very very urgent...metabolism parentage

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metabolism is a child of physiological processes, but not cellular process 0009987?

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/1142":https://sourceforge.net/p/geneontology/ontology-requests/1142

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• milestone: --> 224410
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Original comment by: jl242

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Hi Val - yes that's right. Physiological process includes processes at both the level of the whole organism and at the level of the cell. We don't specify with metabolism whether it's occuring at a cellular or organismal level which is why it isn't under cellular process.

Original comment by: jl242

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Original comment by: jl242

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Hi Jane,

I still have a problem here....this stems from the fact that many terms, for example DNA repair, transcription, RNA metabolism, protein folding, protein targeting, protein modification, protein biosynthesis should surely have cell growth and maintenance....."def: Any process required for the survival and growth of a cell". in their parentage? .......this way they would get the cellular process parentage which is missing.....( cell growth and maintenance is a direct child of both physiological process and cellular process). Then when I start to look at the children of metabolism, I'm not sure what the distinction should be between the physiological level and the cellular level..... So, even if metabolism doesn't need additional parentage, many of its descendent terms do......

If not I have a very strange looking high level process assignment totals for pombe...

GO:0008150 : biological_process (3608) ...GO:0009987 : cellular process (1791) ...GO:0007582 : physiological processes (3493)

does that make sense?

Val

Original comment by: ValWood

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Original comment by: jl242

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Hi Val - I see the problem, won't this will be fixed when David and Tanya split physiological process into cellular physiological process and organismal physiological process?

Original comment by: jl242

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I'm not sure.....I still think the cell growth and maintenance parentage is a separate issue, although I'm sure they'd pick this up when they look

It also seems quite important because it affects the high level terms and the GOslims....it seems bad to have so many fundamentally important processes not under cell growth and maintenance......

I noticed this when I looked at the pombe high level annotations, but it also accounts for why in Joels talk 33% of DNA repair terms had cell growth as a concurrent annotation (because many repair terms will also be annotated to cell growth children,.....but it should be 100% with correct parentage.).....I think it should be fixed quickly if possible because it may have big knock on effects.....if people use this for consistency checking it will probably generate lots of suggestions for ontology and annotation changes which could be averted...it would be even worse if used for annotation comparisons.......it probably removes about 50% of the annotations from under cell growth which should be there for most organisms.....sorry I'm going on a bit.....

Original comment by: ValWood

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Thinking about this a bit more.... I didn't know about the proposed split (I tend to ignore the phys process discussion), but was this proposed to correct errors in the existing structure, or just as a refinement

At the moment things are quite inconsistent...for example DNA replication is a child of cell growth and maintenence but DNA repair isn't.

Original comment by: ValWood

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Val - it's SF item 809298 if you want to have a look - they're keen to take comments. I'll load up their new ontologies later and see if the parentage of things like DNA repair have been sorted out.

Original comment by: jl242

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I've just had a look at the new tree and it looks like the split hasn't fixed this problem. I think we either need a new child of metabolism 'cell metabolism', or we just need to move 'metabolism' so it's a child of 'cell growth and/or maintenance' or 'cellular physiological process'. Is it true to say that all metabolism restricted to cells though?

Original comment by: jl242

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mine is :)

Original comment by: ValWood

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its probably a case of going through one by one and checking whether they should have 'cell growth and or maintenance' as a parent, I suppose som like secondary metabolism won't necessarily need this parentage?

also when this is done can probably kill the term GO:0001557 : metabolism resulting in cell growth which has no associations and will be implicit when the metabolism terms have the correct parentage

Original comment by: ValWood

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this is what Jane and i wrote on a scrap of paper yesterday .....would this work?

physiological process --cellular process ----cellular metabolism ------all the existing metabolism terms (except?) --organismal process ----organismal metabolism ------all the terms which also occur at the oganismal level would need this parentage oxygen, alcohol, carbohydrate etc .--metabolism ----cellular metabolism ----organismal metabolism

this would effectively separate out anything which occured at the level of the cell/organism from things at the level of the cell ONLY ie protein synthesis. Also all the cellular terms ie amino acid biosynthesis, protein sythesis etc would have the cellular metabolism parentage which is currently missing

this doesn't quite cover everthing, as I just reilised protein synthesis, glycolysis, amino acid biosynthesis still don't get a cell growth parent, and metabolic terms would probably need this parentage adding on a case by case basis, excluding terms like secondary metabolism which may not be directly involved in growth?

Original comment by: ValWood

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Hi Jane,

I don't think this would work. I was thinking about it and there are 2 problems with the exisitng arrangement

i) many processes for example, amino acid metabolism, protein biosynthesis, DNA repair do not have a cellular process and/or cell growth parentage

but also ii) many of these processes are not also physiological processes, so moving cellular process under physiologocal process wholesale won't work.

for instance I can think of any instances where any of the above are ever bona fida physiological processes as they only normally occur at the cellular level?

I wonder if we could actually make the organisml metabolism terms the most granular (its not intuitive, as you usually think of the organism asfurther up the heirarchy but it's the only way I can think to avoid TPVs)

for instance phsiological process --physiological metabolism ------physiolocical alcohol metabolism ------physiological carbohydrate metabolism cellular process --cellular metabolism ----alcohol metabolism ------physiological alcohol metabolism ----carbohydrate metabolism ------physiological carbohydrate metabolism

the term names would need some work, but maybe the individaul instances of physiological metabolism are more pertinent to cellular processes

i.e "Processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.

than cellular processes are to physiologocal processes

"Those processes specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms."

or is that just daft?

Original comment by: ValWood

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here are a few things whcih may still need moving protein complex assembly protein complex disassembly protein depolymerization protein folding protein stabilization protein oligomerization protein polymerization

Original comment by: ValWood

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Actually Val - I'm not sure we did decide to exclude these processes from metabolism in the end...the new definition for metabolism is:

Processes that cause many of the chemical changes in living organisms, including anabolism and catabolism. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

I think they'd fall under that wouldn't they? And I'd had a look through the tree and can't see anywhere else they could go...

Original comment by: jl242

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yes I think you are right. I remembered incorrectly

val

Original comment by: ValWood

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Now fixed with metabolism changes. All cellular metabolism terms are children of cellular physiological process.

Original comment by: jl242

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• status: open-works-for-me --> closed-fixed

Original comment by: jl242

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• milestone: 224410 --> PomBase

Original comment by: mah11