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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Problematic spleen terms #6

Closed tmeehan closed 12 years ago

tmeehan commented 14 years ago

There is some confusion in Uberon between spleen follicles, nodules, and germinal centers. I'll state it simply and then suggest some fixes.

Primary follicles contain mature naive B cells. The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles. When B cells become activated during infection or from immunization, activated B cells migrate to the center of the follicles and form germinal centers. Follicles containing germinal centers are considered secondary follicles and have at least two parts: the germinal center (synonyms= central zone, light zone, nodule, or reaction center) and the corona (syn= peripheral zone, dark zone, inactive zone). Secondary follicles are transient structures (ten days after immunization in mice and humans). Thus not all lymph nodes will have secondary follicles.

What works well in Uberon for spleen related terms: primary spleen B cell follicle is_a spleen B cell follicle secondary spleen B cell follicle is_a spleen B cell follicle Spleen B cell follicle part_of white pulp of spleen white pulp of spleen part_of spleen

what is missing spleen B cell follicle is_a lymphoid follicle splenic germinal center part_of secondary spleen B cell follicle splenic corona part_of secondary spleen B cell follicle secondary spleen B cell follicle develops_from primary B cell follicle

what is problematic... lymphoid nodule of spleen (UBERON:0001249) is redundant with the term "spleen B cell follicle"

summary of changes:

  1. merge lymphoid nodule of spleen (UBERON:0001249) with spleen B cell follicle (UBERON:0003969)
  2. make spleen B cell follicle (UBERON:0003969) an is_a type of lymphoid follicle (UBERON:0000444) (merging may have already done this)
  3. Add splenic germinal center term, make it an is_a type of secondary nodular lymphoid tissue (UBERON:0001745), part_of secondary splenic B cell follicle (UBERON:0004042).
    Def= a germinal center that is located in the spleen. syn:central zone, light zone, nodule, or reaction center
  4. add the terms "spleen B cell corona", and its is_a parent "B cell corona". "B cell corona" is_a parent is lymphoid tissue (UBERON:0001744) Def: the area of the (spleen) secondary B follicle that surrounds the germinal center and harbors the small recirculating B lymphocytes. syn= follicle mantle, lymphocytic corona, mantle zone
  5. Add the edge secondary B cell follicle develops_from primary B cell follicle
cmungall commented 12 years ago

all fixed.