go-ontology
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geneontology
Should "epithelialization,” “gliosis,” and “browning" be in GO BP?
@geneontology/ontology should we add epithelialization as a syn for http://amigo.geneontology.org/amigo/term/GO:0060054 "positive regulation of epithelial cell proliferation involved in wound healing"
As the word is written, it should not be specific to wound healing (although one main area it is used in is would healing). Any process involved with growing an epithelial layer should be relevant. Therefore, it probably should not be added as a synonym to GO:0060054.
@geneontology/ontology https://github.com/orgs/geneontology/teams/ontology should we add epithelialization as a syn for http://amigo.geneontology.org/amigo/term/GO:0060054 "positive regulation of epithelial cell proliferation involved in wound healing"
Hare are my thoughts re: gliosis (however, I am not an expert!) We certainly have the GO term 'GO:0061900 glial cell activation' which represents a response of these cells to signals released by injured neurons. However, I would be reluctant to add 'gliosis' as a synonym, as this term appears to be generally associated with detrimental effects of glial cell 'over-activation'.
@vanaukenk @BarbaraCzub
The new suggested name for GO:0061900 is "reactive gliosis".
https://www.ncbi.nlm.nih.gov/pubmed/24462092
"glial cell activation" is better to be changed as a RELATED synonym.
The reason is that the phrase "glial cell activation" could mean the activation of glial cells by neurotransmitters (see the following reference). People nowadays stay away from such an ambiguous term of "glial cell activation" in the respective field if they are very careful about the choice of terminology.
Glial cells and neurotransmission: an inclusive view of synaptic function. https://www.ncbi.nlm.nih.gov/pubmed/14556716
"glial cell activation" in the above paper is totally different from the inflammatory response defined by GO:0061900. The name of a term should be as unambiguously as possible.
Regarding the more precise name of the term, "reactive gliosis" seems to be an even better match to the term definition than just "gliosis".
"gliosis" alone could mean either "reactive gliosis" or the observed (usually by immunolabelling) morphological and proliferative state of glial cells, which is not a process anymore. See an example usage in the following abstract.
https://www.ncbi.nlm.nih.gov/pubmed/27265809
Another synonym is "glial activation" which has even more popular usage than "glial cell activation". But it should also have the ambiguity problem as "glial cell activation". Thus, "glial activation" should be a RELATED synonym.
Just to aid in the discussion, here is the current parentage for 'glial cell activation':
Regarding the issue of "epithelialization", I think the more appropriate name should be "wound reepithelialization". "epithelialization" does not have the meaning of "re".
It also is different from "positive regulation of epithelial cell proliferation involved in wound healing" because it involves more than just "epithelial cell proliferation".
So I suggest adding the term "wound reepithelialization".
Definition: the process of the resurfacing of a wound with new epithelium. It a cooperative multifactorial process dominated by keratinocyte migration, proliferation, and differentiation that restores the intact epidermal barrier to prevent infection and excessive moisture loss.
https://www.ncbi.nlm.nih.gov/pubmed/29981800 https://www.ncbi.nlm.nih.gov/pubmed/26770209
Synonym: EXACT wound re-epithelialization, RELATED re-epithelialization, reepithelialization
"re-epithelialization" does not imply wound. Therefore, such synonyms should be just RELATED. https://www.ncbi.nlm.nih.gov/pubmed/27868276
parent: epithelium regeneration https://www.ebi.ac.uk/QuickGO/term/GO:1990399
Adding the "adipose tissue browning" term
Definition: the emergence of beige adipocytes in white adipose tissue.
Adipose tissue browning and metabolic health. https://www.ncbi.nlm.nih.gov/pubmed/24146030
synonym: RELATED browning
parent: adipose tissue development GO:0060612
Browning could involve the conversion of pre-existing white adipocytes to beige or brown-like adipocytes or de novo formation of beige adipocytes. This parent refers to the latter case. Also, the relation probably should not be is_a. It probably should something like "include".
we need three tickets to discuss this. Barbara please create one for the gliosis discussion
