'intestinal muscle' part_of intestine?

[chris-grove]

@raymond91125 I noticed that the term:

intestinal muscle (WBbt:0005796)

is asserted to be "part of" the intestine (WBbt:0005772). I wouldn't have considered the intestinal muscle to be part of the intestine, but rather part of the alimentary system as a whole. The definition of "intestine" does not appear to accommodate the "intestinal muscle" as part. I would suggest/request that we remove the "part_of intestine" axiom for "intestinal muscle" and instead add the "part_of alimentary_system" axiom.

This comes up because a user is asking for genes expressed in the intestine, but if I use the WormBase Ontology Browser to get the list of genes expressed in the intestine or any of its parts, this will include genes expressed in the intestinal muscle, which I don't think is what they are looking for.

What do you think?

[raymond91125]

In MA and FBbt, muscles of the intestine are related to intestines with part_of. Thus, I am reluctant to remove this relationship in WBbt. It may be prudent to inquire Daniela to see if her curation practices are consistent with the intent of the ontology structure. But I don't think WBbt is wrong in this regard.

[chris-grove]

Hmm, OK. Yes, I do think we should consult Daniela as well. I guess I feel there is then a discrepancy between the existing definitions of intestine and one in which the intestinal muscle would be included as part. For example, the WormAtlas glossary for intestine:

https://www.wormatlas.org/glossary/iglossary.htm#intestine

The definition of "intestine" begins: "A chain of very large cuboidal cells which all descend from a common precursor, the E founder cell and form a wide central lumen lined by many microvilli that form a brush border. Food passes from the posterior pharynx to the intestine where it is digested and then on to the rectum which processes the waste products for excretion."

I don't see any part of the definition in WormAtlas or within the anatomy ontology itself that suggests that it includes the muscle component. There is the WormAtlas definition for "Gut":

https://www.wormatlas.org/glossary/gglossary.htm#gut

that reads:

"A general term which may refer both to the intestine and to related muscles and valves which regulate intake or outflow of its contents."

which may be a more appropriate part_of parent for intestinal muscle. I guess my biggest issue with it is that when people use WOBr to extract intestinally-expressed genes, I would think they are looking for genes expressed in the int cells (derived from E, as in the definition), not the intestinal muscle cells.

[raymond91125]

Intestinal cell WBbt:0005792 is for those who look for exclusively E-derived cell gene expression. Perhaps WA's intestine definition is more in line with the fact that not all nematode intestines have associated muscles. Perhaps gut in nematodes is a better counterpart of intestine in mammals.

[chris-grove]

OK, yeah, that makes sense

[chris-grove]

@raymond91125 Can we revisit this after our discussion with David Hall?