new term request: mammary tissue ?

[ANiknejad]

Hi Chris,

I am trying to annotate the 'Mammary Tissue (Breast, female and male)' from GTEx
Please see this interesting public document:
http://biospecimens.cancer.gov/resources/sops/docs/GTEx_SOPs/BBRB-PR-0004-W1%20GTEx%20Tissue%20Harvesting%20Work%20Instruction.pdf

4.3.6.11
Mammary Tissue (Breast, female and male)

GTEx annotates on
UBERON:0008367
name: breast epithelium

but following the instructions:
'Dissect to an estimated depth 1-2 cm deep to the overlying
skin/nipple (i.e., 1-2 cm 'under' the skin surface of the nipple region)'

'breast epithelium' does not sound to be the correct term, what do you think?

Could
UBERON:0005200
name: thoracic mammary gland
better fit?

Many thanks for your help.
Cheers,
Anne

[cmungall]

I'm not an expert on reading these incision instructions. It seems like goal is to avoid adipose tissue which may not be considered part of the gland proper?

Our design patterns for glands are not as well defined as I would like. It seems there are different conceptualizations of gland partonomy. on the one hand, the central tissue of interest is epithelium. However, we also consider surrounding connective and muscle tissue to be part of the gland, see for example #1151

MA considers adipose tissue to be part of the gland, here are the parts (non-disjoint):

• MA:0000145 ! mammary gland
  • MA:0000788 ! areola
  • MA:0000791 ! mammary gland duct
  • MA:0000792 ! mammary gland epithelium
  • MA:0000793 ! mammary gland lobule
  • MA:0000794 ! mammary gland sebaceous gland
  • MA:0000795 ! mammary gland smooth muscle
  • MA:0000796 ! nipple
  • MA:0002760 ! mammary gland alveolus
  • MA:0002897 ! mammary gland connective tissue
  • MA:0002911 ! mammary gland fat

This broad conceptualization may be the most practical for something like the GTEx protocol,

[RDruzinsky]

MA:0000145 http://purl.obolibrary.org/obo/MA_0000145 ! mammary gland

seems to be synonymous with breast, in which case the parts are
appropriate. However, if mammary gland really only refers to the gland and
the ductal system of the gland, then fat, connective tissue, areola, and
nipple are not parts. The smooth muscle is part of the skin as well. The
contractile cells associated with the glands and the ducts are called
myoepithelial cells, because they have properties of both smooth muscle
cells and epithelial cells. Mammary gland epithelium is also problematic,
since the epithelium of the glands and the ducts is continuous.There should
probably be another term - mammary duct epithelium. Sebaceous glands and
sweat glands are also structures of the skin - nipple and areola.

This is difficult.

Robert E. Druzinsky, Ph.D.
Clinical Associate Professor
Dept. of Oral Biology
College of Dentistry
University of Illinois at Chicago
801 S. Paulina
Chicago, IL 60612
druzinsk@uic.edu

Office: 312-996-0406
Lab: 312-996-0629
Website: www.peerj.com/RobertDruzinsky

On Thu, Nov 19, 2015 at 1:49 AM, Chris Mungall notifications@github.com
wrote:

I'm not an expert on reading these incision instructions. It seems like
goal is to avoid adipose tissue which may not be considered part of the
gland proper?

Our design patterns for glands are not as well defined as I would like. It
seems there are different conceptualizations of gland partonomy. on the one
hand, the central tissue of interest is epithelium. However, we also
consider surrounding connective and muscle tissue to be part of the gland,
see for example #1151 #1151

MA considers adipose tissue to be part of the gland, here are the parts
(non-disjoint):

• MA:0000145 http://purl.obolibrary.org/obo/MA_0000145 ! mammary
  gland
• MA:0000788 http://purl.obolibrary.org/obo/MA_0000788 ! areola
  • MA:0000791 http://purl.obolibrary.org/obo/MA_0000791 ! mammary
    gland duct
  • MA:0000792 http://purl.obolibrary.org/obo/MA_0000792 ! mammary
    gland epithelium
  • MA:0000793 http://purl.obolibrary.org/obo/MA_0000793 ! mammary
    gland lobule
  • MA:0000794 http://purl.obolibrary.org/obo/MA_0000794 ! mammary
    gland sebaceous gland
  • MA:0000795 http://purl.obolibrary.org/obo/MA_0000795 ! mammary
    gland smooth muscle
  • MA:0000796 http://purl.obolibrary.org/obo/MA_0000796 ! nipple
  • MA:0002760 http://purl.obolibrary.org/obo/MA_0002760 ! mammary
    gland alveolus
  • MA:0002897 http://purl.obolibrary.org/obo/MA_0002897 ! mammary
    gland connective tissue
  • MA:0002911 http://purl.obolibrary.org/obo/MA_0002911 ! mammary
    gland fat

This broad conceptualization may be the most practical for something like
the GTEx protocol,

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#1178 (comment)
.

[cmungall]

MA:0000145 http://purl.obolibrary.org/obo/MA_0000145 ! mammary gland seems to be synonymous with breast

Well not quite - look at the subclasses in ontobee. only the 'thoracic mammary gland" would be "breast"?

But I think your analysis is spot on. It seems we need some term for the mereological sum of the gland (or cluster of glands) plus "associated" tissue; the MA 'mammary gland' class would be associated with this more encompassing unit.

[fbastian]

@ANiknejad, how did you annotate these data at the end? Do you need a new term?

[ANiknejad]

we annotated so far as
UBERON:0005200 thoracic mammary gland

[gouttegd]

WARNING: This issue has been automatically closed because it has not been updated in more than 3 years. Please re-open it if you still need this to be addressed addressed addressed – we are now getting some resources to deal with such issues.