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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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align "somite border" with MP #400

Closed cmungall closed 3 years ago

cmungall commented 10 years ago

https://sourceforge.net/p/obo/mammalian-phenotype-requests/1668/

def: anatomical surface separating somites

comments: somite formation requires the physical separation of somitic tissue from the initially continuous presomitic mesoderm (PSM), coalescence of cells in the forming somite, and the establishment of a stable border between the somite and the PSM; when a somite forms in the anterior end of the PSM, an intersomitic boundary (also called a fissure, gap, or cleft) emerges, and it is rapidly followed by a mesenchymal-to-epithelial transition of cells that face a forming gap

ZFA uses "somite border cell" as an exact syn

cmungall commented 10 years ago

See this commit: https://github.com/obophenotype/uberon/commit/0762abb69da187b77f6afaac1f5b3dabda20ba30

cmungall commented 10 years ago

Ideally we would have a GO biological process describing the transition here

mellybelly commented 10 years ago

good papers: http://dev.biologists.org/content/129/4/973.full (describes the formation of the space and vascularization through it. neato.) http://dev.biologists.org/content/137/9/1515.long http://onlinelibrary.wiley.com/doi/10.1111/j.1440-169X.2008.01018.x/full

note similarities to midbrain hindbrain boundary as site of gene expression - cells in a surface that are the boundary themselves

cmungall commented 10 years ago

Bit of a can of worms..

GO regards the development of dermatome, myotome, sclerotome as parts of somite development.

We follow EDHAA2 in making the D/M/Sc etc succeed the somite, via a develops_from relation. This is consistent with ZFA. However, XAO considers the relation one of part_of (consistent with the GO treatment of the "mature structure" of the somite being what it develops into)

See also:

https://sourceforge.net/p/obo/mammalian-phenotype-requests/1667/

MP is effectively collapsing the GO somitogenesis/somite development distinction

mellybelly commented 10 years ago

I think the problem here has to do with when do the sclerotome/myotome/dermatome become independent of the somite. Most developmental biologists still think about them as being part of the somite for some time (all the time whilst one would still call it a somite?), even after they are fully specified. here is a nice pic: http://www.springerimages.com/Images/RSS/1-10.1007_s00381-010-1358-9-8 even wikipedia (albeit poor entry) suggests this: http://en.wikipedia.org/wiki/Sclerotome

The s,m,d terms were originally defined based on fate mapping and cell type derivatives, and this is why dev biologists think of them as being part of the somite. There are also molecular markers in the somite before morphological differentiation that are permissive/obstructive that help define the internal boundaries, see Gilbert for example http://10e.devbio.com/article.php?id=140&search=myotome ....some of the reasons why dev biologists think of them as being part of the somite.

RDruzinsky commented 10 years ago

I agree with Melissa. It is really about what one calls the populations of mesenchyme that go on to become the various structures.

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

On Mon, Feb 17, 2014 at 12:14 PM, Melissa Haendel notifications@github.comwrote:

I think the problem here has to do with when do the sclerotome/myotome/dermatome become independent of the somite. Most developmental biologists still think about them as being part of the somite for some time (all the time whilst one would still call it a somite?), even after they are fully specified. here is a nice pic: http://www.springerimages.com/Images/RSS/1-10.1007_s00381-010-1358-9-8 even wikipedia (albeit poor entry) suggests this: http://en.wikipedia.org/wiki/Sclerotome

The s,m,d terms were originally defined based on fate mapping and cell type derivatives, and this is why dev biologists think of them as being part of the somite. There are also molecular markers in the somite before morphological differentiation that are permissive/obstructive that help define the internal boundaries, see Gilbert for example http://10e.devbio.com/article.php?id=140&search=myotome ....some of the reasons why dev biologists think of them as being part of the somite.

— Reply to this email directly or view it on GitHubhttps://github.com/obophenotype/uberon/issues/400#issuecomment-35309238 .

cmungall commented 10 years ago

Drifting away a bit from the original subject, but I think we need some consistency for part-of vs df across ontologies. See if the diagram helps, it outlines different spatiotemporal possibilities. We tend to see inter-ontology inconsistency for case (a) - in fact I think both relations should hold here. For case (b), part_of is not appropriate. Case (c) is a straightforward class develops_from scenario,

develops-from-vs-part-of

mellybelly commented 10 years ago

way to go to get the biologists to get their story straight :-). This is so helpful and we definitely have all three cases all over the place.

In this particular case though, I don't know if in the different communities we might get different answers for sclerotome <=> somite, for example, but I would think that usage is (a) or (b), but definitely not (c).

A nice description here by Gilbert. Would be interesting to get his opinion. http://www.ncbi.nlm.nih.gov/books/NBK10085/

gouttegd commented 3 years ago

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.