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new term request - suprapubic skin #1272

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jahilton opened this Issue Sep 30, 2016 · 6 comments

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jahilton commented Sep 30, 2016

The ENCODE DCC is requesting NTR for 'suprapubic skin' for GTEx samples
I believe these had been annotated as 'skin of abdomen', but a 'suprapubic skin' term would be more accurate to distinguish the non-sun exposed area

is_a: 'zone of skin' [UBERON_0000014]

section 4.3.6.7 here...
https://biospecimens.cancer.gov/resources/sops/docs/GTEx_SOPs/BBRB-PR-0004-W1%20GTEx%20Tissue%20Harvesting%20Work%20Instruction.pdf

@cmungall cmungall closed this in eb11a80 Sep 30, 2016

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Added:

[Term]
id: UBERON:0036149
name: suprapubic skin
def: "Area of skin in the hypoastric region of the abdomen." [https://github.com/obophenotype/uberon/issues/1272]
synonym: "hypogastric skin" RELATED []
intersection_of: UBERON:0000014 ! zone of skin
intersection_of: part_of UBERON:0013203 ! hypogastrium

this is defined formally in terms of the hypogastrium, which may be a broader than what you need. @ANiknejad can advise

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cmungall commented Sep 30, 2016

Added:

[Term]
id: UBERON:0036149
name: suprapubic skin
def: "Area of skin in the hypoastric region of the abdomen." [https://github.com/obophenotype/uberon/issues/1272]
synonym: "hypogastric skin" RELATED []
intersection_of: UBERON:0000014 ! zone of skin
intersection_of: part_of UBERON:0013203 ! hypogastrium

this is defined formally in terms of the hypogastrium, which may be a broader than what you need. @ANiknejad can advise

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fbastian Oct 5, 2016

@ANiknejad: do we need to update our GTEx annotations following the creation of this term?

fbastian commented Oct 5, 2016

@ANiknejad: do we need to update our GTEx annotations following the creation of this term?

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uberon Oct 5, 2016

In some ways it seems like false specificity? Is the region distinct at the
cellular level? Or is it just a proxy for non sun exposed? (Which should be
captured as an extra qualifier)

On Wednesday, October 5, 2016, fbastian notifications@github.com wrote:

@ANiknejad https://github.com/ANiknejad: do we need to update our GTEx
annotations following the creation of this term?


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#1272 (comment),
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uberon commented Oct 5, 2016

In some ways it seems like false specificity? Is the region distinct at the
cellular level? Or is it just a proxy for non sun exposed? (Which should be
captured as an extra qualifier)

On Wednesday, October 5, 2016, fbastian notifications@github.com wrote:

@ANiknejad https://github.com/ANiknejad: do we need to update our GTEx
annotations following the creation of this term?


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#1272 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/AA2YiPb2_FInlNKimjtr00yyMlqG4opUks5qw6rJgaJpZM4KLPaE
.

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fbastian Oct 5, 2016

Yep, my question exactly.

fbastian commented Oct 5, 2016

Yep, my question exactly.

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ANiknejad Oct 10, 2016

Actually there are some interesting human skin transcriptomics studies

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305515/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882522/

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163054

Main factors sound to be ageing and UV for skin transcriptomics variability, so I guess, there is no reason to specify the localization of the zone of skin, but reasons to qualify the sun exposition status.
pH and microbiota may anyway vary depending of the zone of skin and sex of the individual, while such parameters should not influence human RNA-seq analysis in fine:

https://www.ncbi.nlm.nih.gov/pubmed/11393210

https://www.ncbi.nlm.nih.gov/pubmed/18489300

ANiknejad commented Oct 10, 2016

Actually there are some interesting human skin transcriptomics studies

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4305515/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4882522/

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0163054

Main factors sound to be ageing and UV for skin transcriptomics variability, so I guess, there is no reason to specify the localization of the zone of skin, but reasons to qualify the sun exposition status.
pH and microbiota may anyway vary depending of the zone of skin and sex of the individual, while such parameters should not influence human RNA-seq analysis in fine:

https://www.ncbi.nlm.nih.gov/pubmed/11393210

https://www.ncbi.nlm.nih.gov/pubmed/18489300

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ANiknejad Oct 10, 2016

this is defined formally in terms of the hypogastrium, which may be a broader than what you need. @ANiknejad can advise

so far as available in the literature it is OK to have hypogastrium synonym of suprapubic

ANiknejad commented Oct 10, 2016

this is defined formally in terms of the hypogastrium, which may be a broader than what you need. @ANiknejad can advise

so far as available in the literature it is OK to have hypogastrium synonym of suprapubic

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