Abdominal adipose tissue #259

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paulacalipho opened this Issue May 28, 2013 · 6 comments

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@paulacalipho

"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:

  1. 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. "

  2. 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

@cmungall
Member

For reference, the embedded MP definition seems to indicate viscera

[Term]
id: MP:0008853
name: decreased abdominal adipose tissue amount
namespace: MPheno.ontology
def: "reduction in amount of adipose tissue associated with internal organs" [MGI:csmith]
synonym: "reduced abdominal adipose tissue amount" EXACT []
is_a: MP:0001781  ! abnormal white adipose tissue amount

The ontology has (implicitly) subcutaneous and abdominal adipose but not the intersection of the two:

mp

@cmungall
Member

My inclination would be go with ugly but unambiguous terms:

  • adipose tissue of abdominal region
    • visceral(?) abdominal adipose tissue OR abdominal organ adipose tissue
    • subcutaneous adipose tissue of abdominal region

This seems a bit odd though. The last term may not be of much use for annotation?

@paulacalipho

This sounds ok to me. So would be something like:

. UBERON:0007808 and CALOHA:TS-0002
“adipose tissue of abdominal region” (synonyms: "abdominal adipose tissue", “abdominal fat”)
def: Fatty tissue in the region of the ABDOMEN. It includes the ABDOMINAL SUBCUTANEOUS FAT and the INTRA-ABDOMINAL FAT (from MeSH D050153)

     -> UBERON:XXXXXXX and CALOHA:TS-XXXX
“visceral adipose tissue of abdominal region” 
      (synonyms: “visceral abdominal fat”, “visceral abdominal  adipose tissue”, “intra-abdominal fat”, “intra-abdominal adipose tissue”

      -> UBERON:YYYYYYY and CALOHA:TS-YYYY
“subcutaneous adipose tissue of abdominal region” 
      (synonyms: “subcutaneous fat of abdominal region”, “abdominal subcutaneous fat”, “abdominal subcutaneous adipose tissue”

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

@cindyJax

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:
UBERON:0007808
“adipose tissue of abdominal region” (synonyms: "abdominal adipose tissue", “abdominal fat”)
def: Fatty tissue in the region of the ABDOMEN.

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.

@paulacalipho

Thanks Cindy. So would be:

UBERON:0007808 and CALOHA:TS-0002
“adipose tissue of abdominal region” (synonyms: "abdominal adipose tissue", “abdominal fat”)
def: Fatty tissue in the region of the abdomen.

Only in Caloha (?):

CALOHA:TS-XXXX
“visceral adipose tissue of abdominal region” (synonyms: “visceral abdominal fat”, “visceral abdominal adipose tissue”, “intra-abdominal fat”, “intra-abdominal adipose tissue”

CALOHA:TS-YYYY
“subcutaneous adipose tissue of abdominal region” (synonyms: “subcutaneous fat of abdominal region”, abdominal subcutaneous fat”, “abdominal subcutaneous adipose tissue”

@cmungall cmungall added a commit that closed this issue May 31, 2013
@cmungall cmungall abdominal fat changes. Explicitly broadened grouping class. NTs: adip…
…ose tissue of abdominal region, visceral abdominal adipose tissue. Fixes #259
f58c9c9
@cmungall cmungall closed this in f58c9c9 May 31, 2013
@cmungall
Member
cmungall commented Jun 1, 2013

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

@cmungall cmungall added a commit that referenced this issue Jun 20, 2013
@cmungall cmungall Added EFO slim. Fixes #234
 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
6730349
@cmungall cmungall added a commit that referenced this issue Jul 5, 2013
@cmungall cmungall abdominal fat changes. Explicitly broadened grouping class. NTs: adip…
…ose tissue of abdominal region, visceral abdominal adipose tissue. Fixes #259
baed369
@cmungall cmungall added a commit that referenced this issue Jul 5, 2013
@cmungall cmungall Added EFO slim. Fixes #234
 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
a6cba47
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