Moving hepatobiliary system out from under digestive system

[doughowe]

The Alliance expression working group is planning to use the UBERON terms "digestive system" and "hepatobiliary system" in the gene expression anatomy ribbon. The concensus in the group, also reflected in species-specific anatomies for zebrafish and mouse, is that only parts of the hepatobiliary system are rightly part of the digestive system. Currently in Uberon "hepatobiliary system" is part of "digestive system". One suggestion would be to move "hepatobiliary system" out from under "digestive system" so it is a sibling under "anatomical system" and make the parts of the hepatobiliary system which are part of digestive system..be part of digestive system.

[cmungall]

only parts of the hepatobiliary system are rightly part of the digestive system

I think you mean the HS is not rightly part of the DS?

There is definitely ambiguity here. Sometimes the HS parts, pancreas, are considered "accessory" parts of the DS, sometimes bona fide parts.

The way we model this is in uberon DS = HS + "alimentary part of DS"

• UBERON:0001007 ! digestive system
  • UBERON:0002423 ! hepatobiliary system
  • UBERON:0005409 ! alimentary part of gastrointestinal system

We are more attached to the model than the terminology, but if we do switch labels we want to be consistent

I think the structure the alliance wants is UBERON:0005409. I appreciate that this is an unwieldy string to use as a top level grouping in ribbon. How would people feel about "alimentary system" as the primary label?

If people feel really strongly that they want a string "digestive system" and they want to exclude the liver, we can explore that nomenclature, introducing an unwieldy string for the broader grouping (e.g DS and accessory parts).

I would like to retain terminological consistency as much as possible

The concensus in the group, also reflected in species-specific anatomies for zebrafish and mouse

Uberon is terminologically consistent with XAO, MA, NCIT, FMA.

In contrast EMAPA and ZFA do not place HS under DS

@tfhayamizu - how do you intend to resolve this difference between MA and EMAPA?

Note that ZFA and (implicitly) GO place pancreas (which is often considered an accessory part rather than "true" part). What is the alliance view on pancreas?

Note to self: add this to
https://github.com/obophenotype/uberon/wiki/The-digestive-tract

[cmungall]

Note that Terminologica Anatomica (which we treat as canonical terminology for human) treats alimentary system as the canonical English synonym for latin systema digestorium, and includes pancreas, liver and gallbladder

• https://en.wikipedia.org/wiki/Terminologia_Anatomica#A05:_Alimentary_system_(systema_digestorium)
• http://www.unifr.ch/ifaa/Public/EntryPage/TA98%20Tree/Entity%20TA98%20EN/05.8.01.001%20Entity%20TA98%20EN.htm
• http://www.unifr.ch/ifaa/Public/EntryPage/TA98%20Tree/Entity%20TA98%20EN/05.0.00.000%20Entity%20TA98%20EN.htm

This scuppers my plans to use "alimentary system" as a more digestible (ho ho) string for the restricted entity. But it also suggests that the original proposal to redefine DS in a more restricted way goes against expert usage

[tfhayamizu]

Attempting to resolve disparities between MA and EMAPA -- my 'two cents' here:

It appears that "alimentary" and "digestive" are used synonymously, and that the "alimentary [digestive] system" includes liver and gall bladder. https://en.wikipedia.org/wiki/Human_digestive_system

Personally, I do not have a strong opinion as to the primary label, but it seems "alimentary" would be less contentious. https://www.merriam-webster.com/dictionary/alimentary

Furthermore, I think it would be useful to add a new term "alimentary tract" to the EMAPA (as in the MA, see below). I believe that what the MA is calling the "alimentary system" actually refers to the "alimentary tract" (see synonym). (Would it be better to change MA label, or to merge with parent and then create a new term?)

[Gastrointestinal Tract] https://www.ncbi.nlm.nih.gov/pubmedhealth/PMHT0022855/
The large, muscular tube that extends from the mouth to the anus, where the movement of muscles, along with the release of hormones and enzymes, allows for the digestion of food. Also called the alimentary canal or digestive tract.

I suggest that "gastrointestinal" be avoided, except in synonyms, as it appears to imply exclusion of oral, oropharynx, esophagus and anal regions.

Lastly, it seems that (based on child terms) the current EMAPA terms prefaced by "alimentary system" would be more appropriately labeled "alimentary tract" (e.g. "alimentary tract ectoderm").

[cmungall]

thanks. I agree that the MA term (and the desired AGR) term is really the Digestive Tract. I'm not sure how attached the AGR is to having all of the terms in the slim be "systems"

[cmungall]

@doughowe @sbello thoughts?

alimentary system includes the liver, digestive tract excludes the liver

[cerivs]

Digestive system is used in zebrafish to refer to the "gut"; intestine, esophagus, cloaca and presumptive swim bladder mouth and vent as well as the mouth, pharynx, liver and some other ducts and cells. I think we can either rename or add a synonym to this term so it has alimentary system directly linked. Is there a strong preference for renaming or just adding a synonym?

The gut is sometimes called the digestive tract, enteric tract or alimentary canal. I think we can add mouth terms as children of "gut" and then use whatever grouping term for gut/alimentary canal/ enteric tract/gut tube the expression group comes up with.

Gastrointestinal is inappropriate for zebrafish since they have no stomach.