Hepatobilliary system

[sbello]

Should hepatobilliary system be made a child of digestive system? Email thread:

Hi, MPO colleagues! Shouldn't liver be a part of the digestive system? In the current MP, it is listed separately? See https://www.niddk.nih.gov/health-information/health-topics/Anatomy/your-digestive-system/Pages/anatomy.aspx or is there a different classification for the mouse? -Peter

According to the MA (mouse anatomy ontology) the entire hepatobiliary system is part of the digestive system . I don’t recall why we made this a separate system header - this section had been subject to external expert review, but that was 7-8 years ago. We will look again.
Cindy

Yes, part of the digestive system

not part of digestive tract

develops from part of digestive tract

You should see the inference in protoge Chris Mungall

On 2 Sep 2016, at 15:03, Melissa Haendel wrote:

it should be part of the digestive system. Perhaps we could run checks against Uberon to look for part_of closure omissions like this? I suspect there is already a report somewhere in jenkins?

[sbello]

Need to consider what to do about liver development? Fetal liver is site of hematopoiesis.

[cmungall]

In uberon it's part of the digestive system, and this is consistent with multiple other ontologies.

It develops from a part of the digestive tract (but is not itself a part of the tract)

EDIT this referred to the liver. However, the first part is also true for hepatobiliary system, see below.

[cmungall]

sorry, I didn't read the full ticket, I was responding to the original question on the list which was about the relationship between liver and digestive system (illustrating the distinction that should be made between the system and the main tract).

For the two systems, GO has them as siblings:

In uberon, we hepatobiliary system = liver + biliary system. This seems in itself good justification for including fully within digestive system. In addition, we also make hepatobiliary system part-of the digestive system, as it is in MA (but not EMAPA)

[cindyJax]

We have to be careful about liver physiology terms. Liver detox functions should not be part of digestive system. Manifestations such as jaundice, metabolizing ammonia by-products, or failure of clearance of xenobiotics or blood degradation products should be part of excretory systems

[cmungall]

This is a good time to align definitions to make this decision non-subjective:

We have two candidates in MP, one in Uberon:

id: MP:0001663
name: abnormal digestive system physiology
def: "any functional anomaly of **the organ system that converts 
ingested food to nutrients and energy**" [MGI:cwg]

id: MP:0000462
name: abnormal digestive system morphology
def: "any structural anomaly of **the system dedicated to the 
mechanical, chemical, and enzymatic processing of food**" 
[ISBN:0-683-40008-8, MGI:cwg]

I think these could be combined into one:

"the organ system dedicated to the mechanical, chemical, and enzymatic processing of food, and converts it into to nutrients and energy"

id: UBERON:0001007
name: digestive system
def: "Anatomical system that has as its parts the organs devoted to the 
ingestion, digestion, and assimilation of food and the discharge of 
residual wastes." [FB:gg, NLM:alimentary+system, 
Wikipedia:Digestive_system]

Note that the uberon one includes discharge. This is necessary if the digestive tract is part of the digestive system.

But this makes the whole system much more inclusive....

On 9 Sep 2016, at 7:41, cindyJax wrote:

We have to be careful about liver physiology terms. Liver detox functions should not be part of digestive system. Manifestations such as jaundice, metabolizing ammonia by-products, or failure of clearance of xenobiotics or blood degradation products should be part of excretory systems

You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/obophenotype/mammalian-phenotype-ontology/issues/2199#issuecomment-245933602

[cindyJax]

Agreed that we need to align definitions. However, if we include 'discharge of residual wastes' as part of the definition, do we also include renal system as part of the digestive system? This needs to be defined a bit more carefully.

[cmungall]

Yes, the renal system is a step too far!

The simplest approach may be just to tack on a clause "and includes the full digestive tract, including terminal parts" to the definition of DS

More radically, we could weaken the relationship of DT to DS to overlaps. I don't think this is a good idea but just laying out the options.

The FMA distinguishes between systemic and other kinds of parts, but I feel that complicates things

We have some consistency issues at the other end of the DT too - uberon includes the mouth (and hence teeth, secondary palate etc) as part of the DT (and hence DS), whereas MP/HP excludes it. I can see that a craniofacial classification can be seen as more 'primary' but logically it should be included, especially if we follow MP:0000462 and include mechanical functions (e.g. chewing)

[sbello]

I have a similar issue with the inclusion of mouth as a whole in the digestive system as I do for liver. The mouth could also be considered part of the respiratory system. However, it may be appropriate to add some structures within the mouth, like teeth, to the digestive system. We just need to carefully consider if each tissue always functions as part of the digestive system.

For the digestive system definition what if we modified the one Chris proposed above to "the organ system dedicated to the mechanical, chemical, and enzymatic processing of food, and converts it into to nutrients and energy, and disposes of indigestable waste produced during this process"

[sbello]

Another question, would any of these definitions make the appendix part of the digestive system?

[cmungall]

On 9 Sep 2016, at 13:56, sbello wrote:

I have a similar issue with the inclusion of mouth as a whole in the digestive system as I do for liver.

Hmm, perhaps the real issue here is the inclusion of the whole DT as being within the DS? From an evolutionary perspective, the definition of the DT as the tube extending from mouth to anus is standard and useful. But when we try and place the tract in the DS, the transitivity of part-of ends up making the system term too inclusive.

The mouth could also be considered part of the respiratory system. However, it may be appropriate to add some structures within the mouth, like teeth, to the digestive system. We just need to carefully consider if each tissue always functions as part of the digestive system.

This gets tricky as many structures will have different functions. If a structure always has to function as part of a system to be in that system, this may end up being too restrictive.

Let's take another system, like the nervous system. This includes the brain, which includes both neural cells and supporting structures like blood vessels.

Are all brain vasculature abnormalities NS abnormalities? If the vessels are actually located in the brain (MP:0004950), MP seems to agree.

But this doesn't really fit with the definition of NS abnormality:

"the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan"

Maybe we are trying to get the abnormal-X-system terms to do too much work. Does it help to think of a distinction between an X-system (which may comprise parts that don't always function in X, and may be 'along for the ride') and an X-process (which at any one time only has as participants structures actually functioning to achieve X).

Thus abnormal cerebral artery morphology might always be a NS abnormality (by virtue of anatomic partonomy), but is not itself necessarily an abnormality of nervous system function (though of course, severe abnormalities will lead to NS function abnormalities, e.g. through stroke).

For the digestive system definition what if we modified the one Chris proposed above to "the organ system dedicated to the mechanical, chemical, and enzymatic processing of food, and converts it into to nutrients and energy, and disposes of indigestable waste produced during this process"

I think this works. Not that wikipedia is an authority, but seems consistent: https://en.wikipedia.org/wiki/Digestion#Overview_of_vertebrate_digestion

Hmm, we may need to do some work on GO. GO has defecation sitting outside both 'digestion' and 'digestive system process'...

cross-ontology consistency is hard!