links between metabolicm and homeostasis

[gocentral]

I wondered if links could be established between metabolism terms and their respecticve homeostasis terms? any reason why not?...I feel this has come up before.....

these are the ones I was looking at:

regulation of fatty acid metabolism child of fatty acid homeostasis GO:0055089

regulation of phospholipid metabolism child of phospholipid homeostasis O:0055091

regulation of ergosterol metabolic process child of GONEW: ergosterol homeostasis child of sterol homeostasis GO:0055092

regulation of triglyceride metabolism child of triglyceride homeostasis GO:0070328

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/7177

[gocentral]

I think it's on purpose, and my best guess is that it's because homeostasis of a substance can result from metabolism, transport, or both. Because it's not always just metabolism, we can't say X homeostasis is_a X metabolic process, and because it's not always both we can't use X homeostasis has_part X metabolic process.

Homeostasis is a type of regulation, so I'll assign to D&T in case I got the rationale wrong. m

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> ukemi

Original comment by: mah11

[gocentral]

Midori is 100% correct. Synthesizing or catabolizing something can effect the level of a substance, but not always. We had a difficult time defining homeostasis, but in the end decided it was the regulation of the level. In some cases, metabolic processes can be part of the homeostasis of a substance, but as Midori says, other factors can come into play as well. For example oxygen homeostasis in my body is a very complicated organismal process.

Original comment by: ukemi

[gocentral]

I agree that homeostaasis results from the interplay of multiple procersses I'm still confused about an example of a metabolic process (or a transport) which would not affect homeostasis

i.e. x homeostasis, -x metabolic process -x transport

Original comment by: ValWood

[gocentral]

In our fight or flight responses, we transiently spike the levels of epinephrine in our bloodstream through both transport and metabolism. I don't think this would fit with homeostasis. As I said, when the annotators started asking for all the homeostasis terms, we had a difficult time coming up with a definition for it, but form everything Tanya and I read, it almost always had to deal with reaching an equilibrium or a kind of resting state, so it really didn't fit in with the other processes in a nice way. It is almost because it is a phenotype or a quality rather than a process itself. I agree that metabolism and transport are used to attain this, but I don't think that they always are used in that way.

We originally thought about making those links, but ended up being conservative.

David

Original comment by: ukemi

[gocentral]

There's also an issue of granularity here. If one is looking a regulation of glycolysis by glucagon signaling, for instance, that regulation per se is unidirectional: it promotes glycolysis regardless of glucose abundance or energy needs. Only when one takes a step back to see this one regulatory signal in the context of all the others can one reliably make a statement about homeostasis. Even then, in a disease state like diabetes it doesn't work - the glucagon regulation runs full blast with no insulin regulation to counterbalance it and homeostasis is not achieved.

This may also be an argument to use any homeostasis term only in very limited ways.

A quibble: homeostasis is defined as "Any biological process involved in the maintenance of an internal equilibrium". "Steady state" would be better - cells and tissues are open systems with fluxes through them and if something like glucose levels are stable, that's because input matches output, not because the relevant reactions have reached their equilibrium endpoints. If this issue has already been discussed and resolved, ignore this last comment - it's a bit cranky.

Peter

Original comment by: deustp01

[gocentral]

Peter,

I'd be happy to change the defs to say steady-state. Thanks for your thoughts.

David

Original comment by: ukemi

[gocentral]

OK I will have a think about how I use homeostasis. Val

Original comment by: ValWood

[gocentral]

Fixed all the defs as per Peter's suggestion.

David

Original comment by: ukemi

[gocentral]

• status: open --> closed-fixed

Original comment by: ukemi

[gocentral]

• milestone: --> PomBase

Original comment by: mah11