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#11074 mp for "tail tip morphogenesis" GO:0045138
Hi,
I was wondering why "tail tip morphogenesis" is not related to "male sex differentiation". I am doing PAINT for PTHR12322 and looking at PMID:18550714 and from its definition it is clear that "tail tip morphogenesis" is defined as a male specific process in nemotodes.
PMID:18550714
http://www.ncbi.nlm.nih.gov/pubmed/18550714?dopt=Abstract
Consulting Kimberly for parentage. Thanks for bringing this up, Karen.
Hi Karen and Tanya,
Yes, I think a parent-child relation between the 'tail tip morphogenesis' term and a male-specific development term is a good idea.
I find the definition of male sex differentiation a little bit vague, though:
"The establishment of the sex of a male organism by physical differentiation."
Specifically, what do we mean by 'establishment' and 'physical differentiation'?
What are your thoughts on creating parent terms like 'female anatomical structure morphogenesis' and 'male anatomical structure morphogenesis'?
--Kimberly
This was meant to have been addressed here: http://sourceforge.net/p/geneontology/ontology-requests/9127/
But this seems incomplete.
My recommendation:
Step 3 is harder, it will take a bit of work to get wbbt to be uberon-compliant
https://github.com/raymond91125/Wao/issues/2
Hi,
Wrt the renaming of GO:0045138, I think 'nematode tail tip morphogenesis' is preferred over 'tail spike morphogenesis'. 'Tail spike' is most often used in the literature in association with hermaphrodites, while 'male tail' is used in association with males.
Alternatively, what about 'nematode male tail morphogenesis'?
--Kimberly
+1
Hi,
Doing some more reading (PMID:21408209), I'm wondering if we haven't tried to lump, and annotate, two different processes into this one term, GO:0045138.
Nematode male tail morphogenesis includes formation of the mating structure (which in the literature is usually referred to simply as the 'male tail') as well as morphogenesis of the tail tip which converts it from a spiked shape (retained in the hermaphrodite) to a rounded, blunt-end shape.
So, would something along these lines possibly work:
nematode male tail morphogenesis
part_of male tail tip morphogenesis
part_of male tail mating structure morphogenesis
male reproductive structure morphogenesis
is_a male tail mating structure morphogenesis
The tail tip term would refer to specific hypodermal cells (hyp8-hyp11), while the mating structure term would refer to the rays, hook, and spicules that make up that structure.
Adding in some ids, so that we know what exists and what doesn't:
nematode male tail morphogenesis, GO:new1
--[p] male tail tip morphogenesis, GO:0045138 (exists but currently 'tail tip morph')
--[p] male tail mating structure morphogenesis, GO:new2
male reproductive structure morphogenesis, GO:new3
--[i] male tail mating structure morphogenesis, GO:new2
I'm a little confused. :) Kimberly - Do you have time tomorrow to Skype? I think we should be able to sort this out much more easily that way. I'm on Eastern time.
Sure, any time tomorrow should be fine for a Skype call.
Comment from github issue that Chris opened from Raymond:
"tail spike is a structure shared by both C. elegans sexes until the onset of male-specific morphogenesis. thus this is not the right term to be linked to the GO term in question. we should add a "male tail" term."
Assuming that 'we should add a male tail term' means adding that term to the WB anatomy ontology.
Current plan, pending Kimberly checking whether tail tip is considered part of male genitalia.
move male genitalia development/morphogenesis out from development of primary male sexual characteristics, up to part_of male sex differentiation
male sex differentiation
--[i] male genitalia development
----[p] male genitalia morphogenesis
-------[i]nematode male tail morphogenesis, GO:new1
----------[p] male tail tip morphogenesis, GO:0045138 (currently 'tail tip morph')
----------[p] male tail mating structure morphogenesis, GO:new2
anatomical structure morphogenesis, GO:exists
--[i] male tail tip morphogenesis, GO:0045138 (currently 'tail tip morph'), already there
--[i] male tail mating structure morphogenesis, GO:new2 (add)
New def for GO:0045138: The process by which the anatomical structures of the tail tip are generated and organized. Morphogenesis pertains to the creation of form. The tail tip undergoes morphogenesis to form a copulatory structure. The most posterior hypodermal cells in the tail define a specialized, sexually dimorphic compartment in which cells fuse and retract in the male, changing their shape from a tapered cone or spike to a blunt dome. As in, but not restricted to, the roundworms (Nematoda, ncbi_taxonomy_id:6231).
Should add reproductive organ morphogenesis as a more specific parent (vs. anat stru morph).
Hi,
Here's a slightly revised proposal for these terms, based on some additional reading and references. This proposal has updates based on what is considered an 'organ' vs. a 'structure'.
I also proposed another parent term, 'sensory organ morphogenesis' and took a crack at a definition for that term.
male sex differentiation
--[i] male genitalia development
----[p] male genitalia morphogenesis
-------[i]nematode male tail mating organ morphogenesis, GO:new1
sensory organ development
--[p] sensory organ morphogenesis, GO:new2
------[i] nematode male tail mating organ morphogenesis, GO:new1
anatomical structure morphogenesis
--[i] nematode male tail tip morphogenesis, GO:0045138 (currently 'tail tip morph', see revised definition below)
Proposed definition for nematode male tail mating organ morphogenesis, GO:new1:
The process in which the anatomical structures of the nematode male tail mating organ are generated and organized. The male tail is a sensory organ required for mating and, in C. elegans, consists of ray sensilla, an acellular cuticular fan, a sensory hook, and protracting, copulatory spicules.
PMID:7409314, PMID:1782863, PMID:18050419
Proposed definition for sensory organ morphogenesis, GO:new2:
Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
ISBN:978-0199210893
Revised definition for nematode male tail tip morphogenesis, GO:0045138
The process in which the anatomical structure of the adult male tail tip is generated and organized. In some species of rhabitid nematodes, the male tail tip undergoes a morphological change such that the most posterior hypodermal cells in the tail (hyp8-11 in C. elegans) fuse and retract anteriorly, changing the shape of the tail from a pointed, tapered cone, or spike, to a rounded, blunt dome.
PMID:16806150, PMID:18050419, PMID:21408209
Let me know if this looks okay, or if you think this needs more work.
Thanks,
--Kimberly
Kimberly - Looks pretty good. I need some feedback from Chris on the issue below to proceed.
Chris - I was looking for 'sensory organ' in UBERON but only found 'sense organ' which is defined very narrowly for the sense of smell. Look at the structure of GO under 'sensory organ development' to see how broadly this term is used.
I think UBERON will need some help. Alternatively, I can just create 'sensory organ morphogenesis' without an xref.
Based on current def of UBERON:0000020 (An organ that is capable of detection of chemical stimulus involved in sensory perception of smell. ), this XP is incorrect if you look at all the classes that are children of GO:0007423.
[Term]
id: GO:0007423
name: sensory organ development
namespace: biological_process
def: "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." [GOC:go_curators]
synonym: "sense organ development" EXACT [GOC:dph]
is_a: GO:0044767 ! single-organism developmental process
is_a: GO:0048513 ! organ development
intersection_of: GO:0048856 ! anatomical structure development
intersection_of: results_in_development_of UBERON:0000020 ! sense organ
On 18 Aug 2014, at 13:53, Tanya Berardini wrote:
https://github.com/obophenotype/uberon/issues/549
Will be present in next release, but it's just a textual change so you
can proceed without waiting
Use the uberon class
if go by the logical def in uberon all is good.
Related
Ontology requests:
#11074Hi,
I didn't put this in my comment on Monday, but remembered that we had discussed making another parent term, something like 'male anatomical structure morphogenesis' as a parent of 'nematode male tail tip morphogenesis'. I think this would then address Karen's original question about having a male-specific parent for the 'tail tip morphogenesis' term. Would something like this work?
anatomical structure morphogenesis
--[i] male anatomical structure morphogenesis
----[i] nematode male tail tip morphogenesis
male sex differentiation
--[p] male anatomical structure morphogenesis
----[i] nematode male tail tip morphogenesis
Thanks; let me know if you'd like to Skype about any of this.
If we created 'male anatomical structure morphogenesis', should the full structure look more like this:
male sex differentiation
--[p] male anatomical structure morphogenesis
----[i] male genitalia morphogenesis
-------[p]nematode male tail mating organ morphogenesis, GO:new1
----[i] nematode male tail tip morphogenesis
Yes?
Hi Tanya,
Yes, I think that full structure looks correct.
Thx.
Final structure as added:
sensory organ development
--[p] sensory organ morphogenesis, GO:new2
------[i] nematode male tail mating organ morphogenesis, GO:new1
male sex differentiation
--[p] male genitalia development
----[p] male genitalia morphogenesis
-------[i]nematode male tail mating organ morphogenesis, GO:new1
--[p] male anatomical structure morphogenesis, GO:new3
----[i] male genitalia morphogenesis
-------[i]nematode male tail mating organ morphogenesis, GO:new1
----[i] nematode male tail tip morphogenesis
anatomical structure morphogenesis
--[i] sensory organ morphogenesis, GO:new2
------[i] nematode male tail mating organ morphogenesis, GO:new1
--[i] male anatomical structure morphogenesis, GO:new3
----[i] nematode male tail tip morphogenesis
----[i] male genitalia morphogenesis
-------[i]nematode male tail mating organ morphogenesis, GO:new1
New terms:
[Term]
+id: GO:0090596
+name: sensory organ morphogenesis
+namespace: biological_process
+def: "Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." [GOC:kmv, ISBN:978-0199210893]
+is_a: GO:0009653 ! anatomical structure morphogenesis
+intersection_of: GO:0009653 ! anatomical structure morphogenesis
+intersection_of: results_in_morphogenesis_of UBERON:0000020 ! sense organ
+relationship: part_of GO:0007423 ! sensory organ development
+created_by: tanyaberardini
+creation_date: 2014-08-22T13:23:20Z
+[Term]
+id: GO:0090597
+name: nematode male tail mating organ morphogenesis
+namespace: biological_process
+def: "The process in which the anatomical structures of the nematode male tail mating organ are generated and organized. The male tail is a sensory organ required for mating and, in C. elegans, consists of ray sensilla, an acellular cuticular fan, a sensory hook, and protracting, copulatory spicules." [GOC:kmv, PMID:1782863, PMID:18050419, PMID:7409314]
+is_a: GO:0048808 ! male genitalia morphogenesis
+is_a: GO:0090596 ! sensory organ morphogenesis
+relationship: only_in_taxon NCBITaxon:6231 ! Nematoda
+created_by: tanyaberardini
+[Term]
+id: GO:0090598
+name: male anatomical structure morphogenesis
+namespace: biological_process
+def: "The processes by which anatomical structures that are only present in the male organism are generated and organized." [GOC:kmv, GOC:tb]
+is_a: GO:0009653 ! anatomical structure morphogenesis
+intersection_of: GO:0009653 ! anatomical structure morphogenesis
+intersection_of: results_in_morphogenesis_of UBERON:0014403 ! male anatomical structure
+relationship: part_of GO:0046661 ! male sex differentiation
+created_by: tanyaberardini
+creation_date: 2014-08-22T13:29:45Z
Changes to old 'tail tip morphogenesis' term:
id: GO:0045138
-name: tail tip morphogenesis
+name: nematode male tail tip morphogenesis
new def:
"The process in which the anatomical structure of the adult male tail tip is generated and organized. In some species of rhabitid nematodes, the male tail tip undergoes a morphological change such that the most posterior hypodermal cells in the tail (hyp8-11 in C. elegans) fuse and retract anteriorly, changing the shape of the tail from a pointed, tapered cone, or spike, to a rounded, blunt dome." [GOC:kmv, PMID:16806150, PMID:18050419, PMID:21408209, PMID:7409314]
Last thing:
moved 'male/female genitalia development' out from 'development of primary male/female sexual characteristics' to under male/female sex differentiation