Closed Antonialock closed 1 year ago
I think this deserved wider discussion at the GO meeting. Up to now there have been no guidelines on how to do this...it seems quite arbitrary when a term is accepted or refused, but we need to make annotations consistently.
In case its useful, this is what I wrote before ANtonia created this ticket:
We extend the “transcription factor activity” term in 3 main ways i) The gene(s) regulated by the transcription ii) The response to a specific environmental change iii) If this transcription directly regulates a specific process (NOTE: we only do this when the transcription factor is DIRECTLY CONTROLLING THE PATHWAY (i.e. for metabolic processes the pathway activation is often transcriptional. We would not link to regulation instances where the TF is only ensuring that a gene product present is present at the right time or is constitutively expressed, and the pathway the gene product is involved in are controlled post-transcriptionally in a “NORMAL” cell (e.g most genes regulating cell cycle transitions). This allows us to accurately represent cases where the regulation of the level of a specific gene product is directly regulating a specific process). However, to represent the information fully we often need to link annotations provided for i) ii) and iii);
There are 2 ways to capture the information fully:
Historically we have done this by requesting a composite process term to link to, and would represent, for example:
MF GO:0001078 has regulation target gene y, in_response_to iron ion, part_of “negative regulation of transcription involved in negative regulation ferrichrome biosynthesis” MF GO:0001078 has regulation target gene x, in_response_to iron ion, part_of “negative regulation of transcription involved in negatively regulation of ornithine metabolism”
So in Antonias’s example:
transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding part_of negative regulation of transcription from RNA polymerase II promoter in response to iron (existing process)
this does not tell the full story so Antonia requested
Option1
negative regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron
because it seemed neater than post-composing:
Option2
transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding part_of negative regulation of transcription from RNA polymerase II promoter in response to iron (existing process),negative regulation of transcription from RNA polymerase II promoter involved in negative regulation of ferrichrome biosynthetic process
option1 was vetoed. However, although clunky, but it does follow a previous precedent based on existing terms, and it captures everything completely.
So, if we don’t have these terms we need alternative guidelines of how to do this compliantly.
Option3 A proposal:
MF GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding has_input sib1 part_of (GONEW negative regulation of ferrichrome biosynthetic process, in response to iron) (using a compound extension) has_input sib2 part_of (GONEW negative regulation of ferrichrome biosynthetic process, in response to iron) (using a compound extension)
This captures everything because the MF GO:0001078 already has an ontology encoded F-P link to GO:0000122 negative regulation of transcription from RNA polymerase II promoter
And a biologist reading this page would understand the statement without any loss of information, because the transcriptional repressor is inherently coupled to regulation of transcription from RNA polymerase II in their head (no need to repeat it in the extension, or a precomposed term explicitly).
Thus a DNA binding Transcription Factor like “GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding” would end up with a bunch of Biological Process annotations which included:
This approach would seems to be more LEGO compliant. and, we could easily migrate our existing TF annotations to this format, but could we therefore obsolete the terms in GO that already exist coupling transcriptional processes to the processes that they directly regulate? For example most descendants here: http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006357#term=children
This mught be considered unimportant if LEGO annotation is the long term goal, BUT
@cmungall @ukemi @dosumis @thomaspd
Hi @ukemi and @dosumis , Could one of you take this ticket, please? I think that would make more sense as you'll attend the GOC meeting in person, but let me know if not. Many thanks!
@ValWood could you please add this to the meeting agenda and present your proposals?
added
Thanks @ValWood for adding to the agenda. I'll assign this ticket to myself as well as @ukemi and @dosumis , and set to pending until you discuss at the GOC LA meeting.
Hi @ValWood and @Antonialock , Now that the GOC meeting is over... if you had a chance to discuss the issue above, please comment on this ticket detailing a course of action. Or if further discussion is needed, please make a note here as to when that is scheduled. Thanks!
Hi Paola,
I think in general this was considered to be a good approach at lest for transcription factors. I propose this solution for various modification terms too. There were concerns about this but I think there are alternative ways to capture this information consistently. I need to check. I think a future annotation call is the best place to evaluate this further before a solution is implemented.
I will put this on my list and address it over the coming weeks. in the meantime you can set to "pending"
Sorry this has taken so long. I tidied my slides and added to the Google drive The title is "precomposing GO terms at annotation time" This is probably related to some other tickets too. I think the solution is similar. I don't know that any decision was made, so this probably needs to be revisited on one of the future annotation calls? @ukemi @vanaukenk
Thanks, @ValWood.
Yes, I think it would be good to follow up with this on a future annotation call. Will confer with @ukemi
Hi @vanaukenk and @ValWood,
Given the broad scope and timescale for this ticket, I will unassign myself now, and add Kimberly instead. Thanks.
@pgaudet you may have addressed this already? Anyway I am removing myself becasue I don't think I have a task here?
@Antonialock was asking generally, "could you obsolete all the transcription regulatory terms that we "shouldn't" annotate to (and for which you won't create new sibling terms) - many are descendants of GO:0006357"
There are still a couple of hundred terms that should be obsoleted, and re-annotated as 'regulation of transcription from RNA polymerase II promoter ' part_of' reposnse to x' (for example):
Should we tackled those ?
Most are assigned by SGD and PomBase
Pascale
How did you get the AmiGO numbers. I don't see so many. If it is as many as you see it might not be a good use of time. However I only see 22 under transcription/stress for fission yeast. I would be happy to do those.
That said, these cases do not bother me so much because the stress process is directly regulated by transcription. Previously I objected to the transcriptional regulation of x terms when the process was post-transcriptionally regulated.
I would say SGD's call, because they have the most- but I think the numbers are incorrect (too high) or at least- I can't figure how you got them.
That said, these cases do not bother me so much because the stress process is directly regulated by transcription. Previously I objected to the transcriptional regulation of x terms when the process was post-transcriptionally regulated.
It is confusing as a curator to see a large number of terms available, but we can't add new sibling terms.
@ValWood
These are all the annotations I find for 'regulation of transcription in response to x'
https://docs.google.com/spreadsheets/d/1dXW1T7ZoURb5Wll_pR7FnGfxGMwIY7HT-UnI12lKTyE/edit?usp=sharing
Pombase has 74 in that list (my previous query was probably too wide).
Thanks, Pascale
I would be happy to decompose them, but SGD has a lot and it does not seem to be a priority.
AS long as curators know that these terms will be deprecated? Maybe we can add a comment recommending post compostions using GO-CAm /extension.
My concern is that, if new ones terms like this are not being added, and old ones will be removed, if people continue to use them it makes more work when we eventually come to fix the annotation. It doesn't seem that it should be high priority in the entire scheme of things though?
So in summary, I don't mind either way....it would be good, but it isn't critical...
it's a bunch of annotations to revisit. i've done a few so far (single digits). i don't mind doing it because i think the long combinatorial terms are suboptimal. however it's now in a long list of all the various GO clean-ups that are going on.
i do hope that we stop making new terms like this. my concern, especially around transcription, is that we'll be asked to change them back at some point. (because transcription keeps getting revisited...)
Well hopefully not more than very 10 years !
@srengel Should we then obsolete terms that are not or seldom used, to at least avoid creating new annotations ?
Personally in these situations I think it is good to get rid of the ones that are only used a few times or not at all t odicourage further use.... Also it breaks the task down and makes it less daunting....
These 55 terms all have 0 annotations; I'll send an obsoletion notice:
negative regulation of G1/S transition of mitotic cell cycle by transcription from RNA polymerase II promoter 0
negative regulation of cell-cell adhesion by transcription from RNA polymerase II promoter 0
negative regulation of cellular amino acid biosynthetic process by transcription from RNA polymerase II promoter 0
negative regulation of cellular hyperosmotic salinity response by transcription from RNA polymerase II promoter 0
negative regulation of cellular response to alkaline pH by transcription from RNA polymerase II promoter 0
negative regulation of ceramide biosynthetic process by transcription from RNA polymerase II promoter 0
negative regulation of filamentous growth of a population of unicellular organisms in response to starvation by transcription from RNA polymerase II promoter 0
negative regulation of invasive growth in response to glucose limitation by transcription from RNA polymerase II promoter 0
negative regulation of mating type switching by transcription from RNA polymerase II promoter 0
negative regulation of neuron apoptotic process by transcription from RNA polymerase II promoter 0
negative regulation of phosphatidylcholine biosynthetic process by transcription from RNA polymerase II promoter 0
negative regulation of pseudohyphal growth by transcription from RNA polymerase II promoter 0
positive regulation of arginine biosynthetic process by transcription from RNA polymerase II promoter 0
positive regulation of cellular alcohol catabolic process by transcription from RNA polymerase II promoter 0
positive regulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter 0
positive regulation of ethanol catabolic process by transcription from RNA polymerase II promoter 0
positive regulation of fatty acid beta-oxidation by transcription from RNA polymerase II promoter 0
positive regulation of filamentous growth of a population of unicellular organisms in response to starvation by transcription from RNA polymerase II promoter 0
positive regulation of flocculation via cell wall protein-carbohydrate interaction by transcription from RNA polymerase II promoter 0
positive regulation of peroxisome organization by transcription from RNA polymerase II promoter 0
positive regulation of phospholipid biosynthetic process by transcription from RNA polymerase II promoter 0
positive regulation of phosphatidylcholine biosynthetic process by transcription from RNA polymerase II promoter 0
positive regulation of phosphatidylserine biosynthetic process by transcription from RNA polymerase II promoter 0
positive regulation of pseudohyphal growth by transcription from RNA polymerase II promoter 0
positive regulation of pyrimidine-containing compound salvage by transcription from RNA polymerase II promoter 0
positive regulation of pyrimidine-containing compound salvage by positive regulation of transcription from RNA polymerase II promoter 0
positive regulation of sulfate assimilation by transcription from RNA polymerase II promoter 0
regulation of carbohydrate metabolic process by transcription from RNA polymerase II promoter 0
negative regulation of inositol biosynthetic process by transcription from RNA polymerase II promoter 0
positive regulation of inositol biosynthetic process by transcription from RNA polymerase II promoter 0
regulation of 4,6-pyruvylated galactose residue biosynthetic process by transcription from RNA polymerase II promoter 0
regulation of 4,6-pyruvylated galactose residue biosynthetic process by regulation of transcription from RNA polymerase II promoter 0
regulation of cellular response to oxidative stress by transcription from RNA polymerase II promoter 0
regulation of cellular response to oxidative stress by regulation of transcription from RNA polymerase II promoter 0
regulation of conjugation with cellular fusion by transcription from RNA polymerase II promoter 0
negative regulation of induction of conjugation with cellular fusion by transcription from RNA polymerase II promoter 0
regulation of fungal-type cell wall biogenesis by transcription from RNA polymerase II promoter 0
regulation of fungal-type cell wall biogenesis by regulation of transcription from RNA polymerase II promoter 0
regulation of meiotic nuclear division by transcription from RNA polymerase II promoter 0
positive regulation of meiotic nuclear division by transcription from RNA polymerase II promoter 0
negative regulation of phenotypic switching by transcription from RNA polymerase II promoter 0
positive regulation of phenotypic switching by transcription from RNA polymerase II promoter 0
negative regulation of phenotypic switching by regulation of transcription from RNA polymerase II promoter 0
regulation of pyrimidine nucleotide biosynthetic process by transcription from RNA polymerase II promoter 0
regulation of pyrimidine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter 0
regulation of thiamine biosynthetic process by transcription from RNA polymerase II promoter 0
regulation of thiamine biosynthetic process by regulation of transcription from RNA polymerase II promoter 0
negative regulation of leucine import by transcription from RNA polymerase II promoter 0
negative regulation of leucine import by regulation of transcription from RNA polymerase II promoter 0
positive regulation of sodium ion transport by transcription from RNA polymerase II promoter 0
positive regulation of sulfite transport by transcription from RNA polymerase II promoter 0
regulation of glucose import by transcription from RNA polymerase II promoter 0
regulation of glucose import by regulation of transcription from RNA polymerase II promoter 0
regulation of iron ion transport by transcription from RNA polymerase II promoter 0
OK ?
And open tickets for the other terms left.
Thanks, Pascale
Dear all,
The proposal has been made to obsolete the following pre-composed terms:
GO:0100052 negative regulation of G1/S transition of mitotic cell cycle by transcription from RNA polymerase II promoter GO:0100017 negative regulation of cell-cell adhesion by transcription from RNA polymerase II promoter GO:0100025 negative regulation of cellular amino acid biosynthetic process by transcription from RNA polymerase II promoter GO:0100044 negative regulation of cellular hyperosmotic salinity response by transcription from RNA polymerase II promoter GO:0100043 negative regulation of cellular response to alkaline pH by transcription from RNA polymerase II promoter GO:0100007 negative regulation of ceramide biosynthetic process by transcription from RNA polymerase II promoter GO:0100064 negative regulation of filamentous growth of a population of unicellular organisms in response to starvation by transcription from RNA polymerase II promoter GO:0100040 negative regulation of invasive growth in response to glucose limitation by transcription from RNA polymerase II promoter GO:0100050 negative regulation of mating type switching by transcription from RNA polymerase II promoter GO:0100069 negative regulation of neuron apoptotic process by transcription from RNA polymerase II promoter GO:0100049 negative regulation of phosphatidylcholine biosynthetic process by transcription from RNA polymerase II promoter GO:0100042 negative regulation of pseudohyphal growth by transcription from RNA polymerase II promoter GO:0100046 positive regulation of arginine biosynthetic process by transcription from RNA polymerase II promoter GO:0100037 positive regulation of cellular alcohol catabolic process by transcription from RNA polymerase II promoter GO:1900422 positive regulation of cellular alcohol catabolic process by positive regulation of transcription from RNA polymerase II promoter GO:1900392 regulation of transport by negative regulation of transcription from RNA polymerase II promoter GO:0100005 positive regulation of ethanol catabolic process by transcription from RNA polymerase II promoter GO:0100013 positive regulation of fatty acid beta-oxidation by transcription from RNA polymerase II promoter GO:1904741 positive regulation of filamentous growth of a population of unicellular organisms in response to starvation by transcription from RNA polymerase II promoter GO:0100004 positive regulation of peroxisome organization by transcription from RNA polymerase II promoter GO:0100032 positive regulation of phospholipid biosynthetic process by transcription from RNA polymerase II promoter GO:0100048 positive regulation of phosphatidylcholine biosynthetic process by transcription from RNA polymerase II promoter GO:0100055 positive regulation of phosphatidylserine biosynthetic process by transcription from RNA polymerase II promoter GO:0100041 positive regulation of pseudohyphal growth by transcription from RNA polymerase II promoter GO:0100068 positive regulation of pyrimidine-containing compound salvage by transcription from RNA polymerase II promoter GO:1904001 positive regulation of pyrimidine-containing compound salvage by positive regulation of transcription from RNA polymerase II promoter GO:0100053 positive regulation of sulfate assimilation by transcription from RNA polymerase II promoter GO:0100024 regulation of carbohydrate metabolic process by transcription from RNA polymerase II promoter GO:0100047 negative regulation of inositol biosynthetic process by transcription from RNA polymerase II promoter GO:0100015 positive regulation of inositol biosynthetic process by transcription from RNA polymerase II promoter GO:0100034 regulation of 4,6-pyruvylated galactose residue biosynthetic process by transcription from RNA polymerase II promoter GO:1900416 regulation of 4,6-pyruvylated galactose residue biosynthetic process by regulation of transcription from RNA polymerase II promoter GO:0100038 regulation of cellular response to oxidative stress by transcription from RNA polymerase II promoter GO:1900427 regulation of cellular response to oxidative stress by regulation of transcription from RNA polymerase II promoter GO:0100028 regulation of conjugation with cellular fusion by transcription from RNA polymerase II promoter GO:0100066 negative regulation of induction of conjugation with cellular fusion by transcription from RNA polymerase II promoter GO:0100033 regulation of fungal-type cell wall biogenesis by transcription from RNA polymerase II promoter GO:1900415 regulation of fungal-type cell wall biogenesis by regulation of transcription from RNA polymerase II promoter GO:0100051 regulation of meiotic nuclear division by transcription from RNA polymerase II promoter GO:0100051 positive regulation of meiotic nuclear division by transcription from RNA polymerase II promoter GO:0100057 regulation of phenotypic switching by transcription from RNA polymerase II promoter GO:0100059 negative regulation of phenotypic switching by transcription from RNA polymerase II promoter GO:0100058 positive regulation of phenotypic switching by transcription from RNA polymerase II promoter GO:0100039 regulation of pyrimidine nucleotide biosynthetic process by transcription from RNA polymerase II promoter GO:1900448 regulation of pyrimidine nucleotide biosynthetic process by positive regulation of transcription from RNA polymerase II promoter GO:0100016 regulation of thiamine biosynthetic process by transcription from RNA polymerase II promoter GO:1900382 regulation of thiamine biosynthetic process by regulation of transcription from RNA polymerase II promoter GO:0100065 negative regulation of leucine import by transcription from RNA polymerase II promoter GO:1902574 negative regulation of leucine import by regulation of transcription from RNA polymerase II promoter GO:0100003 positive regulation of sodium ion transport by transcription from RNA polymerase II promoter GO:0100006 positive regulation of sulfite transport by transcription from RNA polymerase II promoter GO:0100018 regulation of glucose import by transcription from RNA polymerase II promoter GO:1900389 regulation of glucose import by regulation of transcription from RNA polymerase II promoter GO:0100021 regulation of iron ion transport by transcription from RNA polymerase II promoter
The reason for obsoletion is that these should be captured as GO-CAM models.
There are 0 experimental annotations to those terms. There are 0 InterPro2GO mappings to those term. Those terms are not included in any subset(s).
Any comments can be added to the issue: https://github.com/geneontology/go-ontology/issues/12739
We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on August 23rd. Unless objections are received by August 23rd, we will assume that you agree to this change.
Thanks, Pascale
Also:
Hi Pascale and Val, This is fine by me, and the earlier proposal by Val seems sensible (17 Oct 2016). We extend the “transcription factor activity” term in 3 main ways i) The gene(s) regulated by the transcription ii) The response to a specific environmental change iii) If this transcription directly regulates a specific process MF GO:0001078 transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding has_input sib1 part_of (GONEW negative regulation of ferrichrome biosynthetic process, in response to iron) (using a compound extension) has_input sib2 part_of (GONEW negative regulation of ferrichrome biosynthetic process, in response to iron) (using a compound extension)
I am concerned about Val's point in the 17 Oct 2016 comment: (NOTE: we only do this when the transcription factor is DIRECTLY CONTROLLING THE PATHWAY (i.e. for metabolic processes the pathway activation is often transcriptional. We would not link to regulation instances where the TF is only ensuring that a gene product present is present at the right time or is constitutively expressed, and the pathway the gene product is involved in are controlled post-transcriptionally in a “NORMAL” cell....This allows us to accurately represent cases where the regulation of the level of a specific gene product is directly regulating a specific process).
I would suggest that ensuring proteins are present at the right time is essential. For example extracellular matrix proteins have to be present in order to create a heart valve. This is not about regulating a process it is about the required consistuents of the tissue or cell being available in order for the cell or tissue to develop or differentiate in an appropriate way. Often this is exactly what the TF is there for, producing this volume of extracellular matrix proteins at the wrong time would lead to a very fibrous probably non-functional heart. But perhaps I am just being oversensitive to this point. Just want to make sure this isn't a new rule ;)
Yes. I think there is a subtle difference here. These genes are switched on in specific cell types, so this is really regulating this developmental programme. The beginning of the programme (decision to develop into x...) is directly controlled by transcription.
With the cell cycle or constitutive processes, you need to ensure the components are present but the transcription is not controlling when the process occurs. Also for cell cycle, a transition needs to occur for the process to begin and this is controlled by the environment, nutrients, size. So for example transcription does not directly control DNA replication, or the G2/M transition, or chromosome segregation.
With beginnings and ends it would be easy to differentiate.
Presumably the developmental programmes begin with the signalling to transcribe cell-type specific genes. For the cell cycle, people who work on this would not say that, for example the regulation of the G2/M transition began with the transcription of the genes. It begins post-trancriptionally with the signalling that activates cdc2 (via phosphorylation events which sense cell size and nutrient status, but not via transcription).
More than anything we need beginnings and ends of the major (i.e. slim level) processes....
Ok I think I understand the difference. thanks Ruth
I've done the first batch. I'll check what annotations are left at the next release and do another group of terms.
Pascale
A few more terms:
No annotations :
Thanks, Pascale
Ready:
Obsoleted:
[x] GO:0035968 regulation of sterol import by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1904788 positive regulation of induction of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1902625 negative regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1900406 regulation of conjugation with cellular fusion by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1902353 positive regulation of induction of conjugation with cellular fusion by negative regulation of transcription from RNA polymerase II promoter by pheromones 0 annot
[x] GO:0035960 regulation of ergosterol biosynthetic process by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:0035961 positive regulation of ergosterol biosynthetic process by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:0072364 regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1900403 negative regulation of cellular amino acid biosynthetic process by negative regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:0072366 regulation of cellular ketone metabolic process by positive regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:0072365 regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1900465 negative regulation of arginine catabolic process by negative regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1900466 positive regulation of arginine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:0072367 regulation of cellular ketone metabolic process by regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:0072368 regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter -> 1 BHF left
[x] GO:0072369 regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter -> 1 BHF left
[x] GO:0035969 regulation of lipid transport by positive regulation of transcription from RNA polymerase II promoter 0 annot
[x] GO:1990872 negative regulation of sterol import by negative regulation of transcription from RNA polymerase II promoter 0 annot
UCL done
UCL done
remaining terms
@ValWood Are you OK to obsolete all the mitotic ones ? I thought you said some of them were pathways.
I think I said that some were direct regulation (i.e there is a feedback loop at G1/S in cerevisiae, where the transcription is directly upregulated and this transcriptional increase directly contributes to the regulation of the transition). In pombe this is all post-transcriptionally regulated as far as we know, so we would never use the precomposed terms.
That said, I think this (whether the transcription is directly part of the process, or causally upstream) could be modelled more clearly without pre-composing these terms....
I think this can close now? GO:0051038 negative regulation of transcription involved in meiotic cell cycle 253 annotations GO:0090419 negative regulation of transcription involved in G2/M transition of mitotic cell cycle 21 annotations GO:0071930 negative regulation of transcription involved in G1/S transition of mitotic cell cycle 820
but the process here is more complex so we can deal with these separately. Needs advice from G1 expert. There is some sort of transcriptional positive feedback required for the transition.
Many terms above have not yet been obsolete (https://github.com/geneontology/go-ontology/issues/12739#issuecomment-696227832)
@RLovering
I will obsolete 'GO:1900094 regulation of transcription from RNA polymerase II promoter involved in determination of left/right symmetry' which you had requested. There are no annotations, it's a parent of 'GO:0038107 nodal signaling pathway involved in determination of left/right asymmetry' which does have annotations, but that can stay under signaling.
Let me know if this causes problems.
Thanks, Pascale
Dear all,
The proposal has been made to obsolete the precomposed terms under GO:0046019 regulation of transcription from RNA polymerase II]). Few terms are left:
Precomposed with heart development:
Precomposed with kidney development:
Precomposed with spermatogenesis
Annotations are here: https://docs.google.com/spreadsheets/d/1v4Vs1zHiySAMqEUEmiF2uuRfTDRZmET52mokg8Qp3oA/edit#gid=0
You can comment here:
We'd like to obsolete these terms by February 10th.
Thanks, Pascale
The proposal has been made to obsolete the precomposed terms under GO:0046019 regulation of transcription from RNA polymerase II]). Few terms are left ; this next list focuses on terms precomposed with yeast mating behavior:
GO:0046019 regulation of transcription from RNA polymerase II promoter by pheromones
GO:0046020 negative regulation of transcription from RNA polymerase II promoter by pheromones
GO:0007329 positive regulation of transcription from RNA polymerase II promoter by pheromones
GO:0001196 regulation of mating-type specific transcription from RNA polymerase II promoter
GO:0001198 negative regulation of mating-type specific transcription from RNA polymerase II promoter
GO:0001197 positive regulation of mating-type specific transcription from RNA polymerase II promoter
30 SGD @srengel
3 CGD @marekskrzypek
4 PomBase @ValWood
3 Complex portal @Kalpanapanneerselvam
Annotations are here: https://docs.google.com/spreadsheets/d/1XJve8auS2BcWn6PaRcUq6S2t66-EbQtW37nINTR1UJ0/edit#gid=0
I am not sure where to move these annotations; perhaps there are signaling terms that are appropriate?
You can comment here: https://github.com/geneontology/go-ontology/issues/12739#issuecomment-1029232870
I'd like to proceed to the obsoletion on February 10th.
Thanks, Pascale
ADDENDUM
Will also obsolete the parent classes (with no annotations: )
Obsolete GO:0060469 positive regulation of transcription involved in egg activation No annotations
Terms left:
'carbon catabolite regulation of transcription from RNA polymerase II promoter' 'nitrogen catabolite regulation of transcription from RNA polymerase II promoter' 'regulation of transcription from RNA polymerase II promoter in response to iron' 'regulation of transcription from RNA polymerase II promoter in response to stress' 'regulation of transcription from RNA polymerase II promoter involved in meiotic cell cycle'
These are probably signaling pathways. I'll open other tickets for these.
No annotations.
Transcription + transport terms:
Annotations are here: https://docs.google.com/spreadsheets/d/1CxgeHVf5NwtX1pYoYgUHyYeODtwVPZfKYOH3tfMnVGE/edit#gid=0
2 ARUK-UCL @RLovering 2 PomBase @ValWood 1 SGD @srengel
Obsolete, no annotations:
So, Val and I think some terms need to be obsoleted in the ontology.
We started talking about it when I requested a long precomposed BP to describe fep1. Fep1 is a DNA binding transcriptional repressor that suppresses transcription of iron starvation genes when there is plenty of iron around. I requested: "negative regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron"
Melanie told me that the term is too specific and I could either annotate to "unconnected" process terms, or string them together using annotation extensions. I definitely want to nest the terms because they "belong" together.
Val then pointed out to me that I was trying to incorporate the function of the enzyme in my process term - and I could make the term a lot less nasty by taking the "MF part" out. We connect MFs to BPs using extensions, and I shouldn't treat the transcription factors any differently.
This is an example annotation for one of our kinases:![example](https://cloud.githubusercontent.com/assets/7359272/19448445/beb1e5e8-9499-11e6-9f5e-3cd8a9c8f1ca.jpg)
The kinase is also annotated to these biological processes as separate annotations, but here they have been connected to the MF.
So, instead of annotating fep1 to "negative regulation of ferrichrome biosynthetic process by negative regulation of transcription from RNA polymerase II promoter in response to iron"
I should annotate it to the MF transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding has_input gene:sib1 part_of negative regulation of ferrichrome biosynthetic process in response to iron
and to the BP negative regulation of ferrichrome biosynthetic process in response to iron
I'm not focussing on transcripton factors at the moment, so it is very confusing that there are terms in the ontology that we "shouldn't" annotate to (if we can't request new sibling terms then I suppose we shouldn't really annotate to the existing terms anyway right?)
So, I'm asking if you could obsolete all the transcription regulatory terms that we "shouldn't" annotate to (and for which you won't create new sibling terms) - many are descendants of GO:0006357
@ValWood @mcourtot