Development terms - Githubissues

gocentral commented 21 years ago

Hi,

I was wondering if we could come up with generic definitons for the terms

formation of x development of x differentiation of x

a bit like the generic definitionas that we already have for metabolism and the other frequently used types of terms.

Also I am working on a secion of ontology at the moment that has a lot of formation and development terms and I'm not sure whether to to make both a formation term and a development term for each thing. Also I'm not sure if there's system to how these terms would be laid out. e.g. as siblings, or have the development terms under develoment and the formation terms under formation or whatever. Does anybody have views on this, and if not please could we discuss it at the next meeting?

Thanks,

Jen

Reported by: jenclark

Original Ticket: "geneontology/ontology-requests/1235":https://sourceforge.net/p/geneontology/ontology-requests/1235

gocentral commented 21 years ago

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Here is the beginning of a small summery of what is currently being done with formation, development and morphogenesis:

%development ; GO:0007275 -%morphogenesis ; GO:0009653

There is no term called 'formation' or 'differentiation'.

High level term definitions:

development ; GO:0007275 def: Biological processes specifically aimed at the progression of an organism over time from an initial condition (eg. a zygote, or a young adult) to a later condition (eg. a multicellular animal or an aged adult).

morphogenesis ; GO:0009653 def:Developmental processes by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.

Some examples of current type definitions:

embryonic morphogenesis ; GO:0009795 def: The developmental processes by which defined structures within an embryo are generated.

Bolwig's organ morphogenesis ; GO:0001746 def: Formation and development of the larval eye in Drosophila, a relatively simple sensory system...

embryonic development ; GO:0009790 def: The development of an organism from zygote formation until the end of its embryonic life stage...

R7 development ; GO:0045467 def: Development of the R7 photoreceptor, the last photoreceptor to develop in the ommatidium.

midgut development ; GO:0007494 def: Development of the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine.

From the St. Croix meeting:

Conclusion: Cell differentiation and its children will have the following structure: cellular process [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)

Original comment by: jenclark

gocentral commented 21 years ago

milestone: 192945 --> TermGenie
assigned_to: nobody --> jenclark

Original comment by: jenclark

gocentral commented 21 years ago

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Part 2 of the summary:

Formation examples:

formation of primary germ layer ; GO:0001704 def: The formation of the ectoderm, mesoderm and endoderm during gastrulation.

formation of extrachromosomal circular DNA during replicative cell aging ; GO:0001313 def: Excision from the chromosome and circularization of a region of chromosomal DNA, generally , but not always, via homologous recombination between direct tandem repeats, in dividing cells as they age.

cell plate formation ; GO:0000919 def: The process of assembly, maturation, and growth of the cell plate to the cell periphery in cells that divide by cell plate formation; often involves deposition of cell wall material in and around the phragmoplast.

Original comment by: jenclark

gocentral commented 21 years ago

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Part 3 of the summary:

differentiation examples:

T-cell differentiation ; GO:0030217 def: The process by which a hemopoietic stem cell acquires characteristics of a T-cell.

R8 differentiation ; GO:0045465 def: The specialization of organization of the R8 photoreceptor.

epithelial cell differentiation ; GO:0030855 def: The process whereby a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.

Original comment by: jenclark

gocentral commented 21 years ago

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Hi Jen,

I think it's a v. good idea to standardise all these terms.

Some suggestions for definitions:

differentiation of X: The specialization of organization of X.

X morphogenesis (modified from ISBN:0582227089): The origin and development of X, [small definition about what X is or does]. Morphogenesis pertains to the development of shape and structure.

development of X: The structural [and functional?] changes that occur to X over time.

formation of X: Establishment of the structure or arrangement of parts of X (Oxford English dictionary).

Also, the cell differentiation/commitment etc structure we have at the moment is different to that shown at the bottom of this SF entry:

cell differentiation --<cell fate commitment ----<cell fate determination ----<cell fate specification

I don't think a generic 'formation' term makes sense. If morphogenesis is 'the creation and development of...., then it sounds like this should be parent to formation of.... and development of.... terms.

It is a bit of a mixed bag at the moment though- some terms we have separate 'development' and 'formation' terms for (eg optic placode terms).

However we do have alot of terms eg heart development, that are very broad and based on it being a child of organogenesis I'd currently use this term to annotate a gene product that's involved in heart formation or the changes that occur to the heart, following its initial formation.

I think we need to decide whether 'development of X' refers to the changes that occur to X (including its formation) or the changes that occur to X, AFTER its initial formation.

Becky

Original comment by: beckyfoulger

gocentral commented 21 years ago

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I have some definite opinions on this issue. I would like to see differentiation be restricted to a cell type or a set of cells of one cell type. Basically, it describes the development of a cell type in the way I describe development below.

The term development is tricky. Do you mean the formation of the structure or what happens to the structure as it matures? I would like to propose that you mean both. Therefore development of something can be broken down into formation of something and "maturation" of something. For example, ectoderm is formed (develops), but it also gives rise to (develops into) the ectodermal portion of the gut. I do not think it is necessary to actually have the specific maturation terms since they will vary completely from structure to structure, and they will be covered under the development of the structure collector term. They can also be expressed as derived_from relationships in the anatomy. However, I do think we need to have the formation of terms, because this concept is very key to developmental biologists. In fact, I would propose that formation and morphogenesis could be used interchangeably in almost all cases.

David

Original comment by: jenclark

gocentral commented 21 years ago

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Hi David,

Yes that sounds sensible.

I suppose one important thing is to work out where one process stops and the next one starts.

e.g.

differentiation to make the cells of a primordium

leads to:

formation of the primordium

then:

development of the primordium

leads to:

the mature structure.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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Suggestions for generic defintions:

development:

def: Biological processes specifically resulting in maturation to this state of being [something] from an intial state of being [something].

e.g. %leaf development def: Biological processes specifically resulting in maturation to this state of being [a mature leaf] from an intial state of being [a leaf primordium].

%larva development def: Biological processes specifically resulting in maturation to this state of being [a larva] from an intial state of being [an embryo].

formation:

%formation of x ; GO:new def: The formation of x from y; x is [description of what x is] and y is [description of what y is].

e.g.

%formation of a leaf primordium ; GO:new def: The formation of a [leaf primordium] from the [leaf primordium intial cells]; x is [description of what x is] and y is [description of what y is].

differentiation:

differentiation of y ; GO:new def: The differentiation of cells of x to form cells of y; y is [description of what y is] and x is [description of what x is].

differentiation of leaf priordium initial cells ; GO:new def: The differentiation of cells of the [shoot apical meristem] to form cells of [the leaf primordium intial]; y is [description of what y is] and x is [description of what x is].

Does this mean that 'formation' is the bit between 'differentiation' and 'development' where the differentiated cells get together and 'form' the 'immature thing' that will develop into the 'mature thing'.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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Yes, so I would actually say that part of the formation would be the differentiation of the different cells. It is really hard to define where one starts and another stops. I think this will be determined case-by- case.

David

Original comment by: jenclark

gocentral commented 21 years ago

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Hi,

I think your definition of differentiation solves the problem quite well. It sounds as if differentiation definately stops at the point where the product can no longer be defined as a cell-type and instead must be defined as a tissue or organ.

e.g. primordium initial cells are more like a group of cells, and you wouldn't maybe define the priordium initial as an organ. By the time the priordium is formed you would definately say it is a developing organ rather than a homogeneous group of primordium cells.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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Hi,

Does that mean that:

--%development --%formation ---<differentiation

or

--%development --%formation --%differentiation

We don't currently have a term that's just 'differentiation' or 'formation' but we do have 'development'.

If we could work that out then we might have a bit of a structure to work with though.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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development, and cell differentiation are already defined. I think their definitions fit what we are saying here. As for formation, I don't think we need to specify the from part.

"x" formation: Biological processes that contribute to the act of giving form or shape to "x"

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

"x" maturation: (in most cases this term will not be needed, but when it is) Biological processes that are involved in the maturation of "x" from a rudimentary structure to its mature state.

"x" development <"x" formation <"y cell" differentiation <"z cell" differentiation <"x" maturation

Please wait for the west coast folks to weigh in on this as well! The plant folks may have some more insights/requirements for the process of maturation since this concept is used in plants a lot.

David

Original comment by: jenclark

gocentral commented 21 years ago

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> > Please wait for the west coast folks to weigh in on this as well! The plant folks may have some more insights/requirements for the process of maturation since this concept is used in plants a lot. > Yes, that seems like a good idea. At the rate we're going we'll have solved all of development between us.

The one things that makes me have reservations about what you've said in that last mail is the situation in Drosophila where there is

embryo development

then

larva development

then

adult development

I think it's important that each development term has both ends of it's phase delineated to its' clear to curators the scope of the term. For example larva development does include gene products for embryo development but if there's a separate term for embryo development then it;s important that we flag that up by delineating the developmental phase covered.

That's all now. I'll stop for a bit and wait for others to reply.

Thanks for all the input.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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I think it's ok to have embryo, larva and adult development. If a gene product is used during any of these processes, then it should be annotated to both. For example, Antp is expressed in both the embryo and the larva. If I remember my graduate days correctly (ancient history) somatic mosaics showed that it functioned during both stages of development, so it would be annotated appropriately to the correct children in embryo development and larval development. O.K. I'll be quiet for a while too.

David

Original comment by: jenclark

gocentral commented 21 years ago

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I'm not sure why you need a new term for 'formation of x'? Isnt' there already 'morphogenesis'?

Sue

Original comment by: jenclark

gocentral commented 21 years ago

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I think at the moment we use morphogenesis and formation terms and I was just thinking that it might be a good idea to standardise our use.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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This is turning into quite a long e-mail discussion so I'll leave the e- mail archive to look after storing the e-mails (17/10/03)

Original comment by: jenclark

gocentral commented 21 years ago

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Hi David, Jen et al. I agree with most comments in this SFitem, but I'm not sure formation and morphogenesis are always synonymous. Looking at the imaginal discs, the term 'imaginal disc morphogenesis' isn't used to describe formation of the discs, but rather the changes in structure and form that occur within the discs, [during the transition from larva to adult body shape]. Maybe these are just a special case? In the definitions most of our current X morphogenesis terms refer to the formation and the development of an organ/structure.

Also 'larval development' refers to the processes that occur between [in flies] the first larval instar (stage) and the final larval instar. Whereas adult heart development, for example, refers to development of the adult heart, which does not neccessarily occur in the adult. Maybe we just need to watch out for these.

Original comment by: beckyfoulger

gocentral commented 21 years ago

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Perhaps we could conform to naming the term one way and using the other convention as a synonym? Since I think many communities for whom this domain is not their expertise will be using GO, the less diversity in the naming convention the better. From Becky's comment, it sounds like formation of x would be a better choice for the term names within the new structure that separates formation, differentiation, and maturation. Perhaps X morphogenesis should be a synonym or X development?

Original comment by: syrhee

gocentral commented 21 years ago

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The problem with using the same convention is that no one would ever use the term heart formation. In this case, it would be better to have heart formation as a synonym of heart morphogenesis. I agree with Becky that formation and morphogenesis are not exactly synonymous, but whenever I try to define them, the defs come out equivalent. I would still be inclined to let the curator specify these terms rather than trying to mold them into one. I also noted a comment on cell differentiation below. The parts were further subdivided as is shown to be more consistent with the process as it is described in Gilbert.

Original comment by: ukemi

gocentral commented 21 years ago

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Really? As a totally naive person in heart development in mamals, I naturally did a google and PubMed search. Results were:

Google 'heart formation' returned 1,990 entries 'heart morphogenesis' returned 1,190 entries (both seem pretty relevant sites)

PubMed 'heart formation' 12,569 entries 'heart morphogenesis' 1,321 entries

Original comment by: syrhee

gocentral commented 21 years ago

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Hi all,

If we decide to go this way:

"x" formation: Biological processes that contribute to the act of giving form or shape to "x"

(Which sounds an awful lot like:
Morphogenesis: Developmental processes by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. )

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

"x" maturation: (in most cases this term will not be needed, but when it is) Biological processes that are involved in the maturation of "x" from a rudimentary structure to its mature state.

"x" development <"x" formation <"y cell" differentiation <"z cell" differentiation <"x" maturation

This may mean revisiting (again) the current development node. I think we really need to come to a decision about what 'morphogenesis' means in GO and what, if anything, 'formation' means that is different from that concept. The sooner we do this and STICK TO IT, the better it will be.

I would be in the camp of saying 'morphogenesis' can be synonymous to 'formation', in other words, morphogenesis is
the creation of the form of X.

Currently, there are quite a few terms that are of the form 'X morphogenesis' with synonym of 'X development'. These would need to be cleaned up.

For history's sake, here's an old email exchange between David and myself:

> Hi David, > Getting a little confused here. Are we saying that 'xxx > development' ='xxx morphogenesis'? > Tanya

>On Thu, 3 Apr 2003, David Hill wrote: > > I think that development and morphogenesis are only > equivalent at the level of a cell. At the level of tissues, > organs and organisms they are different. I would say > morphogenesis has to do with the creation of form > while development includes lots more stuff. > > David

My (more than) 2 cents,

Tanya

Original comment by: tberardini

gocentral commented 21 years ago

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When I made this comment:

"Currently, there are quite a few terms that are of the form 'X morphogenesis' with synonym of 'X development'. These would need to be cleaned up."

I was referring to terms where X is NOT a cell type. I know I've been guilty of this: for example: root development = root morphogenesis. There are probably other examples as well.

Original comment by: tberardini

gocentral commented 21 years ago

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This is really surprising to me! Are you sure the search was on the phrases "heart formation" and "heart morphogenesis"? When I search on heart formation in PubMed, most of the abstracts I get back have the two words, but not the phrase, even if the phrase is in quotes. The Google search gives back the same results you get.

But, if I do the same search with lung, I get back 1940 for morphogenesis and 469 for formation. Kidney gives 817 vs.

Limb gives 1720 vs. 1860. So, the bottom line is I am not sure how to deal with this.

Original comment by: ukemi

gocentral commented 21 years ago

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It sounds to me as if it might be good to have a very carefully written definition for each of the 'formation', 'morphogenesis', 'development' etc. generic terms, as they are to be used by go, and then add synonyms where required to accommodate specific use in other fields.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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O.K. So with Tanya's comments in mind. The definition of morphogenesis is: "Developmental processes by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form."

But, when we go down to embryonic morphogenesis we change this: "The developmental processes by which defined structures within an embryo are generated." We lose the organized bit.

I thing the top level definition is a good one. I think the embryonic def should have the phrase "and organized" added to it. If you look at its parents and children, clearly this def is more correct.

Most of the terms below embryonic morphogenesis include the phrase "The formation and development of", but what I think we really mean is "The formation and structural development (organization) of"

This way, "formation" terms would become a part of "morphogenesis" The other part of "morphogenesis" would be "structural development".

Again though, the diffuculty lies in where these two parts are separated and when does structural development turn into maturation. I think this will have to be based on the structure itself. For example, fly imaginal discs may have different end points than the mammalian spleen.

"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.

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

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

"x" maturation: (in most cases this term will not be needed, but when it is) Biological processes that are involved in the maturation of "x" from a rudimentary structure to its mature state.

"x" development <"x" morphogenesis <"x" formation <"y cell" differentiation <"z cell" differentiation <"x" structural development <"x" maturation

Comments please!

Original comment by: ukemi

gocentral commented 21 years ago

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I agree- I too like the existing morphogenesis definition referring to the generation and organization of structures. I think we should change all current X morphogenesis' definitions to 'generation and organization of X'.

I like the tree structure you have drawn David, with X development being a broad, all-encompassing term.

I think the 'structural development' terms should be made on a case-by-case basis too, since i'm not sure how easy it would be to distinguish between this and the whole process of morphogenesis in most cases. The same for the formation terms perhaps (we don't have many of these terms in GO at the moment anyway). It's not always possible to tell when the formation of a structure ends and its organization begins.

I shall get on with defining and revising the imaginal disc terms when this SF entry is done.

Original comment by: beckyfoulger

gocentral commented 21 years ago

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Is it right that some people have a different concept for 'formation'? Many of the e-mails here have suggested that formation is the whole process that gives rise to mature organisation and shape. I think the way that Becky's suggesting using it is that formation is the initial stage that gives rise to the small initial immature structure and that once formation is complete this small structure organises itself and takes shape to become the large mature structure. Is that right?

Becky: 'It's not always possible to tell when the formation of a structure ends and its organization begins.'

Thanks,

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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"x" development <"x" morphogenesis <"x" formation <"y cell" differentiation <"z cell" differentiation <"x" structural development <"x" maturation

This arrangement is acceptable to me. Is the understanding that each "x" development term may or may not have some/all of the children terms? Are the certain child terms that should be mandatory? Maybe ' x morphogenesis' and 'x maturation' at the least?

Tanya

Original comment by: tberardini

gocentral commented 21 years ago

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I'm Ok with this structure as well. However, 'x structural development' seems a bit esoteric. Could we use 'x organization' instead? I have a particular example of 'petal development' where 'petal organization' is much more appropriate than 'petal structural development'.

BTW, the searches of x formation and x morphogenesis were phrase searches (within quotes).

Thanks!

Original comment by: syrhee

gocentral commented 21 years ago

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Hi,

Should we maybe agree how we define these terms before we make the hierarchy?

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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Structural organization or development is fine with me. I've thrown out some defs. Feel free to comment on them.

Original comment by: ukemi

gocentral commented 21 years ago

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Hi,

I'm completely up to my ears just now, and can't look at the definitions at the moment but I'll keep following the discussion. If you can wait a few days before making any big decisions that would be great.

Thanks,

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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I like all of Davids definitions below, with morphogenesis being the generation and organization of....

Becky.

Original comment by: beckyfoulger

gocentral commented 21 years ago

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Do you mean this?

"x" formation: Biological processes that contribute to the act of giving form or shape to "x"

(Which sounds an awful lot like:
Morphogenesis: Developmental processes by which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form. )

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

"x" maturation: (in most cases this term will not be needed, but when it is) Biological processes that are involved in the maturation of "x" from a rudimentary structure to its mature state.

"x" development <"x" formation <"y cell" differentiation <"z cell" differentiation <"x" maturation

This may mean revisiting (again) the current development node. I think we really need to come to a decision about what 'morphogenesis' means in GO and what, if anything, 'formation' means that is different from that concept. The sooner we do this and STICK TO IT, the better it will be.

Yes, I like those. I think we still need to get the definitons to distinguish between formation and morphogenesis but if we agree to take this set and work from here then that might help to pin the discussion down a bit.

Jen

Original comment by: jenclark

gocentral commented 21 years ago

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yep- though I think the more recent definition of 'x' formation suggested (that sounds less like morphogenesis) was:

"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.

Original comment by: beckyfoulger

gocentral commented 21 years ago

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Actually it was this one wasn't it? I didn't realise that was David's username.