Utilization pathways

[gocentral]

I would like to add some terms in place of the soon-to-be obsoleted 'utilization' terms for those organisms where substrate utilization represents a specific pathway of sensing, transport and metabolism. These will be called 'xxx utilization pathway' and they will be specifically defined so that they cannot be confused with instances where utilization has been used as a synonym of metabolism.

Can interested parties supply me with some substrates for these utilization p'ways and possible defs?

Thanks!

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/2069":https://sourceforge.net/p/geneontology/ontology-requests/2069

[gocentral]

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Hi Amelia,

We would like to discuss this issue little further here at TAIR and thus need sometime. Can we wait for a week atleast? Thanx

Suparna

Original comment by: smundodi

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Hi Amelia,

Here are the ones I have come up with so far: carbohydrate utilization nitrogen utilization phosphate utilization electon acceptor utilization

Thanks, Michelle

Original comment by: mlgwinn

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Ooops - I forgot definitions.

carbohydrate utilization pathway: "The integrated regulatory system which detects the depletion of primary carbohydrate sources, usually glucose, and then activates genes to transport and metabolize alternate carbohydrate sources."

nitrogen utilization pathway: "The integrated regulatory system which detects the depletion of primary sources for nitrogen, usually ammonia, and then activates genes to scavenge the last traces of the prmimary nitrogen source and to transport and metabolize alternate nitrogen sources."

phosphate utilization pathway: "The integrated regulatory system which detects the depletion of inorganic phosphate and then activates genes to scavenge the last traces of inorganic phosphate and to transport and metabolize organic phosphate sources."

electron acceptor utilization pathway: "The integrated reulatory system which detects a lack of molecular oxygen and activates genes for pathways that allow the cell to make use of alternate electron acceptors."

Original comment by: mlgwinn

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Those look good Michelle. I'll wait and see if Suparna has any others to offer and then put them all in in one fell swoop.

Original comment by: girlwithglasses

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Ok, here are the comments from TAIR:

We like Michelle's definitions with few minor changes in some.

In nitrogen utilization pathway, the primary source should be 'ammonium' and not ammonia.

Tree structure change:

Carbohydrate utilization should also be a direct child of carbon utilization.

Definitions:

Carbon utilization: The integrated regulatory system which detects the depletion of primary carbon sources, usually glucose, and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize inorganic carbon sources such as carbon dioxide or carbonic acid.

carbon utilization by fixation of carbon dioxide: The integrated regulatory system which detects the depletion of primary carbon sources, usually glucose, and then activates genes to scavenge the last traces of the primary carbon source and to transport and metabolize inorganic carbon sources such as carbon dioxide.

Term name changing issue:

We are not totally happy with adding the term 'pathway' to the utilization terms, but if that helps distinguish the catabolism synonyms from this, we will live with that. So, my question is, do microbe people look at utilization as same as only degradation? If it is not true, then may be those synonyms could be dropped and we can use the terms without the pathway attached to the term name.

This is it for now.

Suparna

Original comment by: smundodi

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Hello,

No, prok people do not consider these synonomous with degredation. It's fine with me to drop "pathway" from the names.

Michelle

Original comment by: mlgwinn

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The reason for putting 'pathway' into the term names is that 'utilization' is used in lots of different ways in the literature, so by calling these processes 'utilization pathways' it makes it clear that it's talking about something specific.

I'll add these new terms if everyone's happy now.

Original comment by: girlwithglasses

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Having the 'pathway' is misleading and confusing with the way the terms are defined. These processes are clearly not
single, neat 'pathways' but more like a complex collections of processes that are networked. I strongly agree with the suggestion that 'pathway' be dropped from the name.

Original comment by: syrhee

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How do you suggest that we ensure these terms are only used to annotate the specific processes outlined in the defs below, in that case? 'Utilization' is used synonymously with 'metabolism' in papers, and I want some way to alert users who might not bother looking at the defs that in these cases, 'utilization' has a special specific meaning.

Original comment by: girlwithglasses

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That is a general question that I don't think will be solved by adding 'pathway' at the end of the term... In fact, adding 'pathway' may trigger people to to metabolic pathway more than not having it.

I don't mean to insist on this, it's not a huge point and if you insist on having the word pathway, it's fine with me.

Original comment by: syrhee

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I must admit that I have reservations about adding these terms anyway because they seem to be such broad processes. I would've thought it would be better to annotate to a more precise term - would there be cases where you didn't know whether a gene product was involved in sensing, transporting or metabolizing a substrate? 'Utilization' just seems very vague and hand-wavey to me and like it's a catch-all term...

Original comment by: girlwithglasses

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Does anyone have any further comments on this item? Personally I think that these utilization terms are really too vague to be of any use but I will add 'utilization pathway' terms if they really will be useful.

Original comment by: girlwithglasses

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Hello all,

I think these terms are useful - they have a certain meaning in proks that is not currently captured with other GO terms.

I also recognize and share Amelia's fear that the terms would be used inappropriately as surrogates for metabolism terms. However, I don't think the term "pathway" will solve this and agree with Sue that it could cause more confusion.

If Amelia is unhappy without a term like "pathway" and we are unhappy with it, how about something else like "network". Ex: "carbon utilization network"

I would still choose plain "carbon utilization" but it would be good to satisfy everyone's needs if possible.

Michelle

Original comment by: mlgwinn

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So it seems the problem is the word "utilization" is not univocal - we would prefer to have a suffix that means the same thing in all contexts.

I'm not so keen on "utilization pathway" for the reasons outlined below, and also I find the word pathway itself can add to the vagueness. I think there are some issues with the pathway terms in the immune DAG.

I'm not so keen on network, since a network is not really a process. You can take a snapshot of a network and see all it's parts. E.g. a network of neurons connected by axons and synapses. Contrast this with the process of signals traversing the network.

I think we have to have a clear idea of the def before we decide on the word (perhaps you all do, but I don't). Let's see if we can derive a word(s) from the proposed def below:

carbohydrate utilization (pathway): "The integrated regulatory system which detects the depletion of primary carbohydrate sources, usually glucose, and then activates genes to transport and metabolize alternate carbohydrate sources."

The def would suggest "system". I'm not totally happy with the word system for the same reasons as network. My simplistic analogy would be a burglar alarm system - something static. We want to get at the process the system performs, which will help us think of correct DAG placement and so on. We also want to do what David always says and think of the start and end points of the process.

A good way to define things is to give a more general term (genus), and state what differentiates this term from that parent (differentia).

The current def (which is probably more recent than the one proposed below?) starts off well:

Series of processes that involve carbohydrate sensing, carbohydrate transportation and carbohydrate metabolism which lead to the utilization of carbohydrates

but involves a nasty circularity: X is a series of processes involving A, B and C and leading to X!

So if the more general term here is carbohydrate metabolic process, how about:

A carbohydrate metabolic process that unfolds in response to the depletion of primary carbohydrate sources

but this isn't quite satisfactory. I'm not sure that X utilization is_a X metabolism. It seems more like a larger process that has X metabolism as part. In fact the DAG is a little inconsistent here:

nitrogen_utilization is_a nitrogen_compound_metabolism cabrohydrate_utilization is_a multicellular_organismal_process

(at this point I am deeply confused - don't proks do carbohydrate utilization?)

So the questions we have to answer are:

is X utilization (or whatever we call it) a specific kind of metabolism (eg a metabolism that unfolds in certain circumstances), or is it a longer process which has metabolism, sensing/detection and transport as parts? (of course we would not use part_of relations, since not all metabolisms are part_of some utlization)

or in other words, is this diagram correct?

====================================> (time)

[---------- X utilization -----------------------] [--X sensing--][--X transport--][--X metabolism--]

Original comment by: cmungall

[gocentral]

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Hi Chris,

I don't think you should try to make any conclusions from the existing "utilization" terms and their relationships. It was recognized long ago that there were serious problems with them and that (I thought) was one of the goals of this particular SF item - a general clean-up of all these terms.

(and YES proks do carbohydrate utilization)

Regarding your diagram about how the process works.... I think that in general that diagram would be considered true with the added provision that it is not always a one-way progression, that things can loop back and and forth within that set of processes.

I think the term "system" could work here - I like it better than "pathway". I think a better analogy than the burgler alarm for "system" would be "emergency management system" - something that gauges a situation and then directs an appropriate response while efficiently handling developments as they occur.

In this light I think system is a fine word to use.

Michelle

Original comment by: mlgwinn

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at the risk of getting into angels-on-the-head-of-needles type waffling, I'd still say that "system" is usually used to mean a collection of objects that can participate in a process, rather than the process itself. This also goes for an emergency management system - the system is in place even when it is not being used.

We have terms like "endomembrane system" in cellular component, this seems to me where systems belong. Similarly nervous system etc in anatomical ontologies.

Some would say this division is artificial, but I think it is at least useful for consistency in the ontology

so if the diagram is roughly correct, with the looping caveat, then one option is to simply suffix the term with "sensing, transport and metabolism". Not exactly catchy. But probably less prone to mistaken use. It seems that other choices - whether it is utilization, utilization pathway or utilization system are all prone to synonymy errors in annotation, no?

(or perhaps what we really need is a special synonym-class-for-annotators? or software that forces people to read the def...)

Original comment by: cmungall

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I recently has some new terms implemented for 'iron assimilation' which is defined to include soluabilization and transport, It seems like assimilation and utilization are related should iron assimilation have a parent iron utilization?

Also a question, are all instances of 'x utilization' also considered to be a part of some sort of 'scavenging pathway' used when x concentrations are low? This seems to be the distinguishing feature about these pathways/systems ?

if this is the case...perhaps

term x scavenging synonym x utilization would clarify for curators and users?

because although both utilization and scavenging appear to be used to mean this, the word utilization has 'broader connotations' (this may be a totally wrong .but all the defs mention depletion, and the 'iron assimilation' process is used when cellular iron concentrations are low although I didn't say this when I requested the term....)

Val

Original comment by: ValWood

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Hi Val,

No, I would not equate utilization and scavenging. The utilization systems are more about coordinated regulation of various processes in the cell to most effectively make use of whatever resources are available. So for example, if glucose is depleted in the cell's environment but ribose is present it may turn off the genes for glucose transport and metabolism and turn on the genes for ribose transport and metabolism, then when that is depleted it switches to something else and so on.

Scavenging is certainly often a component of this process, but it is just one of many.

I think the distinguishing factor is that it is regulatory system for acquisition and use of a whole class of compounds (carbon sources, nitrogen sources, etc.) not just one.

I'm beginning to wonder if we should just give up on this and get rid of these terms. But I fear an important concept would then be lost from the GO.

Michelle

Original comment by: mlgwinn

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OK thanks Michelle.... and so assimilation and utilization can be seperate also....

Original comment by: ValWood

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Hi Chris,

I don't think you should try to make any conclusions from the existing "utilization" terms and their relationships. It was recognized long ago that there were serious problems with them and that (I thought) was one of the goals of this particular SF item - a general clean-up of all these terms.

(and YES proks do carbohydrate utilization)

Regarding your diagram about how the process works.... I think that in general that diagram would be considered true with the added provision that it is not always a one-way progression, that things can loop back and and forth within that set of processes.

I think the term "system" could work here - I like it better than "pathway". I think a better analogy than the burgler alarm for "system" would be "emergency management system" - something that gauges a situation and then directs an appropriate response while efficiently handling developments as they occur.

In this light I think system is a fine word to use.

Michelle

Original comment by: mlgwinn

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Hi Sorry about that last comment that got added - I accidentally did something to an open sourceforge window that caused it to somehow repost the comment I made a while back - sorry for the spam - please ignore that last entry.

Michelle

Original comment by: mlgwinn

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also see SF 1744740 https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1744740&group\_id=36855

Original comment by: mah11

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MAH & DPH to work on this and SF 710180 together https://sourceforge.net/tracker/index.php?func=detail&aid=710180&group\_id=36855&atid=440764

Original comment by: mah11

[gocentral]

• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Now fixed! Details in log file for go/ontology/editors/gene_ontology_write.obo revision 1.1076 and on wiki at http://wiki.geneontology.org/index.php/Utilization.

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11