paraxial mesoderm development...formation...determination...

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It would be nice to have a set of terms for the development etc. of paraxial mesoderm. Perhaps folks who have a vested interest in this part of the process tree could have a look?

The new terms are being proposed because mutation of specific genes in fish (and I imagine mice) results in defects specifically in paraxial mesoderm formation. A similar future addition of 'axial mesoderm' terms could also be considered. Here is a proposed structure for the new additions. I'm not certain about the is-a's and part-of's.

Feel free to shut me down if this complexity is undesireable. ... mesoderm development (GO:0007498) ---%paraxial mesoderm development (GO:NEW) ---<mesoderm formation (GO:0001707) ------%paraxial mesoderm formation (GO:NEW);<paraxial mesoderm development ------<mesoderm cell fate determination (GO:0007500) ---------%paraxial mesoderm cell fate determination (GO:NEW);<paraxial mesoderm formation

And also the following: regulation of mesoderm cell fate (GO:0042661) ---%regulation of paraxial mesoderm cell fate (GO:NEW)

-Doug

Reported by: doughowe

Original Ticket: "geneontology/ontology-requests/1503":https://sourceforge.net/p/geneontology/ontology-requests/1503

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I think these look OK, but I'll also forward to the GO list to attract attention from the dev biol interest group. Meanwhile, can you help with definitions? Thanks,

m

Original comment by: mah11

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Paraxial mesoderm = that lying alongside the notochord and neural tube.

Original comment by: girlwithglasses

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Here are defs:

mesoderm development (GO:0007498): The processes resulting in development of the mesoderm during gastrulation. Mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.

endoderm development (GO:0007492): The processes resulting in development of the endoderm during gastrulation. Endoderm is the inner germ layer that develops into the lining of the internal organs including the digestive and respiratory systems.

ectoderm development (GO:0007398): The processes resulting in develoment of the ectoderm during gastrulation. Ectoderm is the outer germ layer that develops into skin and nervous tissue.

paraxial mesoderm development (GO:New): The processes resulting in development of the mesoderm located bilaterally adjacent to the notochord and neural tube.

paraxial mesoderm formation (GO:New): The processes resulting in the initial formation of the mesoderm located bilaterally adjacent to the notochord and the neural tube.

paraxial mesoderm cell fate determination (GO:New): A process involved in the cell fate commitment of paraxial mesodermal cells. Once determination has taken place, the cell is irreversibly committed to differentiate as a paraxial mesoderm cell regardless of its environment.

regulation of paraxial mesoderm cell fate (GO:New): The processes involved in regulating the cell fate of paraxial mesoderm cells.

To be consistent, I should also add positive and negative regulation terms as "Is A" children of 'regulation of paraxial mesoderm cell fate', no?...

positive regulation of paraxial mesoderm cell fate (GO:New): Processes which increase the likelyhood that a cell will differentiate as paraxial mesoderm.

negative regulation of paraxial mesoderm cell fate (GO:New): Processes which decrease the likelyhood that a cell will differentiate as paraxial mesoderm.

All defs xref: ZFIN:dh

-Doug

Original comment by: doughowe

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Hi Doug,

I will have a look at this soon. I have got the beginnings of a piece of documentation on the development node: http://www.ebi.ac.uk/~jclark/GOwebsite/text%20in%20development/ development_folder/development.html

I just include that in case it is useful, or in case you would like to contribute anything to it. It's an attempt to summarise the current status of the development node plans.

Thanks,

Jen

Original comment by: jenclark

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Original comment by: jenclark

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Hi,

I have been looking at the definitions with reference to the definitions that were discussed on the sourceforge entry on the development node (summarised http://www.ebi.ac.uk/~jclark/GOwebsite /text%20in%20development/development_folder /development.html)

There are the beginnings of standard definitions for morphogenesis terms and development terms and others related:

"x" development Biological processes specifically aimed at the progression of the "x" over time, from its initial formation to a mature structure.

"x" morphogenesis Developmental processes by which the anatomical structures of "x" are generated and organized. Morphogenesis pertains to the creation of form.

It seems to me from the definitions that you have written that maybe when you made development terms you also wanted morphogenesis terms. Would that seem right? I haven't tried to put these development node guidelines into practise yet so I'd be very interested to use this as a practise run.

It seems to me that maybe what you want is something like:

mesoderm development (GO:0007498) -<mesoderm morphogenesis --<mesoderm formation (GO:0001707) ---<mesoderm cell differentiation ----<mesoderm cell fate determination (GO:0007500) --<mesoderm structural development

paraxial mesoderm development (GO:NEW) -<paraxial mesoderm morphogenesis --<paraxial mesoderm formation (GO:NEW) ---<paraxial mesoderm cell differentiation ----<paraxial mesoderm cell fate determination (GO:NEW) --<paraxial mesoderm structural development

With all the appropriate other parentage of paraxial mesoderm terms under mesoderm terms and the others that you mentioned, as well as the regulation terms.

That way the defs could also be written according to those discussed previously:

mesoderm development def: Biological processes specifically aimed at the progression of the mesoderm over time, from its initial formation to a mature structure. Mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.

mesoderm morphogenesis def: Developmental processes by which the mesoderm is generated and organized. Morphogenesis pertains to the creation of form.

mesoderm formation def: Biological processes that contribute to the act of giving rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.

mesoderm cell differentiation def: Development of the mesoderm cell type. This will involve the change of a cell or set of cells from one cell identity to another.

mesoderm cell fate determination def: Process involved in mesoderm cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate into a mesoderm cell.

mesoderm structural development def: Biological processes that contribute to the act of creating the structural organization of the mesoderm. This process pertains to the physical shaping of a rudimentary structure.

paraxial mesoderm development def: Biological processes specifically aimed at the progression of the paraxial mesoderm over time, from its initial formation to a mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube.

paraxial mesoderm morphogenesis def: Developmental processes by which the paraxial mesoderm is generated and organized. Morphogenesis pertains to the creation of form.

paraxial mesoderm formation def: Biological processes that contribute to the act of giving rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts.

paraxial mesoderm cell differentiation def: Development of the paraxial mesoderm cell type. This will involve the change of a cell or set of cells from one cell identity to another.

paraxial mesoderm cell fate determination def: Process involved in paraxial mesoderm cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate into a paraxial mesoderm cell.

paraxial mesoderm structural development def: Biological processes that contribute to the act of creating the structural organization of the paraxial mesoderm. This process pertains to the physical shaping of a rudimentary structure.

If the others who were involved in the development node discussion could have a look at this as well to see if I've implemented it according to their intensions then I'd really appreciate it. Thanks.

Jen

Original comment by: jenclark

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Jen, If there are agreed upon standards for the development node, Indeed new terms should be created with those standards in mind. I'm only peripherally involved in that effort, so I am probably less aware of it's current status than I should be.

I'd be willing to help in any way I can if this is a good test case for a new structure under development.

I think there is one term missing...perhaps it was implied...I believe 'paraxial mesoderm cell fate specification' should be a 'part-of' child of 'paraxial mesoderm cell differentiation'.

-Doug

Original comment by: doughowe

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Jen, On second thought, cell fate commitment has cell fate specification and cell fate determination as 'part-of' children....so I think the structures you proposed below would require a "x cell fate commitment' term as a child of "x differentiation"..and under that would be "x cell fate specification' and 'x cell fate determination' as 'part-of' children. -Doug

Original comment by: doughowe

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Hi Doug,

Do you have a definition for axial mesoderm and I can make those terms while I'm at it?

Thanks,

Jen

Original comment by: jenclark

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I have put these terms together in DAG-Edit but so far without all the additional parentage. I am going to upload the file here to save a copy before I go ahead and put in all the addition parentage.

I anybody has a spare minute to have a look then that would be very helpful.

Thanks,

Jen

Original comment by: jenclark

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mesoderm terms without additional parentage. (obo)

Original comment by: jenclark

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mesoderm terms with additional parentage. (obo)

Original comment by: jenclark

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Hi,

I have made the additional parentages and uploaded the file again. The GO:ids are meaningless and were just added to make the file work in DAG-Edit. Also some of the terms already exist, so in those cases when the terms are implemented I would just work round the pre-existing terms.

Does this DAG seem like it's the kind of things that's wanted?

Thanks,

Jen

Original comment by: jenclark

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I wrote to the GO list for comments. The e-mail has the subject line 'Development - Practise run.'

Midori made the following suggestion:

One thing you could include: most of the 'x cell differentiation' definitions are standardized on 'the process whereby a relatively unspecialized cell acquires specialized features of a(n) x cell, ...' (ends with a brief description of what an x cell is). The exceptions seem to be for blood cells, for which 'relatively unspecialized cell' is replaced by 'hemopoietic stem cell'.

m

I have done that now.

Jen

Original comment by: jenclark

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A comment on this....

If we are interested in being comprehensive, many people would break the mesoderm down into at least 4 or 5 functional subregions. For example, see this exerpt from chapter 14 part 3 of the 6th edition of the text 'Developmental Biology' available online at NCBI->books.

Not sure if the link will work, but here it is: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=books&doptcmdl=GenBookHL&term=lateral+mesoderm+AND+dbio%5Bbook%5D+AND+131962%5Buid%5D&rid=dbio.chapter.3450

To be this comprehensive at this stage would probably result in the creation of many many GO terms that would get very little usage. For the original need, creating paraxial mesoderm terms would suffice. If you are feeling very ambitious, a homologous set of terms for 'intermediate mesoderm (aka "axial mesoderm'')' and 'lateral mesoderm' terms could be created. I'm not sure where the group stands on such term proliferation.

If there is agreement that this term proliferation should be persued at this stage, I'll go ahead and provide more defs for the various types of mesoderm.

-Doug

Original comment by: doughowe

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For those following the discussion....please see SF# 925921 for a very relevant discussion of the structure of the development node.

Perhaps the outcome of my original term request is contingent on further hashing out and finalizing the desired structure under this node...perhaps in the end we may even wait for a computationally derived development node structure???

-Doug

Original comment by: doughowe

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Hi Doug,

I think it would probably be fine to add those other terms. It would be easiest for me to add the current set and then work on the other ones. If that's okay with you I'll leave this sourceforge item for a week to see if we get comments, and then if it's all fine then I'll commit on Tuesday 13th April. If that all goes well then I'll do the rest of the types of mesoderm next.

Thanks,

Jen

Original comment by: jenclark

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Hi Jen,

I think this structure looks good. Perhaps while we are working on these germ-layer nodes, we should look back into the discussion of mesendoderm and mesectodrm that the worm folks brought up a while ago. I'm not sure we completely resolved that issue.

David

Original comment by: jenclark

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Hi,

There is a term:

regulation of cell fate ; GO:0042659 def: Any process that mediates the adoption of a specific fate by a cell.

It's children include both 'regulation of cell fate' terms and 'regulation of cell fate specification' terms.

I'm not sure how this fits in with the terms you have suggested here:

Jen, On second thought, cell fate commitment has cell fate specification and cell fate determination as 'part-of' children....so I think the structures you proposed below would require a "x cell fate commitment' term as a child of "x differentiation"..and under that would be "x cell fate specification' and 'x cell fate determination' as 'part-of' children. -Doug

Should all the 'regulation of cell fate' terms have 'specification' or 'determination' or something stuck on the end? Regulation of 'cell fate' doesn't seem like a process to me.

Thanks,

Jen

Original comment by: jenclark

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I have sent this to the list:

Hi,

I think this term

regulation of cell fate ; GO:0042659

ought to be

regulation of cell fate specification.

Would anybody mind if I change it over?

Half of it's children are regulation of 'cell fate specification' and half are regulation of 'cell fate', so I'd like to standardize the child terms while I'm at it.

I'll do this next Monday if nobody has any objections.

Thanks,

Jen

Original comment by: jenclark

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Hi,

I have done this so far:

%mesoderm development ; %axial mesoderm development ; <axial mesoderm morphogenesis ; <axial mesoderm formation ; <axial mesoderm cell differentiation ; <axial mesoderm cell fate commitment ; <axial mesoderm cell fate determination ; <regulation of axial mesoderm cell fate determination ; <negative regulation of axial mesoderm cell fate determination ; <positive regulation of axial mesoderm cell fate determination ; <axial mesoderm cell fate specification ; <regulation of axial mesoderm cell fate specification ; <positive regulation of axial mesoderm cell fate specification ; <negative regulation of axial mesoderm cell fate specification ; <axial mesoderm structural development ; <mesoderm morphogenesis ; <mesoderm formation ; <mesoderm cell differentiation ; <mesoderm cell fate commitment ; <mesoderm cell fate determination ; <regulation of mesoderm cell fate determination ; <negative regulation of mesoderm cell fate determination ; <positive regulation of mesoderm cell fate determination ; <mesoderm cell fate specification ; <regulation of mesoderm cell fate specification ; <negative regulation of mesoderm cell fate specification ; <positive regulation of mesoderm cell fate specification ; <mesoderm structural development ; %paraxial mesoderm development ; <paraxial mesoderm morphogenesis ; <paraxial mesoderm formation ; <paraxial mesoderm cell differentiation ; <paraxial mesoderm cell fate commitment ; <paraxial mesoderm cell fate determination ; <regulation of paraxial mesoderm cell fate determination ; <negative regulation of paraxial mesoderm cell fate determination ; <positive regulation of paraxial mesoderm cell fate determination ; <paraxial mesoderm cell fate specification ; <regulation of paraxial mesoderm cell fate specification ; <negative regulation of paraxial mesoderm cell fate specification ; <positive regulation of paraxial mesoderm cell fate specification ; <paraxial mesoderm structural development ;

also with additional parentage where appropriate.

defs:

term: axial mesoderm cell differentiation goid: definition: Development of the axial mesoderm cell type. This will involve the change of a cell or set of cells from one cell identity to another. definition_reference: ZFIN:dh

term: axial mesoderm cell fate commitment goid: definition: The process by which a cell becomes committed to become an axial me soderm cell. definition_reference: ZFIN:dh

term: axial mesoderm cell fate determination goid: definition: Process involved in axial mesoderm cell fate commitment. Once deter mination has taken place, a cell becomes committed to differentiate into a axia l mesoderm cell. definition_reference: ZFIN:dh

term: axial mesoderm cell fate specification goid: definition: The processes involved in the specification of axial mesoderm ident ity. definition_reference: ZFIN:dh

term: axial mesoderm development goid: definition: Biological processes specifically aimed at the progression of the a xial mesoderm over time, from its initial formation to a mature structure. definition_reference: ZFIN:dh

term: axial mesoderm formation goid: definition: Biological processes that contribute to the act of giving rise to t he axial mesoderm. This process pertains to the initial formation of the struct ure from unspecified parts. definition_reference: ZFIN:dh

term: axial mesoderm morphogenesis goid: definition: Developmental processes by which the axial mesoderm is generated an d organized. Morphogenesis pertains to the creation of form. definition_reference: ZFIN:dh

term: axial mesoderm structural development goid: definition: Biological processes that contribute to the act of creating the str uctural organization of the axial mesoderm. This process pertains to the physic al shaping of a rudimentary structure. definition_reference: ZFIN:dh

term: mesoderm cell differentiation goid: definition: Development of the mesoderm cell type. This will involve the change of a cell or set of cells from one cell identity to another. definition_reference: ZFIN:dh

term: mesoderm cell fate commitment goid: definition: The process by which a cell becomes committed to become a mesoderm cell. definition_reference: ZFIN:dh

term: mesoderm cell fate determination goid: definition: Process involved in mesoderm cell fate commitment. Once determinati on has taken place, a cell becomes committed to differentiate into a mesoderm c ell. definition_reference: ZFIN:dh

term: mesoderm cell fate specification goid: definition: The processes involved in the specification of mesoderm cell identi ty. definition_reference: ZFIN:dh

term: mesoderm development goid: definition: Biological processes specifically aimed at the progression of the m esoderm over time, from its initial formation to a mature structure. Mesoderm i s the middle germ layer that develops into muscle, bone, cartilage, blood and c onnective tissue. definition_reference: ZFIN:dh

term: mesoderm formation goid: definition: Biological processes that contribute to the act of giving rise to t he mesoderm. This process pertains to the initial formation of the structure fr om unspecified parts. definition_reference: ZFIN:dh

term: mesoderm morphogenesis goid: definition: Developmental processes by which the mesoderm is generated and orga nized. Morphogenesis pertains to the creation of form. definition_reference: ZFIN:dh

term: mesoderm structural development goid: definition: Biological processes that contribute to the act of creating the str uctural organization of the mesoderm. This process pertains to the physical sha ping of a rudimentary structure. definition_reference: ZFIN:dh

term: negative regulation of axial mesoderm cell fate determination goid: definition: Any process that stops, prevents or reduces the rate of axial mesod erm cell fate determination. definition_reference: ZFIN:dh

term: negative regulation of axial mesoderm cell fate specification goid: definition: Any process that stops, prevents or reduces the rate of axial mesod erm cell fate specification. definition_reference: ZFIN:dh

term: negative regulation of mesoderm cell fate determination goid: definition: Any process that stops, prevents or reduces the rate of mesoderm ce ll fate determination. definition_reference: ZFIN:dh

term: negative regulation of mesoderm cell fate specification goid: definition: Any process that stops, prevents or reduces the rate of mesoderm ce ll fate specification. definition_reference: ZFIN:dh

term: negative regulation of paraxial mesoderm cell fate determination goid: definition: Any process that stops, prevents or reduces the rate of paraxial me soderm cell fate determination. definition_reference: ZFIN:dh

term: negative regulation of paraxial mesoderm cell fate specification goid: definition: Any process that stops, prevents or reduces the rate of paraxial me soderm cell fate specification. definition_reference: ZFIN:dh

term: paraxial mesoderm cell differentiation goid: definition: Development of the paraxial mesoderm cell type. This will involve t he change of a cell or set of cells from one cell identity to another. definition_reference: ZFIN:dh

term: paraxial mesoderm cell fate commitment goid: definition: The process by which a cell becomes committed to become a paraxial mesoderm cell. definition_reference: ZFIN:dh

term: paraxial mesoderm cell fate determination goid: definition: Process involved in paraxial mesoderm cell fate commitment. Once de termination has taken place, a cell becomes committed to differentiate into a p araxial mesoderm cell. definition_reference: ZFIN:dh

term: paraxial mesoderm cell fate specification goid: definition: The processes involved in the specification of mesoderm cell identi ty. definition_reference: ZFIN:dh

term: paraxial mesoderm development goid: definition: Biological processes specifically aimed at the progression of the p araxial mesoderm over time, from its initial formation to a mature structure. T he paraxial mesoderm is the mesoderm located bilaterally adjacent to the notoch ord and neural tube. definition_reference: ZFIN:dh

term: paraxial mesoderm formation goid: definition: Biological processes that contribute to the act of giving rise to t he paraxial mesoderm. This process pertains to the initial formation of the str ucture from unspecified parts. definition_reference: ZFIN:dh

term: paraxial mesoderm morphogenesis goid: definition: Developmental processes by which the paraxial mesoderm is generated and organized. Morphogenesis pertains to the creation of form. definition_reference: ZFIN:dh

term: paraxial mesoderm structural development goid: definition: Biological processes that contribute to the act of creating the str uctural organization of the paraxial mesoderm. This process pertains to the phy sical shaping of a rudimentary structure. definition_reference: ZFIN:dh

term: positive regulation of axial mesoderm cell fate determination goid: definition: Any process that activates or increases the rate of axial mesoderm cell fate determination. definition_reference: ZFIN:dh

term: positive regulation of axial mesoderm cell fate specification goid: definition: Any process that activates or increases the rate of. definition_reference: ZFIN:dh

term: positive regulation of mesoderm cell fate determination goid: definition: Any process that activates or increases the rate of mesoderm cell f ate determination. definition_reference: ZFIN:dh

term: positive regulation of mesoderm cell fate specification goid: definition: Any process that activates or increases the rate of mesoderm cell f ate specification. definition_reference: ZFIN:dh

term: positive regulation of paraxial mesoderm cell fate determination goid: definition: Any process that activates or increases the rate of paraxial mesode rm cell fate determination. definition_reference: ZFIN:dh

term: positive regulation of paraxial mesoderm cell fate specification goid: definition: Any process that activates or increases the rate of paraxial mesode rm cell fate specification. definition_reference: ZFIN:dh

term: regulation of axial mesoderm cell fate determination goid: definition: Any process that modulates the frequency, rate or extent of axial m esoderm cell fate determination. definition_reference: ZFIN:dh

term: regulation of axial mesoderm cell fate specification goid: definition: Any process that modulates the frequency, rate or extent of axial m esoderm cell fate specification. definition_reference: ZFIN:dh

term: regulation of mesoderm cell fate determination goid: definition: Any process that modulates the frequency, rate or extent of mesoder m cell fate determination. definition_reference: ZFIN:dh

term: regulation of mesoderm cell fate specification goid: definition: Any process that modulates the frequency, rate or extent of mesoder m cell fate specification. definition_reference: ZFIN:dh

term: regulation of paraxial mesoderm cell fate determination goid: definition: Any process that modulates the frequency, rate or extent of paraxia l mesoderm cell fate determination. definition_reference: ZFIN:dh

term: regulation of paraxial mesoderm cell fate specification goid: definition: Any process that modulates the frequency, rate or extent of paraxia l mesoderm cell fate specification. definition_reference: ZFIN:dh

New term numbers are as below:

GO:0048318 JIC axial mesoderm development GO:0048319 JIC axial mesoderm morphogenesis GO:0048320 JIC axial mesoderm formation GO:0048321 JIC axial mesoderm cell differentiation GO:0048322 JIC axial mesoderm cell fate commitment GO:0048323 JIC axial mesoderm cell fate determination GO:0048324 JIC regulation of axial mesoderm cell fate determination GO:0048325 JIC negative regulation of axial mesoderm cell fate determ ination GO:0048326 JIC positive regulation of axial mesoderm cell fate determ ination GO:0048327 JIC axial mesoderm cell fate specification GO:0048328 JIC regulation of axial mesoderm cell fate specification GO:0048329 JIC negative regulation of axial mesoderm cell fate specif ication GO:0048330 JIC positive regulation of axial mesoderm cell fate specif ication GO:0048331 JIC axial mesoderm structural development GO:0048332 JIC mesoderm morphogenesis GO:0048333 JIC mesoderm cell differentiation GO:0048334 JIC regulation of mesoderm cell fate determination GO:0048335 JIC negative regulation of mesoderm cell fate determinatio n GO:0048336 JIC positive regulation of mesoderm cell fate determinatio n GO:0048337 JIC positive regulation of mesoderm cell fate specificatio n GO:0048338 JIC mesoderm structural development GO:0048339 JIC paraxial mesoderm development GO:0048340 JIC paraxial mesoderm morphogenesis GO:0048341 JIC paraxial mesoderm formation GO:0048342 JIC paraxial mesoderm cell differentiation GO:0048343 JIC paraxial mesoderm cell fate commitment GO:0048344 JIC paraxial mesoderm cell fate determination GO:0048345 JIC regulation of paraxial mesoderm cell fate determinatio n GO:0048346 JIC positive regulation of paraxial mesoderm cell fate det ermination GO:0048347 JIC negative regulation of paraxial mesoderm cell fate det ermination GO:0048348 JIC paraxial mesoderm cell fate specification GO:0048349 JIC regulation of paraxial mesoderm cell fate specificatio n GO:0048350 JIC positive regulation of paraxial mesoderm cell fate spe cification GO:0048351 JIC negative regulation of paraxial mesoderm cell fate spe cification GO:0048352 JIC paraxial mesoderm structural development

The other terms were already there and have just had their defs updated to the standard version.

I will look through these terms again tomorrow to check that I didn't miss any parentages.

I haven't set the relationships between the terms yet so it's not finished at all, but I just wanted to commit that lot first in case I got a lot of conflicts in the file from working on it for too long. I will go through tomorrow and set the relationships as well.

Thanks,

Jen

Original comment by: jenclark

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I have fixed the relationships now.

Jen

Original comment by: jenclark

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I have standardized all the childern of cell fate specification ; GO:0001708 to end in 'cell fate specification' instead of just 'cell fate'.

Jen

Original comment by: jenclark

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Hi Doug,

You said this below:

'If there is agreement that this term proliferation should be persued at this stage, I'll go ahead and provide more defs for the various types of mesoderm.'

Nobody has objected to this, so if you wanted to provide defs then I could get on and make these terms.

Thanks,

Jen

Original comment by: jenclark

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Hi,

David mentioned another branch of this discussion:

'I think this structure looks good. Perhaps while we are working on these germ-layer nodes, we should look back into the discussion of mesendoderm and mesectodrm that the worm folks brought up a while ago. I'm not sure we completely resolved that issue.'

I wrote and asked where to find this and he sent me the link, so I'll start looking at that sourceforge item too, but keep the two threads separate. Please see: [ 852977 ] additional germ layer specification terms for more information on this.

Thanks,

Jen

Original comment by: jenclark

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Jen, If we consider the mesoderm in three major divisions, axial, paraxial, and lateral, it looks like lateral mesoderm is the one still missing?? Will it be sufficient if I provide a definition for what lateral mesoderm is, so that this can be appended to the std. definitions for all the required lateral mesoderm terms?

-Doug

Original comment by: doughowe

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Yes thanks, that would be great. :-)

Jen

Original comment by: jenclark

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One other thing. Are there plans to integrate the 'mesoderm development', 'gut mesoderm' and 'gonadal mesoderm' terms mentioned in SF925921 into the mesoderm develoment tree we are working on here? If so, there are several items for consideration...

1) The def for 'mesoderm development' provided in that SF item includes more tissues that are derived from the mesoderm, and perhaps would be a useful addition to our mesoderm development def? 2) If gut mesoderm and gonadal mesoderm terms will be considered, we aught to think about cranial mesoderm as well, and there are likely to be others too. However, going down this road will lead to a HUGE proliferation of very detailed terms...perhaps not desireable at this time. I'd be happy with terms for the three major subdivisions of mesoderm as we have been considering them at the moment...lateral, axial, paraxial.

-Doug

Original comment by: doughowe

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Hi Doug,

That's a good question. Perhaps we should send this one to the list? I'm a plant scientist by training and plants don't do any of this stuff so I've been hard at it today with a developmental biology text book trying to find out all the background. Maybe if we invite the rest of the development interest group into the discussion then they would help clarify the potential risks and benefits of this kind of term proliferation?

Thanks,

Jen

Original comment by: jenclark

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Hi,

I wrote to the list with the subject line: 'Re: Development - mesoderm' on the 22nd April. Please see that thread for further information.

Thanks,

Jen

Original comment by: jenclark

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Hi Doug,

From David's comment:

'I think the inclusion of the detailed terms brings us very much down the path of anatomy. The terms will become very species specific very quickly. This is really something for cross-products.'

it seems as if it might be best to wait until we have cross-products. Did you need the lateral mesoderm terms for annotations? I could make those just now if you need then and then leave the others for when we have cross-products.

Thanks,

Jen

Original comment by: jenclark

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Jen, We don't need the lateral mesoderm terms to make annotations at this time. In light of David's comments, perhaps it would be prudent to limit our additions to the paraxial and axial mesoderm terms, and leave lateral mesoderm for the time being. The more detailed terms will be better produced by cross products as David stated. -Doug

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Great, thanks. In that case I'll close this now.

Thanks for all the discussions.

Jen

Original comment by: jenclark

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• milestone: --> TermGenie
• status: open --> closed-accepted

Original comment by: jenclark

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• status: closed-accepted --> open-accepted

Original comment by: jenclark

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We had an e-mail discussion and I will be adding the lateral mesoderm terms, but not the others.

Jen

Original comment by: jenclark

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Hi Doug,

I've added in those lateral mesoderm terms now, with the standard defs. Would it be possible for you to give me a definition for the lateral mesoderm along the lines of those we have for paraxial and axial mesoderm?

Thanks,

Jen

Original comment by: jenclark

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Jen, I've been digging around for some info, and I noticed that the "lateral mesoderm" is commonly referred to as "lateral plate mesoderm", and so "lateral plate mesoderm" should be used as an exact synonym on all the "lateral mesoderm" terms.

Also, here is a nice diagram of the mesodermal regions and their derivative tissues as a reference: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowSection&rid=.09tV5XvbSR4MXmUEf3ElC9oo2Q7IYA9klyi

In light of this information, and other reading I have done, I think we should recognize 4 rather than 3 major subdivisions of mesoderm. So the list would now include:

axial mesoderm paraxial mesoderm intermediate mesoderm lateral mesoderm

Can you derive definitions for intermediate and lateral mesoderm from the diagram I referenced above?

-Doug

Original comment by: doughowe

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I've got some concerns regarding the term "axial mesoderm" as well. What I've been reading suggests that axial mesoderm gives rise to the head mesoderm as well as the notochord. You'll notice in the diagram I cited in my last entry to the SF item that notchord comes from "chordamesoderm" and head mesoderm comes from "paraxial mesoderm". Perhaps what we really want is to either change all the "axial mesoderm" terms to "chordamesoderm" terms.

-Doug

Original comment by: doughowe

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Hi Doug,

Thanks for that diagram, that's really helpful. Just to confirm your points, you're recommending that I:

1) Add intermediate mesoderm terms as with all the others. 2) Add lateral plate mesoderm as synonym of all the lateral mesoderm terms. 3) Change axial mesoderm to chordamesoderm in all cases. 4) Make up defs from that diagram.

I can't see any problem with any of that, and nobody else has mentioned any since you posted this so I could start preparing the intermediate mesoderm terms and commit the whole lot this coming monday if that's okay.

Thanks,

Jen

Original comment by: jenclark

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this item is getting too big for the mailing list ...

m :P

Original comment by: mah11

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This item is continued on [ 951222 ] mesoderm development 2 https://sourceforge.net/tracker/index.php?func=detail&aid=951222&group\_id=36855&atid=440764

Jen

Original comment by: jenclark

[gocentral]

• status: open-accepted --> closed-accepted

Original comment by: jenclark