additional parents?IMP biosynthesis/GMP biosynthesis

[gocentral]

should things like IMP biosynthesis GO:0006188 and GMP biosynthesis GO:0006177 and GTP biosynthesis

also have the parent

GO:0006091 generation of precursor metabolites and energy

The formation from simpler components of precursor metabolites, substances from which energy is derived, and the the processes involved in the liberation of energy from these substances.

Reported by: ValWood

Original Ticket: "geneontology/ontology-requests/2280":https://sourceforge.net/p/geneontology/ontology-requests/2280

[gocentral]

Logged In: YES user_id=451873

Hi Val - I don't think so...the term 'generation of precursor metabolites and energy ; GO:0006091' is the same as they have in MetaCyc, and they don't have any biosynthetic pathways listed there, they have:

MetaCyc Class: Generation of precursor metabolites and energy

Parent Classes: Pathways

Child Classes: Chemoautotrophic energy metabolism (9) , Fermentation (19) , Glycolysis (8) , Methanogenesis (4) , Other (2) , Pentose phosphate pathways (4) , Photosynthesis (6) , Respiration (9) , TCA cycle (17)

Instances: Entner-Doudoroff pathway , superpathway of glycolysis+Entner-Doudoroff

I think it's intended to cover processes where big stuff is broken down so energy can be liberated from it...

Original comment by: jl242

[gocentral]

Logged In: YES user_id=516865

perhaps this def could be tweaked to add catabolic or somthing.

From what you say the def of 'formation from simpler compounds' seems a bit odd if this is meant to refer to their breakdown?

Should it be 'formation of simpler compounds'

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=473796

Is this that awful term that used to be "main pathways of energy generation" or something like that? Hmmmm, it sounds to me like one of those vague terms which causes nothing but trouble. I can think of a simple solution to the problem... ;)

In the mean time, though, I will remove the repeated "the" in the def.

Original comment by: girlwithglasses

[gocentral]

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I don't know what it means! Let me know when you are enlightened.

Original comment by: ValWood

[gocentral]

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Yes - that's exactly what this term used to be! I see what you mean about the def Val - doesn't make any sense. I wrote it when we did all the metabolism changes, clearly not quite knowing what the term meant. It seems that precursor metabolites are the components used to build larger substances or generate energy - I found this definition for them:

PRECURSOR METABOLITES:Intermediate molecules in catabolic and anabolic pathways that can be oxidized to generate ATP or synthesize subunits of macromolecules.

So it's all now clear as mud.

Original comment by: jl242

[gocentral]

Logged In: YES user_id=451873

Looking at the children of 'generation of precursor metabolites and energy ; GO:0006091', perhaps its name should just be changed to 'metabolic energy generation' or something...

or maybe we should just obsolete it considering no-one knows what it means!

Original comment by: jl242

[gocentral]

• summary: additional parents? --> additional parents?IMP biosynthesis/GMP biosynthesis

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=516865 Originator: YES

Can close this, although I liked your term name change suggestion.....

Original comment by: ValWood

[gocentral]

Logged In: YES user_id=436423 Originator: NO

I added that suggested name as a synonym ... icky term! closing ...

Original comment by: mah11

[gocentral]

• status: open --> closed

Original comment by: mah11

[gocentral]

• milestone: --> PomBase

Original comment by: mah11