NTR: dietary nutritional component

LilyAndres commented 3 years ago

Preferred term label

dietary nutritional component

Textual definition

An essential nutrient in food that is necessary to support human and livestock life for good health.

Suggested parent term

material entity - BFO:0000040

LilyAndres commented 3 years ago

Definition suggested by @CropStoreDb and @LilyAndres

A material entity that is ingested and contributes to survival, growth and development

LilyAndres commented 3 years ago

We will open this issue because there are some new point of views that need to be considered by Dr. Britt

bbfreeman commented 3 years ago

The proposed definition may consider material entities that work beyond "survival, growth and development" and contribute to biological function (in humans). Definition may also consider using "or" instead of "and" in all aspects. The current definition is narrow in scope and implies essentiality. Adding "biological function" or other appropriate verbiage will capture components that are not necessary for survival, growth or development but contribute to biological function in the human body. A good example is fiber. It's not essential but contributes to bowel function, as well as having many other functional attributes when consumed. Polyphenols are another example, ie., not required by humans for survival, growth and development but have a growing evidence base of biological function important to human health.

LilyAndres commented 3 years ago

@bbfreeman many thanks for your comment. @Graham-J-King and I think that the nutritional component definition all revolves around what is understood to be ‘nutrition’.

Corollaries: -other material entities may be ingested and not contribute to these.
- key word is ‘contributes’ and the inference of exclusivity to survival, growth OR development.

So, could be modified to:

"A material entity that is ingested and contributes to survival, growth, development or other biological function."

(this allows eg for allergens, toxins, fiber, drugs)

Other OBO definitions we may need to take into consideration/comment on:

'Diet' [XCO:0000013]: The food and drink consumed by an organism day to day.

'Dietary intake' [NCIT:C169077]: A record of the food and liquid consumed by an individual

'Nutrition' [NCIT:C28294]: That which is consumed to fuel necessary life processes of an organism. [ NCI ] Has an alternative definition “The taking in and use of food and other nourishing material by the body. Nutrition is a 3-part process. First, food or drink is consumed. Second, the body breaks down the food or drink into nutrients. Third, the nutrients travel through the bloodstream to different parts of the body where they are used as "fuel" and for many other purposes. To give the body proper nutrition, a person has to eat and drink enough of the foods that contain key nutrients.” [NICHD]

'Nutritional Study' [NCIT:C15820]: “Research that focuses on food, the nutrients and other substances contained therein, their action, interaction, and balance in relation to health and disease.”

What do you think @ddooley, @maweber-bia, @laurenechan, @mateolan?

Graham-J-King commented 3 years ago

This is a question/suggestion: does the definition need to qualify that ingestion relates to an organism? (rather than an inanimate entity), eg: "A material entity that is ingested by an organism and contributes to survival, growth, development or other biological function."

mateolan commented 3 years ago

I like Graham's suggestion, but I think it needs one more step. In the case of specific oligosaccharides contained in human milk, for example--they are ingested by human infants, but not for their own benefit (they indeed lack the saccharidases to metabolize them)--but for the benefit of preferred gut microflora which confer immunity to the infant. So we could see changing this to something akin to:

"*A material entity that is ingested by an organism and that contributes either directly or indirectly to the survival, growth, development, or other biological function* of itself, its bionts, or its holobiont/superorganism."

(I also wordsmithed it a bit.)

For the other terms, I think we should have an issue thread for each one...makes for better tracking.

Best,

~Matthew

On Wed, Aug 18, 2021 at 6:08 PM Graham King @.***> wrote:

This is a question/suggestion: does the definition need to qualify that ingestion relates to an organism? (rather than an inanimate entity), eg: "A material entity that is ingested by an organism and contributes to survival, growth, development or other biological function."

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maweber-bia commented 3 years ago

Hi, this is maweber ;-)

I like the definition for nutrition including the refinement you have proposed, but do we have the definition for holobiont somewhere else ?

I think holobionts called “supraorganisms” not “superorganisms” .

I also like the idea in the alternative definition from [NICHD] which mentions 3 distinct steps because you can have enteral or parenteral nutrition. Perhaps we should restrict the definition to “oral ingestion” in our case ?

Cheers, Magalie

De : Matthew Lange @.> Envoyé : jeudi 19 août 2021 03:58 À : Southern-Cross-Plant-Science/cdno @.> Cc : Magalie Weber @.>; Mention @.> Objet : Re: [Southern-Cross-Plant-Science/cdno] NTR: dietary nutritional component (#30)

I like Graham's suggestion, but I think it needs one more step. In the case of specific oligosaccharides contained in human milk, for example--they are ingested by human infants, but not for their own benefit (they indeed lack the saccharidases to metabolize them)--but for the benefit of preferred gut microflora which confer immunity to the infant. So we could see changing this to something akin to:

"*A material entity that is ingested by an organism and that contributes either directly or indirectly to the survival, growth, development, or other biological function* of itself, its bionts, or its holobiont/superorganism."

(I also wordsmithed it a bit.)

For the other terms, I think we should have an issue thread for each one...makes for better tracking.

Best,

~Matthew

On Wed, Aug 18, 2021 at 6:08 PM Graham King @.<mailto:@.>> wrote:

This is a question/suggestion: does the definition need to qualify that ingestion relates to an organism? (rather than an inanimate entity), eg: "A material entity that is ingested by an organism and contributes to survival, growth, development or other biological function."

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mateolan commented 3 years ago

Ah ha Magalie! I had supraorganism originally, but I changed it because Wikipedia had a disambiguation that led to superorganism! I'm fine to go back to what we both considered more proper...(though my spellcheck is now upset with me about supra vs super also). A nice couple paragraphs about human gut microbiota and holobiont theory can be found in the background and its references in this paper https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0466-8 . If we refine the definition a bit further to remove ingested (which implies oral nutrition) to "consumed" then we can have subclasses that define the mechanisms of consumption, i.e. oral nutritional component, enteral (feeding by tube) nutritional component, parenteral (bypassing the GI tract) nutritional component. Evidently also, there is a history--dubious though it may be, of rectal nutritional therapies--so rectal nutritional component may also be a subclass--this actually may become important as we consider fecal transplants together with therapies designed to keep prefered microorganisms in place.

Does this phrasing and subclassing structure solve the problem you are describing?

Consolidating these changes gets:

"*A material entity consumed by an organism that contributes either directly or indirectly to the survival, growth, development, or other biological function* of itself, its bionts, or its holobiont/supraorganism."

On Wed, Aug 18, 2021 at 11:14 PM maweber-bia @.***> wrote:

Hi, this is maweber ;-)

I like the definition for nutrition including the refinement you have proposed, but do we have the definition for holobiont somewhere else ?

I think holobionts called “supraorganisms” not “superorganisms” .

I also like the idea in the alternative definition from [NICHD] which mentions 3 distinct steps because you can have enteral or parenteral nutrition. Perhaps we should restrict the definition to “oral ingestion” in our case ?

Cheers, Magalie

De : Matthew Lange @.> Envoyé : jeudi 19 août 2021 03:58 À : Southern-Cross-Plant-Science/cdno @.> Cc : Magalie Weber @.>; Mention @.> Objet : Re: [Southern-Cross-Plant-Science/cdno] NTR: dietary nutritional component (#30)

I like Graham's suggestion, but I think it needs one more step. In the case of specific oligosaccharides contained in human milk, for example--they are ingested by human infants, but not for their own benefit (they indeed lack the saccharidases to metabolize them)--but for the benefit of preferred gut microflora which confer immunity to the infant. So we could see changing this to something akin to:

"*A material entity that is ingested by an organism and that contributes either directly or indirectly to the survival, growth, development, or other biological function* of itself, its bionts, or its holobiont/superorganism."

(I also wordsmithed it a bit.)

For the other terms, I think we should have an issue thread for each one...makes for better tracking.

Best,

~Matthew

On Wed, Aug 18, 2021 at 6:08 PM Graham King @.<mailto:@.>>

wrote:

This is a question/suggestion: does the definition need to qualify that ingestion relates to an organism? (rather than an inanimate entity), eg: "A material entity that is ingested by an organism and contributes to survival, growth, development or other biological function."

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mateolan commented 3 years ago

Hmmn, you could be right, and I am generally inclined to remain abstract--but in this case, I am not sure that what you are suggesting is at all implied. Given the last century of nutrition thought, I do think there is a need to clearly state that one is not always merely feeding oneself.. That is--the indirect relationships between feeding the bionts, and our own health outcomes, are not always straightforward...Indeed, I think that in addition to the consumption modality subclasses I mentioned (and rationalize below)--it may be necessary to define subclasses of nutritional components relative to the portion of the system (specific bionts, holobiont, etc) that are being nutrified. Traditionally speaking, oligosaccharides that preferentially feed commensal and synbiotic organisms would not have been considered nutritional components...but since the science has emerged, I do think we need to call this out specifically. Relative to consumption modality subclasses, I think they are important because there may be some specific nutritional components that are specifically found within each type of mode of delivery that are not found within others. Subclassing these terms will likely play a very large role in computable personalized and precision nutrition algorithms.

On Thu, Aug 19, 2021 at 12:08 AM Graham King @.***> wrote:

@mateolan https://github.com/mateolan , @maweber-bia https://github.com/maweber-bia et al. I may be taking a simplistic view, but I would have thought "itself, bionts, supra, etc" and any trophic levels all contribute 'biological functions'. The refinements are therefore just making explicit what is otherwise implicit. I am therefore just testing whether by omitting these qualifications there is any residual information that could be misconstrued or fails to differentiate from these inclusive biological functions.

Remembering also that the nutritional_components per se are the entities in question; roles (perhaps including how ingested) and attributes are intended to belong within other classes. The intersection of component class and structured terms for role/attribute classes etc could therefore provide the necessary precision. Please argue against this view, as required :-)

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Graham-J-King commented 3 years ago

@mateolan @maweber-bia I had removed a comment as originally slightly misread what Matthew had written in his final definition. However, I am re-instating below so that the record is complete I agree with the @mateolan view of the value of sub-classing (somewhere) the different nutritional routes

@mateolan https://github.com/mateolan , @maweber-bia

https://github.com/maweber-bia et al. I may be taking a simplistic view, but I would have thought "itself, bionts, supra, etc" and any trophic levels all contribute 'biological functions'. The refinements are therefore just making explicit what is otherwise implicit. I am therefore just testing whether by omitting these qualifications there is any residual information that could be misconstrued or fails to differentiate from these inclusive biological functions.

Remembering also that the nutritional_components per se are the entities in question; roles (perhaps including how ingested) and attributes are intended to belong within other classes. The intersection of component class and structured terms for role/attribute classes etc could therefore provide the necessary precision. Please argue against this view, as required :-)

maweber-bia commented 3 years ago

Fine ! I think something like A material entity absorbed by an organism that contributes either directly or indirectly to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts could be ok ?

No need to qualify holobionts as supra or superorganisms, but I would prefer to add "absorbed" because for me, "consumed" implicitly refers to the oral route

In addition to what Matthew pointed out (" define subclasses of nutritional components relative to the portion of the system (specific bionts, holobiont, etc) that are being nutrified."), I would say that we have to be careful when defining the "nutrient role" of fiber or phytochemicals ; actually, the nutrient role or essentiality can differ between species or even individuals of different health's status.

Graham-J-King commented 3 years ago

@maweber-bia is fibre/fiber actually absorbed? I understand it enters the digestive system and contributes a biological function, but may not necessarily be absorbed (in my understanding of the word)

maweber-bia commented 3 years ago

Good point ! you are right it seems contradictory…

Fiber are not absorbed “directly but are food for the microbiote in the gut… And they are compositional constituents which have to be listed in the entity classes as well

Cheers, Magalie

De : Graham King @.> Envoyé : jeudi 19 août 2021 14:57 À : Southern-Cross-Plant-Science/cdno @.> Cc : Magalie Weber @.>; Mention @.> Objet : Re: [Southern-Cross-Plant-Science/cdno] NTR: dietary nutritional component (#30)

@maweber-biahttps://github.com/maweber-bia is fibre/fiber actually absorbed? I understand it enters the digestive system and contributes a biological function, but may not necessarily be absorbed (in my understanding of the word)

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maweber-bia commented 3 years ago

perhaps we can use "taken in" instead of "absorbed"? However, I think that absorption is a key notion in defining nutrition/nutrients. Traditionally, absorption is the last step (cf the 3 steps in the [NICHD] definition) but the first 2 steps can be bypassed...

From my perspective, the 3 steps describe the digestion process rather than "nutrition" on its own

laurenechan commented 3 years ago

Hi all, so many great thoughts here! As for ingested vs consumed vs absorbed, I am partial to keeping it very broad as none of them are a perfect fit in my mind given the variety of routes for receiving nutrients and the lack of absorption that occurs in some cases. To @maweber-bia 's note of absorption being a key part to nutrition/nutrients, I think that's largely true, but for instances of parenteral nutrition (IV) then you don't actually see any absorption occurring because the nutrients are provided directly into the vessel. Same with fiber not being absorbable directly, yet it feeds microbiota and they can produce short chain fatty acids which are absorbed. I think we need some level of ambiguity that allows for these use cases to still fit even if they don't include direct absorption of the entity in question. Could we consider "utilized"? I think "taken in" is also fine, although may still seem to imply absorption.

"A material entity utilized by an organism that contributes either directly or indirectly to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts"

maweber-bia commented 3 years ago

yes, indeed, "utilized" does not necessarily imply digestion (oral /stomach phase) and/or absorption (enteral phase) so it fits well

mateolan commented 3 years ago

I like utilized by, but it is perhaps a bit broad. In that sentence the material entity could be the BBQ I used to cook my food, or any tool used by an organism. I realize that one of the definitions of consume is to ingest, but not all of them are... Perhaps we just need to point to the right one?

On Thu, Aug 19, 2021, 07:50 maweber-bia @.***> wrote:

yes, indeed, "utilized" does not necessarily imply digestion (oral /stomach phase) and/or absorption (enteral phase) so it fits well

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laurenechan commented 3 years ago

Is it too cumbersome to say "biologically utilized"? Perhaps that might help distinguish from tools being used? @mateolan

mateolan commented 3 years ago

So a caterpillar climbing a tree is biologically utilizing the bark as a scaffold upon which to climb... I do think "consumes" is ok, especially if we have subclasses which define modes of consumption, and oral ingestion is one of those modes. Parenteral injection is another mode of consumption, etc.

On Thu, Aug 19, 2021, 10:55 Lauren @.***> wrote:

Is it too cumbersome to say "biologically utilized"? Perhaps that might help distinguish from tools being used? @mateolan https://github.com/mateolan

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laurenechan commented 3 years ago

Hmm maybe "metabolically" if "biologically" is too broad? I am ok with consumes so long as clear routes are provided somewhere (would this be in CDNO?), just trying to give options!

ddooley commented 3 years ago

"metabolically" - just what I was thinkin!

Graham-J-King commented 3 years ago

So does the 'metabolically' imply the contribution to nutrition, whereas other material entities may not necessarily be metabolized but still contribute to gastrointestinal health? For example my (non-expert) understanding is that a dietary component such as insoluble fiber may have some additional contributions beyond being fermented - by retaining water and bulking up stool. Is this function considered 'nutritional' or some other role not involving metabolism ?

Graham-J-King commented 3 years ago

or, more simply - are there parts of diet that are non-nutritional ?

mateolan commented 3 years ago

Graham, indeed I would agree that there are nutritional components that are non-metabolic in nature, and your example of stool bulkers is a great one.

On Thu, Aug 19, 2021 at 3:50 PM Graham King @.***> wrote:

or, more simply - are there parts of diet that are non-nutritional ?

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maweber-bia commented 3 years ago

Actually, "metabollically" implies nutrition; other non-metabolic dietary parts may play a biological, physiological, or a simple mechanical role. In other words, not all the dietary compounds that are ingested are playing a metabolic/nutritional role. Only those considered as nutrients are playing a metabolic role.

bbfreeman commented 3 years ago

This is a fabulous discussion and so many great points are being made. From my perspective, keeping some level of broadness is important. In this way, we should lean away from the word "nutrient" because the material entities we are talking about under the definition of nutritional components are much broader than traditionally defined nutrients (i.e., a substance that provides nourishment essential for growth and the maintenance of life). I like the discussion around fibers, oligosaccharides, etc and think it is quite relevant for the reasons already stated. I think we can add "contributes directly and indirectly" but I wonder if its necessary to be this explicit or is it captured just by the mere definition of "contributes to survival, growth, development or biological function....". Might it be implied directly or indirectly? Does it need to be stated?

Metabolized - Since not all these chemical entities that have biological function are "metabolized" I would suggest not including "metabolized" in the definition because it narrows the scope.

Subclasses of routes of intake - this is another interesting point. Indeed, I think we tend to think of oral ingestion first, but there are other modes of "entry" into the body (other modes may be through the skin and lungs) and perhaps these will be more favorable for some chemical entities in years to come. I can't really come up with any better words, so of the suggested words to use (consumption, take in, ingest, etc...), perhaps "taken in by organism..." or "taken into an organism..."

Organism - I am wondering if we are talking about humans only or indeed including other "organisms" in the definition of "dietary nutritional component". Noticed the word "organism" has been included as the definition has evolved so wanted ask the question.

Graham-J-King commented 3 years ago

@bbfreeman For the nutritional component class, we had left this at the general organism level. However, for the proposed ‘dietary role’ class, it has been suggested that there be defined a major subclass ‘human dietary role’ and subclasses for other organisms. @LilyAndres also reminded me that within the definition of available carbohydrate (CDNO_0000003) we included the term “monogastric animals” so that this was also applicable for livestock.

maweber-bia commented 3 years ago

Finally, are we defining "nutritional component" class or "dietary nutritional component" class (or both) ? From the previous discussions, I think we have "dietary component" on one side, and "nutritional component" on the other.

@bbfreeman, could you please give an explanation or an example for your statement about "Metabolized"

"Metabolized - Since not all these chemical entities that have biological function are "metabolized" I would suggest not including "metabolized" in the definition because it narrows the scope."

In my opinion, if we are defining "nutritional component" we have to refer to the metabolism/metabolic use of the component that has been taken in...

bbfreeman commented 3 years ago

@maweber-bia, responding to "could you please give an explanation or an example for your statement about "Metabolized".

When written I was thinking about certain flavonoid compounds that are absorbed and excreted intact (no apparent "metabolism" per se, but associated with biological activity).

Graham-J-King commented 3 years ago

@bbfreeman, @maweber-bia, indeed, entities may be involved in 'metabolism' as a biological activity, without necessarily being 'metabolized' (changing energy state) themselves.

This discussion was initially focused on 'dietary nutritional component'. The word ‘dietary’ was included to differentiate from other uses of the term nutrition (eg in plants). It may help to test whether these statements are true or false:

All (human) nutrition derives from diet
Diet may include nutritional and non-nutritional components
All nutritional components have a biological role
All nutritional components are involved in metabolism
Some non-nutritional components of diet also have a biological role
Not all non-nutritional components of diet have a biological role

We may therefore wish to consider how the class named dietary component may differ from dietary nutritional component if at all.

mateolan commented 3 years ago

Great thought exercise Graham. My answers below. But before I go there--I would challenge the group to think in terms of the Gene Ontology's root classes under 'biological process' (what is it doing), 'molecular function' (how does it work), and 'cellular component' where in the organism does this process/mechanism occur. FWIW, I also think this is a good read https://pubmed.ncbi.nlm.nih.gov/31769838/, and also this is a must read https://ods.od.nih.gov/pubs/bioactivefoodcomponents/American%20Dietetic%20Association%20-%20ADA%20-%20comments%20on%20defining%20bioactive%20food%20components.pdf. We should also probably compare definitions from here https://ods.od.nih.gov/HealthInformation/dictionary.aspx, and (as an example) these 7 definitions https://www.ebi.ac.uk/ols/search?q=nutrient&groupField=iri&exact=on&start=0 of "nutrient". I also think that the terms in these links should be on our list of items to discuss--(maybe we should be using a shared Google doc or sheet?) for this shortlist, so we can see discrepancies? I would also recommend that one of the students among us make this purchase https://www.eatrightstore.org/product-type/subscriptions/electronic-nutrition-care-process-terminology . Also, I added a 7th question. Finally, I think that this discussion will yield a paper like the Frank paper linked above, but actually, much much stronger, since we will encode the logical relationships.

All (human) nutrition derives from diet FALSE Rationale: Diet implies alimentation. It is entirely possible (though I would not want to) meet one's nutritional needs on parenteral nutrition, which by definition avoids the gastrointestinal system--and therefore, "diet".
Diet may include nutritional and non-nutritional components. TRUE Rationale: Pica https://www.nationaleatingdisorders.org/learn/by-eating-disorder/other/pica is all you need to know here.
All nutritional components have a biological role. TRUE Rationale: Let us consider that a biological role is to effect a biological_process change in an organism. In the case of a nutritional component, it would be to "improve" that process. (Which ultimately may or may not be healthy for that organism at that point in time.)
All nutritional components are involved in metabolism. FALSE Rationale: Fiber is an example of what I would argue is an important nutritional component, without being either a nutrient, or involved in metabolism.
Some non-nutritional components of diet also have a biological role. TRUE Rationale: That biological role may be deleterious, as in eg inappropriate calcification.
Not all non-nutritional components of diet have biological roles. MAYBE (your double negative is leaving open holes) Rationale: I would argue that just about anything that is consumed dietarily will have a biological role, no matter how undesirable. I would be delighted to be turned wrong here.
A "nutritional component" is the same thing as a nutrient. (If not, how do they differ?) FALSE Rationale: I believe that "nutritional component" is a broader class of molecules with types like bioactive component (which may be multi-homed), and nutrient which may have subclasses, like essential and non-essential as well as micronutrient, and macronutrient. I would argue that Carbohydrates are a class of non-essential macronutrients. I would further put forth that bioactive components may include essential or non-essential nutrients, or other classes of molecules altogether like the indigestible carbohydrates (oligosaccharides) or bioactive peptides that I mentioned previously.

PS. @bbfreeman https://github.com/bbfreeman, @maweber-bia https://github.com/maweber-bia how would you feel about adding your names to your github profiles so that we who update the issues list via email get to see your names when the email comes in?

On Sun, Aug 22, 2021 at 6:57 PM Graham King @.***> wrote:

@bbfreeman https://github.com/bbfreeman, @maweber-bia https://github.com/maweber-bia, indeed, entities may be involved in 'metabolism' as a biological activity, without necessarily being 'metabolized' (changing energy state) themselves.

This discussion was initially focused on 'dietary nutritional component'. The word ‘dietary’ was included to differentiate from other uses of the term nutrition (eg in plants). It may help to test whether these statements are true or false:

1.
 All (human) nutrition derives from diet
2.
 Diet may include nutritional and non-nutritional components
3.
 All nutritional components have a biological role
4.
 All nutritional components are involved in metabolism
5.
 Some non-nutritional components of diet also have a biological role
6.
 Not all non-nutritional components of diet have a biological role
We may therefore wish to consider how the class named dietary component may differ from dietary nutritional component if at all.

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maweber-bia commented 3 years ago

Good job Matthew, I fully agree with all your answers and rationales

I would just add some comments for Question 6 and 7

--> I think it is right that anything consumed dietarily will have a biological role if we consider the definition of a biological role: CHEBI:24432 http://purl.obolibrary.org/obo/CHEBI_24432 A role played by the molecular entity or part thereof within a biological context.
If we consider the definitions of "nutrient role" and "nutrient" below nutrient roleOBI:0000204 http://purl.obolibrary.org/obo/OBI_0000204 a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.

nutrientONS:0000077 http://purl.obolibrary.org/obo/ONS_0000077 A nutrient is a food component used by the body for normal physiologic functions that guarantee survival and growth. It must be supplied in adequate and defined amounts from foods consumed within a diet. Malnutrition occurs when the right amount of nutrient is not provided

nutrientCHEBI:33284 http://purl.obolibrary.org/obo/CHEBI_33284 A nutrient is a food component that an organism uses to survive and grow.

--> I actually think that we have to distinguish "nutrients" (or nutritional dietary components) that provide nourishment to an organism from "bioactive components" ( or biologically active compounds) that have a (broader) biological role within an organism.

I also think that we have to specify that the "dietary component" (either nutritional or non-nutritional) refers to human nutrition.

Matthew, does that kind of hierarchy fit your view?

PS I have added my name to my Github profile, thank you for the tip!

mateolan commented 3 years ago

Magalie, Yes! A few caveats at this end. A nutritional component, or even nutrient may or may not be a dietary or food component (we actually get some essential minerals from the air)--also, again, parenteral nutrition--so this means that we are diverging from the ONS and ChEBI definitions you cited. I like biological role definition from ChEBI. I also like the nutrient role from OBI, tough some of their other definitions around food and nutrition are more spurious. I agree with your supposition that we need to clarify "for humans" not just for "dietary component" but for just about all of the items we are speaking about.

On Mon, Aug 23, 2021 at 12:40 AM Magalie WEBER @.***> wrote:

Good job Matthew, I fully agree with all your answers and rationales

I would just add some comments for Question 6 and 7

1.

--> I think it is right that anything consumed dietarily will have a biological role if we consider the definition of a biological role: CHEBI:24432 http://purl.obolibrary.org/obo/CHEBI_24432 A role played by the molecular entity or part thereof within a biological context. 2.

If we consider the definitions of "nutrient role" and "nutrient" below nutrient roleOBI:0000204 http://purl.obolibrary.org/obo/OBI_0000204 a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.

nutrientONS:0000077 http://purl.obolibrary.org/obo/ONS_0000077 A nutrient is a food component used by the body for normal physiologic functions that guarantee survival and growth. It must be supplied in adequate and defined amounts from foods consumed within a diet. Malnutrition occurs when the right amount of nutrient is not provided

nutrientCHEBI:33284 http://purl.obolibrary.org/obo/CHEBI_33284 A nutrient is a food component that an organism uses to survive and grow.

--> I actually think that we have to distinguish "nutrients" (or nutritional dietary components) that provide nourishment to an organism from "bioactive components" ( or biologically active compounds) that have a (broader) biological role within an organism.

I also think that we have to specify that the "dietary component" (either nutritional or non-nutritional) refers to human nutrition.

Matthew, does that kind of hierarchy fit your view? [image: image] https://user-images.githubusercontent.com/64576528/130408221-0e8d5276-d051-496b-9aaf-be6d8b0a7859.png

PS I have added my name to my Github profile, thank you for the tip!

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LilyAndres commented 3 years ago

Amazing points thanks @bbfreeman, @maweber-bia and @mateolan thanks for the references, I checked them all, they are very useful.

Finally, are we defining "nutritional component" class or "dietary nutritional component" class (or both) ? From the previous discussions, I think we have "dietary component" on one side, and "nutritional component" on the other.

@maweber-bia we are discussion 'dietary nutritional component' but we proposed to check if the label we are looking for is actually 'dietary component'.

I also think that the terms in these links should be on our list of items to discuss--(maybe we should be using a shared Google doc or sheet?) for this shortlist, so we can see discrepancies?

Great idea @mateolan I copied all the definitions in the following doc I also added at the end the 'dietary nutritional component' with the last definition, hopefully, it makes sense now that we can see the other definitions for nutrient.

Finally, I think that this discussion will yield a paper like the Frank paper linked above, but actually, much much stronger, since we will encode the logical relationships.

@mateolan Absolutely, I think so too.

I also think that we have to specify that the "dietary component" (either nutritional or non-nutritional) refers to human nutrition.

@maweber-bia thanks. I think this can be good but at the same time we want to provide some general terms for people working with livestock, otherwise, somebody else will need to create new terms for a livestock nutrition ontology...

maweber-bia commented 3 years ago

I think this can be good but at the same time we want to provide some general terms for people working with livestock, otherwise, somebody else will need to create new terms for a livestock nutrition ontology...

@LilyAndres Thanks for the clarification! yes, humans and livestock should be targeted in addition to plants, but what I wanted to point out is that we have to specify for what kind of organism we are referring to when stating that the material entity (food/feed component) has a nutrient role and this is tricky because we can not really have a class for "essential" compounds that apply to all organisms...

In any case, we have some interesting leads in this discussion; my last point is that for me if we are referring to "dietary component", it would imply "oral ingestion" (and thus digestion and absorption but not necessarily metabolism, as refer to the flavonoid compounds for example); if we are referring to a broader scope for nutrients (let's call them "nutritional components") then we should point to the administration route (oral, cutaneous, enteral, parenteral...)

If we want to cover all aspects, I definitively think that "taken in" is the most appropriate term in the definition of nutritional component :

A material entity taken in by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts

A subclass could be for dietary nutritional component

A material entity ingested by an organism that contributes to the survival, growth, development, or other biological function of itself, its bionts, or its holobionts cheers, Magalie

LilyAndres commented 2 years ago

Hello everybody, I would like to keep going with the conversation about the definition of the 'dietary nutritional component'. Here are some points to discuss:

1. Nutritional We will change the label to 'dietary chemical component' or 'dietary component'. We decided to do this change because we have terms that are not necessary 'nutritional components' as discussed in issue #70 and highlighted by @laurenechan

In issue #191 from FoodOn @kaiiam proposed to modify our CDNO hierarchy to:

have a nutritional disposition class, with a definition like: A role which 1) inheres in a material entity 2) is realized when that entity is taken in by an organism and contributes to the survival, growth, development, or other biological function of such organism, its bionts, or its holobionts.

change dietary nutritional component to dietary component and modify it's definition to be something like: A material entity which is taken in by an organism during a dietary process.

Add the axiom has disposition some nutritional disposition to the relevant classes in the CDNO dietary component hierarchy making sure not to assign the axiom to terms like lead or gold etc. Similarly, back to the original discussion of chemical food component perhaps FOODON

2. Now, one important point to highlight here is the term 'dietary', as mentioned by @mateolan: FALSE Rationale: Diet implies alimentation. It is entirely possible (though I would not want to) meet one's nutritional needs on parenteral nutrition, which by definition avoids the gastrointestinal system--and therefore, "diet". So, NOT all (human) nutrition derives from diet.

I think the scope of the CDNO might not involve other types of "feeding" (i.e. acquisition of food) at this point but it's good to have this discussion here:

Enteral Feeding (involving or passing through the intestine, either naturally via the mouth and oesophagus, or through an artificial opening) o Eating o Tube feeding – liquid nourishment. Similar to what you would get from food and digested the same way
Parenteral Feeding o TPN – Supplying nutrients to the body, bypassing the digestive system and dripping nutrient solution directly into the vein

In this we will only involve enteral process so we will have 'dietary' in the label.

Happy to discuss any of this subjects. Let me know what you think @ddooley, @maweber-bia, @Graham-J-King

ddooley commented 2 years ago

So we can safely say "Diet" involves the process of oral or enteral feeding, while parenteral and intravenous feeding involve a different (more direct) biochemical chain, so that sounds like a good distinction. Most esoterically, does this suggest a top-level food consumption hierarchy:

gastro-intestinal feeding process
    oral feeding
    enteral feeding
veinal feeding process (or arterial? Either? cardiovascular system feeding process?)
    intravenous feeding
    parenteral feeding

"Dietary component" sounds fine to me! And by emphasizing potential roles of chemicals rather than type of host organism, we can then use the same hierarchy regardless of human or other animal application. @FrancescoVit your feedback appreciated too!

Graham-J-King commented 2 years ago

A. I would suggest that 'dietary' is being used here as an adjective, derived from the root word 'diet', in the sense defined in Merriam-Webster as "habitual nourishment" or "food and drink regularly provided or consumed". From Wikipedia we have "In nutrition, diet is the sum of food consumed by a person or other organism". (some diverse definitions of 'food' in C. below

B. @ddooley suggests 'feeding process' to distinguish the type of feeding. This seems reasonable. However, NCIT appears to have this process as a formal conceptual entity named ‘route’ in which 'parenteral' is a subclass of ‘dietary route’. This would suggest dietary route is not exclusive to an (eg enteral) dietary system (eg as opposed to cardiovascular system etc).

NCIT give: Conceptual Entity -Route --------- Route of Administration ---------------------Dietary Route of Administration](http://purl.obolibrary.org/obo/NCIT_C78373) ------------------- Administration by way of food stuff ---------------------------Enteral Route of Administration --------------------------Parenteral Route of Administration

C. Food definitions....... • (general) any nutritious substance that people or animals eat or drink or that plants absorb in order to maintain life and growth. • http://purl.obolibrary.org/obo/**NCIT_C62695 A group of materials of either plant, animal or artificial origin containing essential body nutrients that can be ingested by an organism to produce energy, stimulate growth, and maintain life. • http://purl.obolibrary.org/obo/ONS_0000079 a complex matrix that is consumed by a person through the process of eating or drinking. Food are bearer of the nutrients, bioactives and sometimes other food components. Food consumption, through the meal consumption, follows a certain dietary pattern, which define the diet. Nutrients and bioactives contained in food can be exploited by the human organism thanks to the process of digestion, absorption, metabolization, or through the intervention of the gut microflora • http://purl.obolibrary.org/obo/CHEBI_33290** A physiological role played by any substance of either plant, animal or artificial origin which contains essential body nutrients that can be ingested by an organism to provide energy, promote growth, and maintain the processes of life.

Food material • http://purl.obolibrary.org/obo/**FOODON_00002403** Any substance that can be consumed by an organism to satisfy nutritional or other health needs, or to provide a social or organoleptic food experience

Food or food product • http://purl.obolibrary.org/obo/**NCIT_C1949** Processed or unprocessed substances obtained from animal, plant, microorganism and mining source that provide nutrients for living organisms to maintain biological processes or functions.

maweber-bia commented 2 years ago

Hi there!

I fully agree with the argument "Diet" involves the process of oral or enteral feeding, while parenteral and intravenous feeding involve a different (more direct) biochemical chain and "Dietary component" sounds fine to me! And by emphasizing potential roles of chemicals rather than type of host organism, we can then use the same hierarchy regardless of human or other animal application.

@ddooley, this is right, using "roles or dispositions" is the best way in my views as we can also connect chemical food components (or ingredient, contaminant,...) with nutritional disposition, or other functional disposition (acidifying role, anti-oxydative role,...). In the case of contaminants, those may have a toxic role !

@Graham-J-King based on the definitions collected, I think that we should take "diet" in the broadest sense : as "habitual nourishment" or "food and drink regularly provided or consumed", irrespective of the way of absorption/consumption. This would allow combination with different ways of administration, namely "routes" or "feeding processes"

Once again, we must not confuse diet (or food) and nutrition : nutrition involves different routes and different nutrients (which have a nutritional role or disposition) , when diet is intimately linked to food and digestion process (oral and/or gastro-intestinal routes). Oral ingestion is not exclusive but the most regular way for feeding humans (and most of other animals !

For bacteria or microbes (or plants), we rather speek about "nutrients" which are metabolized to produce metabolites...

I think we now have the big picture! @FrancescoVit your feedback appreciated too!

maweber-bia commented 2 years ago

in the NCIT definition, I am confused about "Administration by way of food stuff"

food stuff = food and/or the nutrients derived from it ?

Graham-J-King commented 2 years ago

@maweber-bia - in NCIT if you go to this link you'll see a long list of 'routes'. "Route of Administration' is defined as "Designation of the part of the body through which or into which, or the way in which, the medicinal product is intended to be introduced. In some cases a medicinal product can be intended for more than one route and/or method of administration." So I think we can only refer to the "route' concept by analogy for food stuff, rather than explicitly reuse the NCIT term in CDNO, as the higher NCIT entity appears to be defined in relation to 'medical product' (eg delivering a polio vaccine on a sugar cube would fit that definition).
Hope this comment helps!

maweber-bia commented 2 years ago

Thank you! this is clearly a point of differentiation with the biomedical context (the enteral and parenteral routes are "derived" from the normal route of nutrition for human, which is oral ingestion)

laurenechan commented 2 years ago

Hi all, I agree with many of the comments being stated. In particular, @maweber-bia point about differentiating diet and nutrition provisions. Parenteral nutrition (at least in the US) is considered a pharmaceutical product/medication, so while to me it is clearly a nutrition provision it is not what I would consider diet. However, I think common language surrounding parenteral nutrition still includes the term "feeding" but I am uncertain if "feeding" has to be fully aligned with dietary intake (which I would not say includes parenteral nutrition).

CompositionalDietaryNutritionOntology / cdno