cellular transcription???

[gocentral]

There is a new term cellular transcription, child of transcription, how come? I have direct annotations to this term, even though I know I have never used it.

What is non-cellular transcription?

In fact, something odd has happened around here because the old transcription term is now defined as 'x' ;)

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/7071

[gocentral]

for tanya: oops, missed a def (let me know if I can help ... and thanks again for doing the rest!!)

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• assigned_to: nobody --> tairtb

Original comment by: mah11

[gocentral]

I think this might be a case where we needed to know about the changes in advance. Where have the old terms gone? regulation of transcription, DNA dependent etc, why aren't they synonyms?

Original comment by: ValWood

[gocentral]

I've just added a def.

Val, will explain when I'm back at work tomorrow. Today is a holiday. It's a long story.

Original comment by: tberardini

[gocentral]

I wonder if it was meant to be "cytoplasmic transcription", which by that I would assume to be transcription in an organelle like mitochondrion or chloroplast? Just guessing.

Original comment by: hdrabkin

[gocentral]

Harold - I've lived through the back story that Tanya alludes to, so I know it wasn't meant to be "cytoplasmic transcription."

ugh. m

Original comment by: mah11

[gocentral]

OK, I look forward to the short version, It must be because of viral transcription? v

Original comment by: ValWood

[gocentral]

ah! of course; vaccina !

Original comment by: hdrabkin

[gocentral]

Short version: Jen in her taxon checking work found that viral transcription needed a parent that would not lead to cellular process. We decided that rather than creating a new term 'cellular transcription' and moving ALL of the other current children of transcription to that one and sorting out the children terms, regulation and all (which would have been a gigantic job), we would rename the old transcription term as 'cellular transcription' which is really what is was all along, create a new term called just 'transcription' and have 'cellular transcription' and 'viral transcription' as kids of that term.

For more details, please ask Midori or Jen. Hope that helps.

The old terms are still all there, under 'cellular transcription'.

Original comment by: tberardini

[gocentral]

I'm still confused. From what you say "cellualr transcription is a new "child" of transcriotion which was inserted to be a parent of the non viral terms. However, I have direct annotations to this term, even though I never used it. This implied the term already existed, but was called something esle. What was it called previously ? It is likely I need to reannotate things

Thanks

Val

Original comment by: ValWood

[gocentral]

>"rather than creating a new term 'cellular transcription' ..."we would rename the old transcription term as >'cellular transcription' which is really what is was all along,"

'cellular transcription' was 'transcription'

Original comment by: tberardini

[gocentral]

OK got you

Original comment by: ValWood

[gocentral]

:)

Can we close this?

Original comment by: tberardini

[gocentral]

Well you can but i'm still confused why the term was needed

now its transcription --cellular transcription --transcription DNA, dependent ----cellular transcription DNA dependent ----mRNA transcription

I thought it was because of viral transcription, but I don't see how this fits in here. If it is because of viral transcription, why can't this be under cellular ? it happens at the cellular level Also, why did we need mRNA transcription?

...can skype me if its easier ;)

Original comment by: ValWood

[gocentral]

Hi Val,

Discussion is going on further between Midori, David and myself as we sort through the ramifications of the terms that Jen created on January 26th. We hope to sort this out in the next week when David is back from vacation.

What is your skype id?

Also, viral transcription falls here: transcription --cellular transcription --transcription DNA, dependent ----cellular transcription DNA dependent ----mRNA transcription ------cellular mRNA transcription ------viral transcription***

Re:mRNA transcription - there are also rRNA transcription, tRNA transcription, snoRNA transcription terms, etc.

Tanya

Original comment by: tberardini

[gocentral]

Hmmm, I'd like to see exactly what the justification was for needing a new parent for "viral transcription" and why it was placed where it is. Most viruses don't have their own RNA polymerases, so transcription of their genomes only occurs when they coopt host enzymes, which occurs in the cell. Even for things like vaccinia, which do have their own polymerases, I'm not aware of this occurring outside of a cell, so I am not clear at all on the need for a non cellular parent for any kind of transcription.

-Karen

Original comment by: krchristie

[gocentral]

Hi Jen,

It looks like some annotators need more background information than they have -- not everyone has been closely involved in the taxon work, so how it's influencing ontology development needs more explanation.

Could you please provide a summary of the reasons the taxon work led to the addition of new 'cellular' terms for replication, transcription, etc., and respond to Karen's concern about the transcription terms?

Thanks, m

Original comment by: mah11

[gocentral]

• assigned_to: tairtb --> jenclark

Original comment by: mah11

[gocentral]

I was also slightly concerned abotu the new term mRNA transcription here.

This only has 76 annotations so it is very incomplete (and most from viruses). I would need to propagate all of my transctiption from RNA polymerase II promoter annotations to this term, maybe this is because I should have used mRNA transcription from RNA polymerase II promoter, but is anything else transcribed by PolII (I don't know the answer to this.....) , I'm very confused.....

Original comment by: ValWood

[gocentral]

Hi,

I'll fix the 'x' definition, but I have also written to Tanya to ask if she could follow up further. Friday is my last day so I won't be able to follow the rest of the story through.

Thanks,

Jen

Original comment by: jenclark

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• assigned_to: jenclark --> tairtb

Original comment by: jenclark

[gocentral]

Hi,

I see the 'x' def is actually fixed. I hadn't received amy mails on this SF item before. Thanks for sorting. :-)

Jen

Original comment by: jenclark

[gocentral]

Hi Jen,

Reassigning to you so that you can address Midori's request from

Date: 2010-02-19 10:37.

Scroll down to see it.

Thanks,

Tanya

Original comment by: tberardini

[gocentral]

• assigned_to: tairtb --> jenclark

Original comment by: tberardini

[gocentral]

Yes, Tanya and David added a definition in place of the 'x'. What we still need is the rationale for the broader set of changes -- as I said in the 2010-02-19 comment, not everyone is quite up to speed with the ways the taxon work has been interpreted.

Original comment by: mah11

[gocentral]

Hi,

I'm not sure what he current status of this, as Tanya has taken over the project, but I can tell you what led to the creation of 'cellular' terms.

The original thinking is documented at:

http://gocwiki.geneontology.org/index.php/Taxon-GO\_Checks\_and\_Commentary\_-\_Part\_4

then further similar discussion also at:

http://gocwiki.geneontology.org/index.php/Taxon-GO\_Checks\_and\_Commentary\_-\_Response\_to\_GOA\_-\_Part\_5\#Ontology\_Corrections

and finally as the problem seemed to be quite a far reaching one I made a proposal at :

http://gocwiki.geneontology.org/index.php/Are\_multi-organism\_process\_and\_cellular\_process\_disjoint%3F

Some problems came to light after my initial edits and Tanya and David took over making changes. I also took the proposal (linked above) to the GO list and from there I understand that there is a plan to take it to the Consortium meeting for discussion.

My general feeling just now is that these edits made sense at the time, but that a different solution may be needed in the long run. I'm hoping that the proposal above can be discussed, and the problem resolved as soon as possible, so that we can either change the graph properly and explain the ramifications to everyone, or change it back and properly define the top terms. At the moment it seems to me that the only way is to wait for that discussion. I'm not sure it makes sense to make radical changes one way or the other until we have a policy decision.

Does that help?

Thanks,

Jen

Original comment by: jenclark

[gocentral]

It seems that the problem here is the intepretation of the term "celluar process" as being specific to a cellular organism, when it is defined as occurring at the level of the cell.

I didn't see a problem with viral processes occuring in a host cell and using host machinery being defined as cellular processes (occuring at the level of the cell).

These high level terms (cellular process, multicellular process) were originally introduced to disambiguate processes which have different cell level and multicellular level mechanisms (i.e alcohol metabolism in a single cell, or alcohol metabolism in the liver), but are also useful to capture generally the information about whether a process is a cell level, or an multicellular (organ or tissue level) process.

It seems that the need to make this distinction does not occur when discussing viral transcription and any other transcription

BTW, for the same reason I don't have a problem with a multispecies process occurrung at the cellular level (i.e conjugation) also being a "multi organism process"......

These are my thoughts....

Original comment by: ValWood

[gocentral]

Another thought, before big (high level) changes are made as a result of the taxon work, could a SF item be submitted to warn us. Hardly any of us would know how we would know about these changes in advance.

Original comment by: ValWood

[gocentral]

Hi Val,

Thanks for your thoughts. I do actually always let people know if I'm doing anything that will have a big effect, but in this case the ramifications were not obvious until I was a little way done the editing route. Hopefully a conclusion can be reached soon and everything fixed to everyone's satisfaction.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

I completely agree wtih Val's comments about "It seems that the problem here is the intepretation of the term "celluar process" as being specific to a cellular organism, when it is defined as occurring at the level of the cell.

I also completely agree with Val's comments about warning us before changes are made to such high level terms. Not only would that have avoided the current situation where terms have been created that seem likely to get removed, but I think that the input Val and I are providing now, after the fact, could have saved you a lot of work, if we had had the opportunity to comment in advance. So, I think we need to be more systematic in alerting people to proposed changes, especially effecting high level terms, even if that means changes occur a little more slowly.

-Karen

P.S. If the similar terms for "cellular DNA replication" were also recently created due to the taxon work on the basis of Vaccinia biology, then it may suffer from the same flaw as the "cellular transcription" term. If there's something else though where DNA replication really occurs outside the context of the cell, you can disregard this comment.

Original comment by: krchristie

[gocentral]

Hi Everyone,

Thank you for all the comments!

Taking all your input into consideration, David and I have reverted the changes made to the ontology on Jan. 26th that pertain to the following terms and their children:

id: GO:0055132 name: cellular DNA metabolic process

id: GO:0055133 name: cellular DNA replication

id: GO:0055134 name: cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

and those made on Feb.8th that were an attempt to bring the ontology in line with the new terms.

By reviewing the diff files line by line from those two time periods, we think we've been able to sort out everything and restore the previous state. However, should you spot anything that still looks amiss, please let us know and we'll fix it up right away.

I'll leave this issue open till the end of this week. If nothing pops up, I'll close it. If you find something after this Friday, please just open a new SF item.

Tanya

Original comment by: tberardini

[gocentral]

• assigned_to: jenclark --> tairtb

Original comment by: tberardini

[gocentral]

closing.

Original comment by: tberardini

[gocentral]

• status: open --> closed-fixed

Original comment by: tberardini

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• milestone: --> PomBase

Original comment by: mah11