology-requests:#10156] </p/geneontology/ontology-requests/10156/> definition of primosome
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Mon May 13, 2013 04:30 PM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
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Dr. Birgit Meldal IntAct Curator European Bioinformatics Insitute Welcome Trust Sanger Centre Hinxton Cambridgeshire CB10 1SD
+44 1223 494107 bmeldal@ebi.ac.uk http://www.ebi.ac.uk/intact/
Original comment by: bmeldal
gocentral
commented
11 years ago Could you also please add is_a GO:0033202 DNA helicase complex
Thanks, Birgit
Original comment by: bmeldal
gocentral
commented
11 years ago Hi Jim, Have you had any feedback from your replication colleague? There's a number of terms from Birgit in the TermGenie queue (children of primosome) that I'm keen to add in, which depend on the outcome of the primosome discussion. Thanks, Becky
Original comment by: rebeccafoulger
gocentral
commented
11 years ago not yet. I will follow up.
Sent from my iPad
On May 22, 2013, at 5:32 AM, "RFoulger" rfoulger@users.sf.net wrote:
Hi Jim, Have you had any feedback from your replication colleague? There's a number of terms from Birgit in the TermGenie queue (children of primosome) that I'm keen to add in, which depend on the outcome of the primosome discussion. Thanks, Becky
[ontology-requests:#10156] definition of primosome
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Tue May 14, 2013 10:38 AM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
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Original comment by: jimhu
gocentral
commented
11 years ago Hi Rebecca,
Response from Tania Baker at MIT. The reference to her shoulder is that she was injured in a bike accident on the way to the memorial service for the MIT policeman who was killed by the Boston bombers.
Are there followup questions needed?
Jim
Hi Jim:
I did see it---but I haven't had a chance to respond..
I basically agree with your comments "understanding".... although of course not everyone would agree with this (or any) nomenclature call.
I'd go for the "more inclusive"
is that enough help?
(shoulder had a bit of a set back... hurts etc... back on pain meds and imobilization----I may need surgery, but trying to avoid it!)
best,
tania
On May 22, 2013, at 10:21 AM, Jim Hu wrote:
Hi Tania,
Did you see this before?
Jim
Hi Tania,
How is your shoulder? I'm having a discussion with people in the GO consortium about whether these two terms should have eukaryotic in their definitions.
http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006267_!_pre-replicative_complex_assembly
My sense is that the definitions are too narrow. Actually, I think the whole set of terms relating to DNA replication could use an overhaul, but for now my question is whether it is useful to think of the complexes at the origin as analogous.
My understanding is that for both bacteria and eukaryotes the same basic steps happen, but there are differences in the order
Origin recognition - DnaA, lambdaO, ORC Origin unwinding (not in euks) Helicase recruitment (DnaB, lambdaP, MCMs) (additional helicase-dependent unwinding?) Recruitment of the holoenzyme Leading strand initiation Lagging strand initiation at some point after that we wouldn't think of it as initiation anymore... where would that be?
Thanks!
Best,
Jim
Jim Hu Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054
On May 22, 2013, at 5:32 AM, RFoulger wrote:
Hi Jim, Have you had any feedback from your replication colleague? There's a number of terms from Birgit in the TermGenie queue (children of primosome) that I'm keen to add in, which depend on the outcome of the primosome discussion. Thanks, Becky
[ontology-requests:#10156] definition of primosome
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Tue May 14, 2013 10:38 AM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
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Jim Hu Professor Dept. of Biochemistry and Biophysics 2128 TAMU Texas A&M Univ. College Station, TX 77843-2128 979-862-4054
Original comment by: jimhu
gocentral
commented
11 years ago Hi Jim,
(just back after the bank holiday).. Thanks for following this up. I'm going to make a taxon-generic term for pre-replicative complex, and make the existing GO:0005656 Eukaryotic-restricted.
I'll expand the pre-IC term (GO:0031261) to make it taxon-generic.
I'm still confused about how the primosome (GO:1990077) fits with the pre-RC and pre-IC complexes (if atall). Could you please ask Tania how they are connected.
Thanks again… and I hope her shoulder injury heals quickly. Becky
Original comment by: rebeccafoulger
gocentral
commented
11 years ago These 4 complex terms (submitted by Birgit to TG freeform) may need rehousing under more specific primosome or pre-RC terms, once the primosome/pre-RC terms have been finalised:
DnaB-DnaC complex ; GO:1990100 DnaA-oriC complex ; GO:1990101 DnaA-DiaA complex ; GO:1990102 DnaA-HU complex ; GO:1990103
Original comment by: rebeccafoulger
gocentral
commented
11 years ago Created new taxon-agnostic pre-RC terms: pre-replicative complex ; GO:0036387 pre-replicative complex assembly ; GO:0036388
and renamed the existing terms to be Eukaryotic, based on their existing parentage: pre-replicative complex ; GO:0005656 pre-replicative complex assembly ; GO:0006267
nuclear pre-replicative complex ; GO:0005656 nuclear pre-replicative complex assembly ; GO:0006267
Created new bacterial pre-RC terms: bacterial pre-replicative complex ; GO:0036389 bacterial pre-replicative complex assembly ; GO:0036390 (discussed in office, and couldn't think of better name that doesn't contain 'bacterial')
STILL TO DO ON THIS TICKET: ! Sort out how primosome fits in with the pre-RC and pre-RI complexes. ! Rehouse Birgits DnaA/DnaB complex terms accordingly (see above)
Original comment by: rebeccafoulger
gocentral
commented
11 years ago Thanks, Becky :)
On 05/06/2013 17:06, RFoulger wrote:
Created new taxon-agnostic pre-RC terms: pre-replicative complex ; GO:0036387 pre-replicative complex assembly ; GO:0036388
and renamed the existing terms to be Eukaryotic, based on their existing parentage: pre-replicative complex ; GO:0005656 pre-replicative complex assembly ; GO:0006267
nuclear pre-replicative complex ; GO:0005656 nuclear pre-replicative complex assembly ; GO:0006267Created new bacterial pre-RC terms: bacterial pre-replicative complex ; GO:0036389 bacterial pre-replicative complex assembly ; GO:0036390 (discussed in office, and couldn't think of better name that doesn't contain 'bacterial')
STILL TO DO ON THIS TICKET: ! Sort out how primosome fits in with the pre-RC and pre-RI complexes. ! Rehouse Birgits DnaA/DnaB complex terms accordingly (see above)
[ontology-requests:#10156] http://sourceforge.net/p/geneontology/ontology-requests/10156/ definition of primosome
Status: open Labels: Other term-related request Created: Mon Apr 29, 2013 08:42 AM UTC by Birgit Meldal Last Updated: Mon Jun 03, 2013 04:17 PM UTC Owner: RFoulger
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/geneontology/ontology-requests/10156/
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Dr. Birgit Meldal IntAct Curator European Bioinformatics Insitute Welcome Trust Sanger Centre Hinxton Cambridgeshire CB10 1SD
+44 1223 494107 bmeldal@ebi.ac.uk http://www.ebi.ac.uk/intact/
Original comment by: bmeldal
gocentral
commented
10 years ago Original comment by: rebeccafoulger
gocentral
commented
10 years ago Reassigning 'CC complex' SF items to David O-S, before I finish.
Original comment by: rebeccafoulger
gocentral
commented
10 years ago Original comment by: dosumis
gocentral
commented
10 years ago Original comment by: dosumis
pgaudet
commented
6 years ago @bmeldal Can you please tell me what is the action remaining on this ticket ?
Thanks, Pascale
bmeldal
commented
6 years ago On 5 June 2013 Becky signed off with:
STILL TO DO ON THIS TICKET:
- [ ] Sort out how primosome fits in with the pre-RC and pre-RI complexes.
- [ ] Rehouse Birgits DnaA/DnaB complex terms accordingly (see above)
I don't think anything further was done away from this ticket. However, we've started started looking at the TFs with Astrid and Ruth, so I may be able to answer these points once I got my teeth into the TF philosophy! (although the GREEKC grant only seems to look at human)
I'll keep a note to come back to this ticket soon :)
pgaudet
commented
6 years ago hi Birgit,
I am assigning the ticket to you so that you can give us more information as to how to move forward.
Thanks :)
Pascale
bmeldal
commented
6 years ago @RLovering we should keep this ticket in mind when we discuss TFs with Astrid (what's her GH id?)
RLovering
commented
6 years ago sorry I don't know
pgaudet
commented
6 years ago Hi @bmeldal
This is DNA replication; are you sure it's related to tx factors ?
Thanks, Pascale
bmeldal
commented
6 years ago Doh! Yes, not the same thing! Although, both synthesise nt chains ;-)
I’ll look into it.
pgaudet
commented
6 years ago Hi @bmeldal - any progress on this one ?
ValWood
commented
1 year ago Closing as out of date. If any action is required please summarize in a new ticket.
Hi,
I requested a term for the primosome on Friday but now saw that there are already names in the ontology biological process lineage that refer to this complex in eukaryotes:
GO:0071163 DNA replication preinitiation complex assembly, and GO:0006267 pre-replicative complex assembly.
I'm struggling to see the difference between these two terms, they are entirely parallel in the ontology and don't really differ in their definition.
Although they refer to eukaryotic replication it looks as if they could also be applicable to prokaryote replication. In that case we could call the primosome complex either pre-replicative complex or replication preinitiation complex. I would probably prefer pre-replicative complex as then it can also refer to the complexes formed during restart of replication at a stalled replication fork (see SF request 3612171)
Thanks, Birgit
Reported by: bmeldal
Original Ticket: geneontology/ontology-requests/10156