NTR: Intestinal Material Terms

[mkuhn]

I'm maintaining and expanding the Metalog database of contextual data for metagenomic samples, where we combine metadata from the primary publications and do our best to use the proper ontology terms. While fecal material (ENVO:00002003) is the most common sample type, there are also many studies (especially in animals) where samples were taken directly from the digestive tract. Here, "fecal material" does not fit, and neither do the various UBERON terms that describe the actual anatomical structure and not its contents. We therefore do not have a good way at the moment to store this information properly.

I'm therefore suggesting to add a new subtree under "bodily fluid material" (ENVO:02000019):

Proposed Term Hierarchy

Level 1: General intestinal material

intestinal material (new ENVO term)

• Definition: A bodily fluid material which is composed primarily of intestinal contents, including partially digested food, digestive secretions, epithelial cells, mucus, and associated microorganisms present within the lumen of the intestine.
• Links to: intestine (UBERON:0000160)
• Parent: bodily fluid material (ENVO:02000023)
• Subclasses: small intestinal material, large intestinal material

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Level 2: Small vs. Large intestine

small intestinal material (new ENVO term)

• Definition: An intestinal material which is composed primarily of contents present within the lumen of the small intestine, characterized by ongoing enzymatic digestion and nutrient absorption.
• Links to: small intestine (UBERON:0002108)
• Parent: intestinal material
• Subclasses: duodenal material, jejunal material, ileal material

large intestinal material (new ENVO term)

• Definition: An intestinal material which is composed primarily of contents present within the lumen of the large intestine, characterized by water absorption, electrolyte balance, and microbial fermentation of indigestible materials.
• Links to: large intestine (UBERON:0000059)
• Parent: intestinal material
• Subclasses: caecal material, colonic material, rectal material

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Level 3: Segment-specific terms

Small intestine segments:

duodenal material (new ENVO term)

• Definition: A small intestinal material which is composed primarily of contents present within the lumen of the duodenum, characterized by acidic chyme mixed with bile and pancreatic secretions.
• Links to: duodenum (UBERON:0002114)
• Parent: small intestinal material

jejunal material (new ENVO term)

• Definition: A small intestinal material which is composed primarily of contents present within the lumen of the jejunum, the primary site of nutrient absorption.
• Links to: jejunum (UBERON:0002115)
• Parent: small intestinal material

ileal material (new ENVO term)

• Definition: A small intestinal material which is composed primarily of contents present within the lumen of the ileum, the distal portion of the small intestine where bile salts and vitamin B12 are absorbed.
• Links to: ileum (UBERON:0002116)
• Parent: small intestinal material

Large intestine segments:

caecal material (new ENVO term)

• Definition: A large intestinal material which is composed primarily of contents present within the lumen of the caecum, characterized by active microbial fermentation of complex carbohydrates and fiber.
• Links to: caecum (UBERON:0001153)
• Parent: large intestinal material
• Synonyms: cecal material

colonic material (new ENVO term)

• Definition: A large intestinal material which is composed primarily of contents present within the lumen of the colon, undergoing water absorption and formation of semi-solid waste.
• Links to: colon (UBERON:0001155)
• Parent: large intestinal material

rectal material (new ENVO term)

• Definition: A large intestinal material which is composed primarily of contents present within the lumen of the rectum, representing waste material immediately prior to defecation.
• Links to: rectum (UBERON:0001052)
• Parent: large intestinal material

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Relationship to Existing Terms

chyme material (ENVO:02000026)

• Links to: chyme (UBERON:0006314)
• Parent: bodily fluid material (ENVO:02000019)
• Current definition: Specifically stomach contents before entering the duodenum
• Relationship to proposed terms:
  • As currently defined, chyme material represents gastric (stomach) contents and would be a sibling term to "intestinal material"
  • However, physiologically "chyme" describes the semi-liquid digestive contents throughout the small intestine
  • Potential overlap: Should "small intestinal material" be considered a type of chyme, or are they distinct?

fecal material (ENVO:00002003)

• Links to: feces (UBERON:0001988)
• Parent: excreta material
• Relationship: Fecal material is excreted waste material expelled from the digestive tract. It is semantically distinct from intestinal materials, which remain within the organism.