Development -- suggested defs and a few questions

[gocentral]

Hello,

This is an offshoot of Doug's SF request for the paraxial mesoderm terms (SF:889881).

First off, some suggested defs - def refs are Dorlands, aka ISBN: 0721601464

ectoderm development, GO:0007398 The formation and development of the ectoderm, the outermost layer of cells of the three primary germ layers of the embryo. From it are developed the epidermis and the epidermal tissues, such as the nails, hair, enamel of teeth, and glands of the skin, the nervous system, the external sense organs such as the ear and eye, and the mucous membrane of the mouth and anus.

endoderm development, GO:0007492 The formation and development of the endoderm, the innermost of the three primary germ layers of the embryo; from it are derived the epithelium of the pharynx, respiratory tract (except the nose), digestive tract, bladder, and urethra.

mesoderm development, GO:0007498 The formation and development of the mesoderm, the middle layer of the three primary germ layers of the embryo, lying between the ectoderm and the endoderm. From it are derived the connective tissue, bone and cartilage, muscle, blood and blood vessels, lymphatics and lymphoid organs, notochord, pleura, pericardium, peritoneum, kidney, and gonads.

gut mesoderm development, GO:0007502 The formation and development of gut mesoderm cells, the middle layer of the three primary germ layers of the embryo which will go on to form the gut of the organism.

gonadal mesoderm development, GO:0007506 The formation and development of gonadal mesoderm cells, the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism.

Next up, some of those "what's the difference" questions. What's the difference between:

• 'epidermal differentiation ; GO:0008544' and 'epidermal cell differentiation ; GO:0009913'
• 'mesoderm cell migration ; GO:0008078' and 'mesoderm migration ; GO:0007509'
• 'xxx formation' and 'xxx development' - we could do with standard defs for both if they are different concepts.

Lastly, under histogenesis, things don't always adhere to the principles laid down in the St. Croix meeting relating to the relationships between cell development terms. Are these principles applicable to tissue development? If not, can we formulate some rules for tissue development? Cell differentiation terms should be arranged thus:

[i] cell differentiation ---[p] cell fate commitment (exact synonym: cell fate specification) ---[p] cell fate determination ---[p] cell development (exact synonyms: cell morphogenesis, cell maturation)

Doing a search for 'ectoderm', there are loads of terms scattered all over the place. eg. in the ectoderm section, we have: histogenesis [i]ectoderm development ---[p]ectoderm formation ------[p]ectoderm cell fate determination

Elsewhere, under 'cell fate commitment', we have: ectoderm cell fate commitment [p]ectoderm cell fate determination [p]ectoderm cell fate specification

and elsewhere still, we have: ectodermal gut morphogenesis [p]anterior midgut (ectodermal) morphogenesis

How do these tissue terms relate to each other and to the tissue cell terms (eg. ectoderm cell differentiation vs. ectoderm differentiation)?

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/1628":https://sourceforge.net/p/geneontology/ontology-requests/1628

[gocentral]

Logged In: YES user_id=579762

Comments only on the defs. From an old email between David and myself that didn't make it into SF (or reality evidently)

---

Hmm. I thought we defined them as well. Since each of them has children of formation, I think we should define them as "The formation and subsequent development of the "GERM LAYER".

Then one of the following three sentences and whatever you need to add for plants. (NOTE from TANYA: plants don't have these layers)

1) In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.

2) In animal embryos, the mesoderm is the middle germ layer of the embryo, formed during gastrulation.

3) In animal embryos, the endoderm is the inner germ layer of the embryo, formed during gastrulation.

Does this work?

David

At 03:25 PM 4/23/2003 -0700, you wrote: >Hi David, > >I'm adding a bunch of plant histogenesis terms and noticed >that 'endoderm evelopment', 'mesoderm devt' and 'ectoderm >devt' don't have definitions. I'm almost 100% sure that we >defined these way back when, do you recall? >If so, we need to bring these definitions back! > >Tanya

Original comment by: tberardini

[gocentral]

Logged In: YES user_id=631592

I don't think that the rules for cell development can be used to describe tissue development since tissues add another level of complexity. In general I think we should stick to the concept that tissues develop and cells differentiate. Tissue development should not be confused with cell differentiation. However, cell differentiation (including cell development) can be used to describe the development of cell-types in tissues. So, for the example of the ectoderm formation above. This term refers to the formation of the tissue layer which includes the movements of gastrulation. The formation of the tissue also involves the formation of ectodermal cells and should ectoderm cell fate commitment and its necessary part_of children; ectoderm cell fate determination and ectoderm cell fate specification, but not ectoderm cell development as this would go under later morphogenic stages of ectoderm development. These latter stages would include the formation of all of the things that ectoderm gives rise to (serious incorporation of anatomy is required here). That is why the specific terms that go beyond the formation of the primary germ layers are only added on an as-needed basis. The hope is that they will at some point take extensive advantage of the anatomies. In addition, the cell type ontology has great derived_from relationships that can at some point be used to construct the cell differentiation parts of the graph. I think much of the confusion here is due to the following that was based on Gilbert. All types of cell differentiation should have two necessary parts, cell fate commitment [GO:0045165] and cell development or cellular morphogenesis [GO:0000904]. All types of cell fate commitment should have two necessary parts, cell fate determination [GO:0001709] and cell fate specification [GO:0001708]. These parts of cell differentiation may take place during different phases of tissue development and this varies a great deal from tissue to tissue. For example, the commitment of germs cells in many animals takes place very early in embryogenesis and they are sequestered away as the embryo develops, but they don't mature until much later. But for something like a hematopoeitic cell, the commitment to a late lineage may not take place until the organism is an adult.

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=473796

David - do you think there is a difference between tissue formation and tissue development?

Re: cell fate commitment, etc. - what is the current policy on cell fate specification and cell fate commitment? There's a whole branch of separate specification and commitment terms - is this correct? Is there a new relationship between cell differentiation, cell fate commitment, determination, specification et al?

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=631592

Hi Amelia,

I would like to distinguish formation and development. Formation would have to do with the processes that happen to establish a tissue. A couple of examples of these would be primary embryonic induction and epithelial to mesenchymal transition. As in other parts of the development graph, the development of a tissue would include much more than this, includin morphogenic shaping of cell layers, patterning, selective apoptosis etc, depending on the tissue.

As for the cell differentiation stuff:

All of the terms for every cell type should be related in the following way:

cell differentiation <cell fate commitment <cell fate determination <cell fate specification <cellular morphogenesis during differentiation %x-cell differentiation <x-cell fate commitment %cell fate commitment <x-cell fate determination %cell fate determination <x-cell fate specification %cell fate specification <x-cell development %cellular morphogenesis during differentiation

I actually believe that this whole subtree of the graph could be constructed for every cell type in the cell-ontology using the type_of and develops_from relationships in that ontology. You and I should get together and discuss this, because I think you could do it using your programming skills. Of course, doing this would make the cellular part of GO essentially complete, but we would still have to use our embryology knowledge to put the right cell types in the right places with respect to histogenesis and organogenesis.

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=473796

Added the defs suggested below (in Tanya's email).

Could we formulate some standard defs for these kind of terms? It would be good to have defs that don't include the term name in the def. eg. xxx formation: The processes involved in establishing xxx tissue.

development: The formation and subsequent ... growth? maturation? evolution?

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473796

Have a look at the paraxial mesoderm term request from Doug Howe - Jen is coming up with some std defs there.

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=735846

The development node docs are a work in progress still but if it's any use you could have a look:

http://www.ebi.ac.uk/~jclark/GOwebsite/text%20in%20development/ development_folder/development.html

Each time a new point is decided upon I am adding it in.

Jen

Original comment by: jenclark

[gocentral]

• assigned_to: nobody --> jenclark

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

Hi,

I could change these development defs a bit to the standard that was agreed upon:

Biological processes specifically aimed at the progression of the "x" over time, from its initial formation to a mature structure. [Followed by the information on what "x" is.]

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

For the formation and development standard def question above, we currently have:

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

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

I will include a bit more about the meaning of this in the documentaion that I am writing.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

For this question:

Next up, some of those "what's the difference" questions. What's the difference between:

• 'epidermal differentiation ; GO:0008544' and 'epidermal cell differentiation ; GO:0009913'
• 'mesoderm cell migration ; GO:0008078' and 'mesoderm migration ; GO:0007509'

I had a look and it seems to me that

- 'epidermal differentiation ; GO:0008544' is describing the establishment of a tissue, and so should maybe be called

epidermis formation', def: ' Biological processes that contribute to the act of giving rise to epidermal tissue. This process pertains to the initial formation of a structure from unspecified parts.'

whilst

'epidermal cell differentiation ; GO:0009913' is describing the differentiation of a cell type, and so should be defined 'Development of epidermal cell type'

This way we can also give parentage:

%'epidermal formation ; GO:0008544' --<'epidermal cell differentiation ; GO:0009913'

For the other question:

- 'mesoderm cell migration ; GO:0008078' and 'mesoderm migration ; GO:0007509'

I presume that there should just be parentage since one is cell migration and the other is tissue migration:

% 'mesoderm migration ; GO:0007509' --<'mesoderm cell migration ; GO:0008078'

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=631592

Jen,

You are correct on both issues. Epidermal should be epidermis and mesodermal cell migration is a part of the migration mesodermal tissue.

David

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=735846

Thanks David. :-)

Is that also right to change epidermal differentiation to epidermis formation ?

Thanks,

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=631592

Yes, it could actually be epidermis formation or epidermis development and regulation of epidermis formation or development.

Original comment by: ukemi

[gocentral]

Logged In: YES user_id=735846

I have made the following changes:

id: GO:0008544 name: epidermal differentiation namespace: process relationship: part_of GO:0007398

changed to:

[Term]

id: GO:0008544 name: epidermis development namespace: process def: "Biological processes specifically aimed at the progression of the epidermis over time\, from its initial formation to a mature structure

also given part_of child 'epidermal cell differentiation ; GO:0009913'

New child relationship made %'mesoderm migration ; GO:0007509' --<'mesoderm cell migration ; GO:0008078'

This child term was previously a child of mesoderm development ; GO:0007498

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

These are the defs adapted for the new standard versions:

ectoderm development, GO:0007398 Biological processes specifically aimed at the progression of the ectoderm over time, from its initial formation to a mature structure. The ectoderm is the outermost layer of cells of the three primary germ layers of the embryo. From it are developed the epidermis and the epidermal tissues, such as the nails, hair, enamel of teeth, and glands of the skin, the nervous system, the external sense organs such as the ear and eye, and the mucous membrane of the mouth and anus.

endoderm development, GO:0007492 Biological processes specifically aimed at the progression of the endoderm over time, from its initial formation to a mature structure. The endoderm is the innermost of the three primary germ layers of the embryo; from it are derived the epithelium of the pharynx, respiratory tract (except the nose), digestive tract, bladder, and urethra.

mesoderm development, GO:0007498 Biological processes specifically aimed at the progression of the mesoderm over time, from its initial formation to a mature structure. The mesoderm is the middle layer of the three primary germ layers of the embryo, lying between the ectoderm and the endoderm. From it are derived the connective tissue, bone and cartilage, muscle, blood and blood vessels, lymphatics and lymphoid organs, notochord, pleura, pericardium, peritoneum, kidney, and gonads.

gut mesoderm development, GO:0007502 Biological processes specifically aimed at the progression of the gut mesoderm over time, from its initial formation to a mature structure. The gut mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gut of the organism.

gonadal mesoderm development, GO:0007506 Biological processes specifically aimed at the progression of the gonadal mesoderm over time, from its initial formation to a mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism.

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

Hi,

I just checked and in the second comment on this item the sentence:

'The formation of the tissue also involves the formation of ectodermal cells and should ectoderm cell fate commitment and its necessary part_of children; ectoderm cell fate determination and ectoderm cell fate specification, but not ectoderm cell development as this would go under later morphogenic stages of ectoderm development.' should read

'The formation of the tissue also involves the formation of ectodermal cells and should include ectoderm cell fate commitment and its necessary part_of children; ectoderm cell fate determination and ectoderm cell fate specification, but not ectoderm cell development as this would go under later morphogenic stages of ectoderm development.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

Hi,

On rereading the comments and searching the ontology I realised that Amelia has already added an amended version of the defs, but they are not fixed up for the standard definitions that the development interest group has come up with recently, since she didn't know that was being done. I will fix them up to correspond to these new standards. The current defs are:

ectoderm development, GO:0007398 def: The formation and subsequent development of the ectoderm. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.

endoderm development, GO:0007492 The formation and subsequent development of the endoderm. In animal embryos, the endoderm is the inner germ layer of the embryo, formed during gastrulation.

mesoderm development, GO:0007498 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.

gut mesoderm development, GO:0007502 The formation and subsequent development of the gut mesoderm, the middle layer of the three primary germ layers of the embryo which will go on to form the gut of the organism.

gonadal mesoderm development, GO:0007506 The formation and subsequent development of the gonadal mesoderm, the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

This is the standardized version of the term defs which I could add if nobody objects.

ectoderm development, GO:0007398 def: Biological processes specifically aimed at the progression of the ectoderm over time, from its initial formation to a mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation.

endoderm development, GO:0007492 Biological processes specifically aimed at the progression of the endoderm over time, from its initial formation to a mature structure. In animal embryos, the endoderm is the inner germ layer of the embryo, formed during gastrulation.

mesoderm development, GO:0007498 Biological processes specifically aimed at the progression of the mesoderm over time, from its initial formation to a mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue.

gut mesoderm development, GO:0007502 Biological processes specifically aimed at the progression of the gut mesoderm over time, from its initial formation to a mature structure. The gut mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gut of the organism.

gonadal mesoderm development, GO:0007506 Biological processes specifically aimed at the progression of the gonadal mesoderm over time, from its initial formation to a mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

Hi,

I have sent this to the list to ask if it would be a problem to fill in all the terms as suggested below. The subject line is 'proliferation of terms' and the date is 26/4/4.

Jen

Hi,

I have a question about proliferation of development terms. In the development interest group we've discussed the standard terms for development:

"x" development --<"x" morphogenesis ----<"x" formation ------<"x cell" differentiation ----<"x" structural development --<"x" maturation

and we talked about how some structures do not require all of these terms to be added (e.g. some do not require the maturation term). However, I have found a whole lot of things in the ontology that already have an 'x' morphogenesis term, but not an 'x' development term, and I need the 'x' development term as a parent for a terms that I am adding.

For example:

I am adding 'root cap mucilage metabolism' and I would like to make this a child of 'root development', but 'root development' does not exist, and there is only 'root morphogenesis'. It makes sense to me just to add the five or six development terms that I need just now.

However, I wondered if this means that I could also go through and add development terms for all the morphogenesis terms that are already present?

Also if I am doing that anyway then would it make sense at some point to fill in all the missing development standard terms as suggested in sourceforge [ 925921 ] (Development -- suggested defs and a few questions) https://sourceforge.net/tracker/index.php? func=detail&aid=925921&group_id=36855&atid=440764. This could be done manually but it also might be a good thing to do with the prolog plugin once it is ready to go.

This could also be applied to the cell development terms:

%cell differentiation --<cell fate commitment ----<cell fate determination ----<cell fate specification --<cellular morphogenesis during differentiation

This would be very helpful for filling in all the development section of the ontology but I'm not sure if the proliferation of terms would be a problem.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

The conclusion of this discussion was that it would be good to start with development and morphogenesis term pairs. In some situations this would be very straight forward and we could just add morphogenesis or development if it is missing. In other situations it is only appropriate to have morphogenesis or development but not both, and that we should consider these situations individually. The current plan is that we can start to look through the development and morphogenesis terms, and where we see something that we think may need fixing we can make a new sourceforge item so that each case can be considered properly before modifications are made. There turned out to be too many exceptions to the rules for the whole thing to be done automatically. Becky pointed out that this was often because different biological fields use the terms development and morphogenesis subtly differently. This is something that we need to look at so we can properly document the use of the terms.

Jen

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=735846

I have commited the revised defs that I posted on 2004-04-23.

The new docs on cell differentiation are in the middle of being written and revised now and we can start going through and fixing the relationships once this is done. I have opened a new page to discuss this:

[ 948372 ] fixing cell differentiation terms https://sourceforge.net/tracker/index.php? func=detail&aid=948372&group_id=36855&atid=440764

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-later

Original comment by: jenclark

[gocentral]

• assigned_to: Jennifer Deegan --> nobody
• Group: Plant Ontology --> None

Original comment by: cooperl09