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new terms request: for Porifera and Cnidaria #578

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ANiknejad opened this Issue Oct 6, 2014 · 9 comments

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@ANiknejad

ANiknejad commented Oct 6, 2014

Hi Chris,

http://www.ncbi.nlm.nih.gov/pubmed/24844197

"Thus, while sponges contain only a limited number of direct orthologues of genes involved in body plan patterning in the eumetazoans, all of them are expressed in patterns supporting Haeckel’s view that body plans of sponges and cnidarians are homologous: choanoderm corresponds to the gastrodermis and osculum to the mouth of the polyp. Clearly, the described expression patterns of the developmental regulatory genes, while highly suggestive, do not prove homology of the body plans. Rather, they provide the necessary first step and a framework for studies aimed at determining the regulatory networks governing development of sponges. Once established, these networks can be further compared with developmental regulatory networks in other animals and provide insights into the molecular mechanisms underlying diversification of animal body plans."

so maybe worth to have the following new terms?

*(sponge) choanoderm
*(sponge) osculum
*(cnidaria) gastrodermis

see also
ISBN:978-0030259821 "Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003)
pages 78-79 for Porifera
page 100 'gastrodermis' in eumetazoa

Comments?
Cheers,

Anne

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cmungall Oct 6, 2014

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Fascinating stuff! cc @bobthacker

Please use:

I can add PORO to the composite-metazoan release next time around.

There is also CTENO_0000003 gastrodermis, but of course ctenophores are not cnidarians. Does the same paper discuss how this all fits in with recent discussions as to the origins of ctenophores?

I would like to 'bud off' a cnidarian ontology at some point, but for now we can add gastrodermis to uberon. Do you have a definition? I don't have my copy of Barnes at the office

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cmungall commented Oct 6, 2014

Fascinating stuff! cc @bobthacker

Please use:

I can add PORO to the composite-metazoan release next time around.

There is also CTENO_0000003 gastrodermis, but of course ctenophores are not cnidarians. Does the same paper discuss how this all fits in with recent discussions as to the origins of ctenophores?

I would like to 'bud off' a cnidarian ontology at some point, but for now we can add gastrodermis to uberon. Do you have a definition? I don't have my copy of Barnes at the office

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ANiknejad Oct 8, 2014

Hi Chris, thanks again, here what is provided by
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003)

p.100
"Except for sponges and placozoans, almost all animals have an internal gut cavity that opens to the outside through an opening called the mouth. The gut cavity is lined by an epithelium, called the gastrodermis (=stomach skin), that joins the epidermis at the mouth"

ANiknejad commented Oct 8, 2014

Hi Chris, thanks again, here what is provided by
ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003)

p.100
"Except for sponges and placozoans, almost all animals have an internal gut cavity that opens to the outside through an opening called the mouth. The gut cavity is lined by an epithelium, called the gastrodermis (=stomach skin), that joins the epidermis at the mouth"

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So there is a strong argument for making 'gastrodermis' a synonym of UBERON:0003929 'gut epithelium' (which I would prefer to relabel as 'digestive tract epithelium', 'gut' can be ambiguous, here I think we mean the full tract, starting with the mouth, extending to the anus, if present)

We could also make it a subclass, with an additional differentia - e.g. a gastrodermis is a digestive tract epithelium that borders the mesoglea?

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cmungall commented Oct 8, 2014

So there is a strong argument for making 'gastrodermis' a synonym of UBERON:0003929 'gut epithelium' (which I would prefer to relabel as 'digestive tract epithelium', 'gut' can be ambiguous, here I think we mean the full tract, starting with the mouth, extending to the anus, if present)

We could also make it a subclass, with an additional differentia - e.g. a gastrodermis is a digestive tract epithelium that borders the mesoglea?

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ANiknejad Oct 13, 2014

Hi Chris,

I guess, having 'gastrodermis' as a synonym of UBERON:0003929 would be fine (yes, I agree with relabeling like you propose).
In fact, Barnes himself defines the 'gastrodermis' as an adult epithelium in Bilateria:
p.217
"...a three-layered (triploblastic) embryo is not unique to bilaterians - ctenophores also have three layers - but bilaterian animals, in general, diversify and specialize the layers to a greater extent than do their radial relatives. In most bilaterians, each of the embryonic germ layers differentiates into an adult epithelium:....endoderm becomes gastrodermis."

And in the literature 'gastrodermis' is not exclusively used for Cnidaria and Ctenophora (as does the term 'mesoglea'), but also for basal Bilaterian such as Nemertodermatida
http://www.ncbi.nlm.nih.gov/pubmed/21680408
or for Schistosoma
http://www.ncbi.nlm.nih.gov/pubmed/24921634

So the synonym option is ok from my point of view.
Any other comments? Bob?

Cheers,

Anne

ANiknejad commented Oct 13, 2014

Hi Chris,

I guess, having 'gastrodermis' as a synonym of UBERON:0003929 would be fine (yes, I agree with relabeling like you propose).
In fact, Barnes himself defines the 'gastrodermis' as an adult epithelium in Bilateria:
p.217
"...a three-layered (triploblastic) embryo is not unique to bilaterians - ctenophores also have three layers - but bilaterian animals, in general, diversify and specialize the layers to a greater extent than do their radial relatives. In most bilaterians, each of the embryonic germ layers differentiates into an adult epithelium:....endoderm becomes gastrodermis."

And in the literature 'gastrodermis' is not exclusively used for Cnidaria and Ctenophora (as does the term 'mesoglea'), but also for basal Bilaterian such as Nemertodermatida
http://www.ncbi.nlm.nih.gov/pubmed/21680408
or for Schistosoma
http://www.ncbi.nlm.nih.gov/pubmed/24921634

So the synonym option is ok from my point of view.
Any other comments? Bob?

Cheers,

Anne

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bobthacker Oct 13, 2014

Hi Anne and Chris,

Chris pointed out that "osculum" and "choanoderm" are already in PORO.

Since the homology of "choanoderm" vs. "gastrodermis" is debatable and under investigation by several evo/devo lab groups, I think you could list their relationship as "analogous to" for now, but please include the Barnes reference in the definition of analogy so that anyone wanting to look up the justification can find it.

I would also use as a reference: http://www.dbbe.fcen.uba.ar/contenido/objetos/EPITELIOSYESPONJAS2009.pdf

Epithelia and integration in sponges.
Leys SP, Nichols SA, Adams ED.
Integr Comp Biol. 2009 Aug;49(2):167-77. doi: 10.1093/icb/icp038. Epub 2009 Jun 22.

I am not sure how to express in an ontology that sponges do not contain "gastrodermis" but instead the terms "choanoderm" and "pinacoderm" are used, but if possible, I think "analogous to" would be good.

Bob

bobthacker commented Oct 13, 2014

Hi Anne and Chris,

Chris pointed out that "osculum" and "choanoderm" are already in PORO.

Since the homology of "choanoderm" vs. "gastrodermis" is debatable and under investigation by several evo/devo lab groups, I think you could list their relationship as "analogous to" for now, but please include the Barnes reference in the definition of analogy so that anyone wanting to look up the justification can find it.

I would also use as a reference: http://www.dbbe.fcen.uba.ar/contenido/objetos/EPITELIOSYESPONJAS2009.pdf

Epithelia and integration in sponges.
Leys SP, Nichols SA, Adams ED.
Integr Comp Biol. 2009 Aug;49(2):167-77. doi: 10.1093/icb/icp038. Epub 2009 Jun 22.

I am not sure how to express in an ontology that sponges do not contain "gastrodermis" but instead the terms "choanoderm" and "pinacoderm" are used, but if possible, I think "analogous to" would be good.

Bob

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We already have an (inferred) axiom in Uberon 'gut epithlium' only in taxon 'Eumetazoa' - so if gastrodermis is equivalent or a subclass then it inherits this.

Re analogy vs homology: the bgee similarity table records the hypothesis stated in the paper, which in this case is homology. It is however, not encumbent on anyone to believe this... there are conflicting statements and this is to be expected

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cmungall commented Oct 13, 2014

We already have an (inferred) axiom in Uberon 'gut epithlium' only in taxon 'Eumetazoa' - so if gastrodermis is equivalent or a subclass then it inherits this.

Re analogy vs homology: the bgee similarity table records the hypothesis stated in the paper, which in this case is homology. It is however, not encumbent on anyone to believe this... there are conflicting statements and this is to be expected

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ANiknejad Mar 10, 2015

Hi Chris,

I would appreciate to have 'gastrodermis' as a synonym of
UBERON:0003929
name: gut epithelium

As you proposed, UBERON:0003929 can be renamed 'digestive tract epithelium'

Cheers,

Anne

ANiknejad commented Mar 10, 2015

Hi Chris,

I would appreciate to have 'gastrodermis' as a synonym of
UBERON:0003929
name: gut epithelium

As you proposed, UBERON:0003929 can be renamed 'digestive tract epithelium'

Cheers,

Anne

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are we good to close this now?

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cmungall commented Mar 23, 2016

are we good to close this now?

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ANiknejad Mar 24, 2016

yes, thank you Chris!

ANiknejad commented Mar 24, 2016

yes, thank you Chris!

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