Authors and contributors:

• Chris Mungall (author)

Date: 2012

Document Type: ontology_design_pattern

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We follow Kardong in defining the digestive tract as a tube extending from mouth to anus. We use this definition across bilateria.

Note that various other terms are used for other divisions or parts of the digestive system, for example

• alimentary tract - in Kardong, the portion of the DT after the pharynx
• digestive system - DT plus various organs
• gut - ambiguous term, sometimes synonymous with DT, sometimes intestines

Reference: Kardong, fig 13.1

Like any tube, the DT can be subdivided along its main axis, which we call the proximal-distal axis (terminology may vary across species; e.g. in some metazoans the terms oral-aboral may be used)

Multiple overlapping subdivisions may exist.

A standard list of divisions order proximal-distal for vertebrates is

• mouth
• pharynx
• esophagus
• stomach
• intestine

Note that some subdivisions may simultaneously be considered organs and tube subdivisions.

Note that the the same 4 terms may also be used in non-chordates for analagous structures. We tend to reserve these labels for vertebrates, and use functional grouping classes such as food storage organ.

There are variations and subdivisions of this scheme in vertebrates; e.g. the esophageal structures of avians; the stomachs of ruminants; divisions of the intestine in mammals. See Kardong for details.

A 'combined' vertebrate pattern may be

• mouth
• pharynx
• nasopharynx
• oropharynx
• hypopharynx
• esophagus (may have: crop)
• stomach (may have: proventriculus, gizzard, multiple 'sub-stomachs'; absent in species such as zebrafish)
• intestine
• small intestine
• duodenum
• jejunum
• ileum
• large intestine
• colon
• rectum

Note we treat the caecum as a diverticulum and not a true section of the DT

The DT can be subdivided along a proximal-distal axis. Each subdivision will typically have similar parts. Minimally: a wall, and a lumen, bounded by the wall.

We use the class subdivision of digestive tract for any section of the tube, including the wall and lumen.

In vertebrates the a subdivision typically contains:

• mucosa
• epithelium
• lamina propria (lamina propria mucosae)
• muscularis mucosa (lamina muscularis mucosae, lamina muscularis) - smooth
• submucosa
• muscularis propria (muscular coat, muscle/ular layer, muscularis externa) - typically smooth
• circular muscle
• longitudinal muscle
• serosa or adventita

Glands may occur in the mucosa, submucosa or outside the walls

Sometimes it is also useful to create a class 'smooth muscle of X'. Note that this may encompass both muscularis mucosa and the non-adjacent muscular coat - although in some sections, such as the esophagus, this is skeletal muscle. At the time of writing, some parts of the ontology may need to be verified for consistency - in some cases, smooth muscle may be bundled together with the muscularis propria

In metazoans, the DT is typically open at both ends - the mouth and the anus.

We attempt to clearly distinguish between the opening itself (an orifice or aperture), the terminal portion of the tube (which encompasses the opening an extends along the tube some distance), and the lumen of that terminal portion. Terminology is often quite loose here.

For the proximal section we have:

• oral opening - orifice
• mouth - terminal subdivision
• oral cavity - lumen of mouth, aka buccal cavity

We propose that these classes can be used across metazoans. In vertebrates the mouth typically contains tongue, teeth, etc, and extends to the pharynx.

There is some inconsistency in various anatomy ontologies as to the extent of the mouth. See section on AOs below

For the distal section we have:

• anus - orifice
• terminal part of digestive tract
• lumen of terminal part of digestive tract

We propose that these classes are also used across metazoans.

The term 'rectum' may sometimes be used as a synonym for the terminal portion, but in vertebrates it used more specifically for the terminal portion of the large intestine, which is not necessarily the terminal portion of the DT when a cloacal chamber is present.

We use the term cloaca to refer exclusively to the chamber present in many mostly non-mammalian vertebrates into which the digestive and urogenital system empties.

The cloaca may be considered part of the DT, but it is also part of the genitourinary system. In vertebrates with a cloaca, we consider the rectum to be the terminal part of the intestine, emptying into the cloacal chamber.

Note that in vertebrates the anus is considere to be the opening at the end of the rectum. If the DT is considered to extend past the rectum and include the cloaca and the cloacal opening, then the anus is no longer the end of the DT. For simplicity we may consider the DT proper to end with the rectum/anus in vertebrates, and the cloaca to be a hindgut derivative that is not part of the DT proper, but still part of the digestive system (and urogenital and excretory system). TBD.

Mammals have an embryonic cloaca.

One subdivision of the gut is as follows

• foregut
• midgut
• hindgut

These are defined very generally for bilateria. For vertebrates, standard borders are used. See ontology for details.

Some structures start as diverticula of the embryonic DT. We consider these to be not part of the DT, but they may still be part of the digestive system. Different subdivisions apply for systems.

MA has distinct classes for mouth an oral region, with the following parts:

• tonsil: O
• tongue: O
• oral epithlium: O
• soft palate: O
• salivary gland: O, M
• oral region cartilage bone: O, M
• tooth: O, M
• gingiva: O, M
• oral mucosa: M
• lip: M
• palate: M

We merge these in Uberon

In FMA, the mouth contains salivary glands, dentition, lips, mucosa, soft palate.

EHDAA2 has no class 'mouth', but 'oral region' corresponds to mouth

The tongue and the palate are considered part of the face in FMA (as well as part of the mouth)