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Abdominal adipose tissue #259
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For reference, the embedded MP definition seems to indicate viscera
The ontology has (implicitly) subcutaneous and abdominal adipose but not the intersection of the two: |
My inclination would be go with ugly but unambiguous terms:
This seems a bit odd though. The last term may not be of much use for annotation? |
This sounds ok to me. So would be something like: . UBERON:0007808 and CALOHA:TS-0002
I did not included “abdominal organ adipose tissue” because when google "abdominal organ adipose tissue" found 0 results, so not sure it is used, but if you think it is, go ahead. I think that “subcutaneous adipose tissue of abdominal region” may be useful for annotations because studies showing that the different contribution of “subcutaneous adipose tissue of abdominal region” and “visceral adipose tissue of abdominal region” to obesity |
Adipose tissue is one of many examples where the mouse differs from humans. Paula's examples are all from papers describing human adipose tissue. I have it a bit confounded and skewed towards mouse descriptions in the MP, but I tried to be purposefully vague at the higher levels. For example, rodents do not have semi-solid visceral fat packed around abdominal internal organs and in the peritoneal cavity as humans do- but they do have four main abdominal encapsulated fat pad depots that have a more cohesive appearance (mice never get a "pot-belly"). While mice do have some subcutaneous fat in skin, especially abdomen, it is not in the same proportion or distribution as in humans, who require an overall thicker layer for insulation from heat/cold and for energy storage. I'm not sure about adipose tissue in other animal species, although I expect that it is well known in livestock. So at least in the mouse/rat, if you discuss "abdominal fat" you are almost always referring to the abdominal fat pads… visceral fat doesn't exist and subcutaneous fat is generally considered separate. I do have a term "decreased abdominal adipose tissue amount [MP:0008853]" that I should reconsider. There are only a handful of MGI mouse annotations and the few I checked are really about the fat pads, for which I have a similar term ("decreased abdominal fat pad weight" [MP:0009287]). I'm not sure how best to make subterms, but this much is fine: The rest of the definition from above gets more human-centric. The two proposed subterms are okay for human annotations but we could not use the “visceral adipose tissue of abdominal region” in the rodent community as it implies visceral fat. |
Thanks Cindy. So would be: UBERON:0007808 and CALOHA:TS-0002 Only in Caloha (?): CALOHA:TS-XXXX CALOHA:TS-YYYY |
With the changes above, the existing uberon class was retained as a broad grouping class. Subclasses include visceral abdominal, subcutaneous and encapsulated fat depots. These will be in the next release. I think there's still some work to be done in this area - not quite happy with panniculus adiposus and related structures |
Added has_parts for epithelium and BM. Addresses #269 Added taxon constraints for BM. Addresses #269 Adding relationships for septal nuclei structures added and obsoleted adult eye primordium (EFO) Changed def of tongue - Robert Druzinsky. Addresses #256 Added dermatocranium part_of dermal skeleton. This ensures any bones in the dermatocranium are auto-classified as dermal bones/ Fixes #265 dc-rights added Renamed alula. Fixes #264 NT: extraperitoneal space. Additional axioms for: epidural space, retroperitoneal space abdominal fat changes. Explicitly broadened grouping class. NTs: adipose tissue of abdominal region, visceral abdominal adipose tissue. Fixes #259 fixed equiv between integumentary adnexa and integumentary projection modified axioms for dorsal fin - was in_median_plane_of some dorsum, changing to median plane of organism and a separate axiom for part_of dorsum. Addresses #262 merged hypodermis fat layer into subcutaneous adipose tissue modifying relationships and label for hypodermal muscle layer (muscle is now located in adipose tissue rather than a part) fat pad synonyms split many latin synonyms derived from dbpedia that were previously accidentally concatenated Fixed relationship between PA 2 skeleton and PA 2. Addresses #258 Removed part_of link between hyoid arch skeleton and facial skeleton. Mistake arising from viscerocranium confusion. Addresses #258 Modified definition of cricoid cartilage from Robert Druzinsky, modified from AAO definition. Also disambiguated tissue composition from primary classification. Fixes #257 NTs for subtypes of gustatory epithelium and removed restriction that taste buds were always on (papillae of) tongue
…ose tissue of abdominal region, visceral abdominal adipose tissue. Fixes #259
Added has_parts for epithelium and BM. Addresses #269 Added taxon constraints for BM. Addresses #269 Adding relationships for septal nuclei structures added and obsoleted adult eye primordium (EFO) Changed def of tongue - Robert Druzinsky. Addresses #256 Added dermatocranium part_of dermal skeleton. This ensures any bones in the dermatocranium are auto-classified as dermal bones/ Fixes #265 dc-rights added Renamed alula. Fixes #264 NT: extraperitoneal space. Additional axioms for: epidural space, retroperitoneal space abdominal fat changes. Explicitly broadened grouping class. NTs: adipose tissue of abdominal region, visceral abdominal adipose tissue. Fixes #259 fixed equiv between integumentary adnexa and integumentary projection modified axioms for dorsal fin - was in_median_plane_of some dorsum, changing to median plane of organism and a separate axiom for part_of dorsum. Addresses #262 merged hypodermis fat layer into subcutaneous adipose tissue modifying relationships and label for hypodermal muscle layer (muscle is now located in adipose tissue rather than a part) fat pad synonyms split many latin synonyms derived from dbpedia that were previously accidentally concatenated Fixed relationship between PA 2 skeleton and PA 2. Addresses #258 Removed part_of link between hyoid arch skeleton and facial skeleton. Mistake arising from viscerocranium confusion. Addresses #258 Modified definition of cricoid cartilage from Robert Druzinsky, modified from AAO definition. Also disambiguated tissue composition from primary classification. Fixes #257 NTs for subtypes of gustatory epithelium and removed restriction that taste buds were always on (papillae of) tongue
"Abdominal adipose tissue" (UBERON:0007808 and CALOHA:TS-0002) is defined differently in UBERON and CALOHA
CALOHA took the definition from MeSH that considers that "Abdominal adipose tissue" includes "Abdominal subcutaneus fat" and "Intra-abdominal fat".
Seems that literature definition matches MeSH.
See for example:
From: http://edrv.endojournals.org/content/21/6/697.full
"As described by Märin et al. (21), abdominal fat is composed of abdominal subcutaneous fat and intraabdominal fat, as clearly shown by CT and magnetic resonance imaging (MRI); intraabdominal adipose tissue is composed of visceral, or intraperitoneal, fat, mainly composed of omental and mesenteric fat and retroperitoneal fat masses by a delineation along the dorsal borderline of the intestines and the ventral surface of the kidney. "
From: http://physrev.physiology.org/content/93/1/359.long
"Furthermore, by scanning the abdomen, these investigators showed for the first time that it was possible to dissociate adipose tissue located in the abdominal cavity, the so-called intra-abdominal or visceral adipose tissue, from the abdominal adipose tissue located subcutaneously (567)"
UBERON took the definition from Brenda-Wikipedia that excludes from "Abdominal adipose tissue" the "Subcutaneus fat" and considers "Abdominal adipose tissue" synonym of "visceral adipose tissue", "intra-abdominal fat".
definition: Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively. [database_cross_reference: BTO:0004041]
See http://en.wikipedia.org/wiki/Adipose_tissue#Abdominal_fat
I do not really see the BRENDA-Wikipedia reason for such exclusion. Do you have any clue?
Many thanks in advance
Paula from Calipho group
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