search

geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
Creative Commons Attribution 4.0 International
219 stars 40 forks source link

Growth pattern or patterned growth #2046

Closed gocentral closed 9 years ago

gocentral commented 19 years ago

I have some quibbles with the term 'growth pattern ; GO: 0007150'.

- 'growth pattern' as a concept doesn't describe a series of events, so it's not really a process. 'growth' is a process, so perhaps this term could be renamed 'patterned growth' - ie. growth which exhibits a pattern. Does the current def still fit in this case?

"A process whereby cells develop a specific morphology under a specific set of circumstances."

Is it the cells that are developing the specific morphology or is it whether or not cells develop in certain areas / conditions that results in a particular growth pattern? Or could it be both?

At the moment, this term only has 'filamentous growth' children; there are plenty of development terms involved in patterned growth, so perhaps if this term is to stay, they can be added as children.

Reported by: girlwithglasses

Original Ticket: "geneontology/ontology-requests/2053":https://sourceforge.net/p/geneontology/ontology-requests/2053

gocentral commented 19 years ago

Logged In: YES user_id=735846

Hi Amelia,

Yes I can see what this term is getting at. I'm not sure whether it's a sensible go term but if it is then it wants renamed at least. Here's an example of what it's trying to say, as it might happen in plants.

Sometimes in ferns the spore (in the dark) starts its development by growing into a long thin cell that grow straight upwards, and periodically divides to make a long chain of filamentous cells. If the spore was in soil then eventually the topmost filamentous cell would eventually break through the surface of the soil and into the light. At this point the tip receives an environmental signal which is blue light. In response to the environmental signal, the topmost, newest cell would expand into a sphere instead of a filament. So as a response to an environmental signal the fern cells are determined to develop either as a filament of a sphere. This is what the person meant by 'growth pattern'.

Is this a sensible thing to have as a GO term or would it be better just to annotate to 'response to blue light' and 'isotropic (sphere) cell morphology' or 'anisotropic (filamentous) cell morphology'

The mechanism that sends the signal from the blue light receptor to the morphogenesis department wasn't known when I last looked.

The difficulty with the name of this term is that it could be confused with 'pattern specification' GO:0007389 which is entirely different thing. It's just to do with the establishment of axes and patterns in an organ or organism by the diffusion of protein along a gradient, and things like that.

Jen

Jen

Original comment by: jenclark

gocentral commented 19 years ago

Logged In: YES user_id=735846

Hi Amelia,

I was just thinking more about that and I think that currently the term that would cover 'anisotropic (filamentous) cell morphogenesis' would be 'tip growth' GO:0009932 which is a child of 'growth'.

Jen

Original comment by: jenclark

gocentral commented 19 years ago

Logged In: YES user_id=735846

Hi,

Should 'monopolar cell growth', 'tip growth', and 'filamentous growth' be related to one another in some way other than just via 'growth' and 'growth pattern'?

Jen

Original comment by: jenclark

gocentral commented 19 years ago

Logged In: YES user_id=473796

Jen, does your understanding of 'growth pattern' fit the use of growth pattern in the terms underneath it?

I am really not convinced by this term. The def makes it sound like it's a 'response to ...' type term, but the children terms use it as if it means a particular mode of growth. Of course, cells will grow in different ways according to their circumstances, but I presume there is also a 'default mode', a way in which cells will grow if they don't receive any outside stimulus. Those terms under 'growth pattern' may well describe default growth modes, which would make the current def seem wrong. To my mind there doesn't seem to be any point in having a term that groups 'modes' of growth - may as well just stick them all under 'growth'.

Original comment by: girlwithglasses

gocentral commented 19 years ago

Logged In: YES user_id=436423

This may not solve the present problem, but I can provide a smidge of this term's history: it is part of the Antediluvian GO, and was included at the behest of us yeasties to help deal with the bud-form vs. hyphal/pseudohyphal/filamentous growth modes observed in Saccharomyces and a passel of other fungi.

The child term is actually a better guide than the def to the original intended purpose of 'growth pattern'. Although it maywell apply to the spore growth patterns Jen describes, that certainly wasn't the process we had in mind six years ago!

If we keep the term, the best rewording might thus be 'regulation of growth pattern', or possibly 'establishment of ...'; either way the definition could be adjusted to fit.

If the term were to be made obsolete instead of renamed (and more accurately defined), the yeast people would have to be satisfied that the processes that (a) determine whether cells will grow as bud form or filamentous form and (b) actually bring about growth in that mode are adequately covered by other terms.

Incidentally, the definition of 'filamentous growth' could be adjusted to sound more process-y (e.g. 'The process by which cells grow so as to form filamentous chains' ... could be improved, no doubt).

m (only feeling a little like an old-timer)

Original comment by: mah11

gocentral commented 19 years ago

Logged In: YES user_id=473796

I'm happy with whatever the yeasties want to do, as long as the term name is changed and the def is altered so it refers to the term string. Ta!

Original comment by: girlwithglasses

gocentral commented 19 years ago

Logged In: YES user_id=735846

Hi,

Yes the process I'm describing is quite different from that and would require a different filamentous growth child. It fits into the idea of the 'growth pattern' term though.

There's a whole big field in plant sciences called 'photomorphogenesis' that is to do with how plants grow in particular shapes in response to environmental light signals. That might be worth a look when considering this term.

Jen

Original comment by: jenclark

gocentral commented 19 years ago

Logged In: YES user_id=439222

Hi

Midori, I intuitively see the yeastie angle represented by this term. But I'm confused about whether this is supposed to represent the pattern a group of cells makes or the 'growth pattern' of a single cell (is that possible?).

Since it's under 'cell growth', it should be about the 'growth pattern' of a cell...? But it seems like to me, filamentous growth is described in GO and in literature as a phenotype describing a group of cells or a colony.

BTW, if it's a process for 'groups of cells', where would it get placed? Under development?

or maybe the string should be called 'filamentous cell growth' to mean individual cells.

ugh. sorry for the rambling. I jsut don't get this term 'patterned growth'. I feel like we're trying to shoe horn in the yeasty terms under this general term with a vague meaning.

I can bring this up with curators to see if they have any more thoughts. Maybe Maria and CGD will have more specific thoughts on this.

no help here, Chandra

Original comment by: clt4

gocentral commented 19 years ago

Logged In: YES user_id=473796

It seems to me that there is enough confusion and mystery surrounding this term to warrant its obsoletion. The def is wrong and anyway, it's only got 4 direct annotations. If there is a call for GO representation of 'growth patterns', perhaps some new terms can be suggested by interested parties.

Original comment by: girlwithglasses

gocentral commented 19 years ago

Logged In: YES user_id=735846

I'd be happy with that suggestion. The processes that I was thinking of belongs under photomorphogenesis ; GO:0009640. Do we need a new grouping term to take things like photomorphogenesis and other processes where growth pattern is altered in response to external stimuli?

Jen

Original comment by: jenclark

gocentral commented 19 years ago

Logged In: YES user_id=473796

Concerning the obsoletion of this term - I would advise that annotations are transferred to the parent term 'cellular morphogenesis ; GO: 0000902'.

Original comment by: girlwithglasses

gocentral commented 19 years ago

Logged In: YES user_id=616548

I don't have any problems with obsoletion of this term. I'm also wondering whether 'filamentous growth' should not be a child of 'cellular morphogenesis'. Even for single-celled organisms, the term and its children refer to the relationships between cells - the overall pattern of the group of organisms - rather than to the shape of each cell. I think it would make sense for 'filamentous growth' to be a direct child of 'growth', i.e.

development -%growth --%filamentous growth

and to remove its 'cellular morphogenesis' parentage. However, I'm aware that cells exhibit different shapes during the different kinds of filamentous growth, so I'm not 100% sure whether this is a good idea... I'd appreciate comments from other fungal people!

Maria

Original comment by: mariacostanzo

gocentral commented 19 years ago

Logged In: YES user_id=777884

I agree that it's a good idea to obsolete the term 'growth pattern'. Regarding changing the parentage of 'filamentous growth', the definition of 'filamentous growth' does not refer to cell morphology at all:

Definition: A pattern of growth where colonies are composed of filamentous chains of cells

So, unless we want to expand the definition to include something about cell morphology, I would agree with Maria's suggestion to remove 'cellular morphogenesis' as a parent of 'filamentous growth'.

Jodi

Original comment by: jodih

gocentral commented 19 years ago

Logged In: YES user_id=473796

How about I suggest annotations are directed towards the terms 'growth' or 'cell growth' instead? I agree with reparenting 'filamentous growth', and if anyone wants to give it (or suggest) a more process-like definition, that would be great!

Original comment by: girlwithglasses

gocentral commented 19 years ago

Logged In: YES user_id=616548

Yikes! The definition of filamentous growth, in addition to not being process-y, is way too yeast-specific; it's more specific than some of its children. It really refers only to "growth as a filament"; this can be hyphal growth (a tube of connected cylindrical cells, or a continuous multinucleate tube) or pseudohyphal growth (chains of attached cells). How about "The process by which a multicellular organism or a group of unicellular organisms grow in a threadlike, filamentous shape." ??

Original comment by: mariacostanzo

gocentral commented 19 years ago

Logged In: YES user_id=735846

Maria's def would allow this term to be used for the plant situation I was talking about, which would be good because that process would be called filamentous growth.

Jen

Original comment by: jenclark

gocentral commented 19 years ago

Logged In: YES user_id=473796

OK, so the plan is

I'll carry that out tomorrow if there are no complaints.

Original comment by: girlwithglasses

gocentral commented 19 years ago

Logged In: YES user_id=473796

All done!

Original comment by: girlwithglasses

gocentral commented 19 years ago

Original comment by: girlwithglasses

gocentral commented 11 years ago

Original comment by: cooperl09