Changes to 'developmental process'

[pgaudet]

Hello,

For the BP refactoring, we want to untangle multi-cellular organism processes from cellular processes.
For the 'developmental process' branch, we propose to move 'cellular developmental process' under 'cellular process' and rename 'developmental process' -> 'multi-cellular organism developmental process'

@thomaspd

Thanks, Pascale

[raymond91125]

Proposed changes:

• move 'GO:0048869 cellular developmental process' to 'is_a 'GO:0009987 cellular process'

• CREATE NEW TERM 'multicellular organismal-level developmental process' under which to move organism-level processes (embryonic development?? see https://en.wikipedia.org/wiki/Animal_embryonic_development)

Review children of developmental process:

• 'GO:0048532 anatomical structure arrangement' > move under new term 'multicellular organismal-level developmental process'
• 'GO:0048856 anatomical structure development' > move under new term 'multicellular organismal-level developmental process'
• 'GO:0048646 anatomical structure formation involved in morphogenesis' > move under new term 'multicellular organismal-level developmental process'
• 'GO:0009653 anatomical structure morphogenesis' > move under new term 'multicellular organismal-level developmental process'
• 'GO:0060033 anatomical structure regression' > move under new term 'multicellular organismal-level developmental process'
• GO:0043697 cell dedifferentiation > move under GO:0048869 cellular developmental process
• GO:0043696 dedifferentiation > obsolete, unnecessary grouping class
• GO:0031128 developmental induction' > move under new term 'multicellular organismal-level developmental process'
• GO:0021700 developmental maturation' > move under new term 'multicellular organismal-level developmental process'
• GO:0048757 'pigment granule maturation' > not a developmental process (remove is_a developmental maturation')
• GO:0061792 secretory granule maturation > not a developmental process/ is_a GO:0033363 secretory granule organization sufficient (remove LD)
• GO:0016188 synaptic vesicle maturation > not a developmental process/ is_a 'vesicle organization' sufficient (remove LD)
• GO:0060074 'synapse maturation' not a developmental process is_ GO:0050808 synapse organization sufficient (remove is_a developmental maturation')
• GO:0048469 cell maturation: move under 'GO:0048869 cellular developmental process'
• GO:0003006 developmental process involved in reproduction': to be reviewed separately, has many cellular processes
• GO:0022611 dormancy process: is a developmental process?
• GO:0098727 maintenance of cell number: is_a ​​GO:0048871 multicellular organismal-level homeostasis ?

[raymond91125]

@pgaudet
CREATE NEW TERM 'multicellular organismal-level developmental process' under which to move organism-level processes (embryonic development?? see https://en.wikipedia.org/wiki/Animal_embryonic_development)
IS_A developmental process?
If we are to keep the grouping term developmental process, shouldn't cellular developmental process stay? cellular developmental process has dual IS_A parentage.

[raymond91125]

Perhaps we would keep developmental process, IS_A children include
---cellular developmental process
---multicellular organism-level
---- NTR animal developmental process
---- NTR plant developmental process
---unicellular organism-level (or merge with cellular)
---cellular component-level

[pgaudet]

Discussion with @thomaspd and @raymond91125

• cellular component-level should go under 'organelle biogenesis' (or something like this, depending on the term

• for now we can keep the top level term ' developmental process', and decide later when looking more broadly at the ontology

• specifically: under ' developmental process', we can keep for now:

• cellular developmental process

• multicellular organism-level

• NTR animal developmental process

• NTR plant developmental process

• unicellular organism-level (or merge with cellular) (maybe we create later, when we see whether we need it?)

• cellular process

• • GO:0032989 cellular component morphogenesis

[raymond91125]

New term proposal
animal organism-level developmental process "Any multicellular organismal process whose specific outcome is the progression of a metazoa over time from an initial condition to a later condition." [WIKIPEDIA:Developmental biology]
plant organism-level developmental process "Any multicellular organismal process whose specific outcome is the progression of a viridiplantae over time from an initial condition to a later condition." [WIKIPEDIA:Developmental biology]

[pgaudet]

Sound good. Could we simplify the labels:
'animal developmental process' and 'plant developmental process' ?

Thanks, Pascale

[raymond91125]

I just noticed that there is already a term multicellular organism development with LD 'anatomical structure development'
and ('results in developmental progression of' some 'multicellular organism') and two other IS_A parents developmental process, multicellular organismal process.

[raymond91125]

I think the animal and plant terms can be placed under multicellular organism development and revise the definition accordingly. One concern is that there maybe developmental processes that are beyond clearly identifiable anatomical structures, e.g. gender identity, gender euphoria. GO currently does not cover these psychological processes.

[pgaudet]

Suggestion on the ontology call by @cmungall

---- NTR animal gross anatomical part developmental process
---- NTR plant gross anatomical part developmental process

LD for animal term -> there is no uberon term suitable yet - 'gross anatomical part ' under discussion

LD for plant term: need to coordinate with PO to create a suitable grouping class

[pgaudet]

Hi @raymond91125

Following on on yesterday's call - if you create the new terms 'animal gross anatomical part developmental process' and 'plant gross anatomical part developmental process', then these terms could be used as the general for the logical definitions, that would generate correct classification. Is that also what you had in mind?

Thanks, Pascale

[raymond91125]

I was thinking using something like developmental process as the genus and animal anatomical parts as the differentia. e.g. 'developmental process'
and ('results in development of' some 'adrenal cortex')

[pfey03]

Anatomical structure development we have as it is an ok term for Dicty. Plus in Dicty the development is not cellular but multicellular. I do not agree with the planned changes

[raymond91125]

We could have a term about Dictyosteliida multicellular anatomical part developmental process. We should discuss to decide on the level of phylogeny and term name. The goal is to make groupings that are more likely to have internal conservation.

Would that work @pfey03?

[pfey03]

@raymond91125 and @pgaudet I don't know why we always must have these complicated names when developmental process simply would do for us and anatomical structure development as well. It is always annoying for us. multicellular anatomical part developmental process is a stupid sounding term, just repetitive and I don't like it.

[pgaudet]

@raymond91125 Perhaps the best (simplest) solution for now is to keep the dicty terms under 'developmental process', we'll figure out later if we need another grouping term for these. What do you think?

[raymond91125]

An example

[pgaudet]

I dont see the issue - this can be kept as-is for now, and you can still create the distinction between plant and animal development, right ?

[raymond91125]

Yes, I think so. We are not obsoleting any exiting but create new grouping terms.

[pfey03]

Dicty is neither plant nor animal, though because it's from the base in phylogeny where plants and animals divide, it has many (about 30% mammalian ortholgs but no plant orthologs, and of cause general orthologs from yeast to up, and then purely amoeba genes. We even have several disease genes like Huntington, or presenilin A and B genes involved in Alzheimer, several genes involved in mitochondrial diseases and many more.

[raymond91125]

Propose to add two new terms as below. Please comment.

+[Term]
+id: GO:0160084
+name: animal gross anatomical part developmental process
+def: "Any developmental process whose specific outcome is the progression of the gross anatomical parts of an animal over time from an initial condition to a later condition." [WIKIPEDIA:Developmental_biology]
+synonym: "animal development" RELATED []
+is_a: GO:0032502 ! developmental process
+property_value: term_tracker_item "#22994" xsd:string
+created_by: rynl
+creation_date: 2023-07-19T23:48:44Z
+scope: biological_process
+
+[Term]
+id: GO:0160085
+name: plant gross anatomical part developmental process
+namespace: biological_process
+def: "Any developmental process whose specific outcome is the progression of the gross anatomical parts of a plant over time from an initial condition to a later condition." [WIKIPEDIA:Developmental_biology]
+synonym: "plant development" RELATED []
+is_a: GO:0032502 ! developmental process
+property_value: term_tracker_item "#22994" xsd:string
+created_by: rynl
+creation_date: 2023-07-20T00:05:55Z
+

[pgaudet]

Hi @raymond91125

I wonder, can we be more specific than "from an initial condition to a later condition" ? This is not what is described in the wikipedia page you cite. Can we have something that mentions that it starts with a zygote and ends with a fully formed/mature organism?

@ukemi is that too restrictive?

Thanks, Pascale

[pgaudet]

Or maybe to cover specific organ development processes (for example), that start later than at the zygote stage, we could have something that indicates an immature stage to a mature stage?

[raymond91125]

I thought the goal is to focus on developmental processes of gross anatomical parts: such as the heart, the limb, or the nervous system, defined by Uberon for animals; we are not modelling development as temporal progressions of life cycles per se.

[pgaudet]

we are not modelling development as temporal progressions

But your definition states "progression over time" - I guess this is what I would like to see clarified. We need to be very clear about what these grouping terms are to make sue they only cover the terms we want.

Maybe "Any developmental process whose specific outcome is the progression of a gross anatomical part of an animal from an initial immature state, to a later, more mature state" ... along these lines?

Thanks, Pascale

[raymond91125]

The definition I proposed is following the definition we have for the parent term GO:0032502 developmental process. Perhaps the reference can be better but I haven't found one.
The logical definition, when we have a Uberon term would be 'developmental process' and ('results in development of' some 'animal gross anatomical part')

[raymond91125]

Ontology editor meeting 2023-07-31:

1. We should specify the initial conditions for terms of specific anatomical parts; an example may be included in the comment of these grouping terms.
2. PO does not have a term of plant gross anatomical part

[pfey03]

What about Dicty? It has cell differentiation when it fruits and is a really multicellular organism then. It also has this epithelium like organization GO term as it has alpha and beta catenins. Dicty is always different and the development is not strictly a cellular process there is a lot more to it.

[raymond91125]

How about a social amoeba gross anatomical part developmental process? Is there an anatomy term that we can use for LD?

[pfey03]

We have many anatomy terms that represent the complexity. Just a selection here:
DDANAT:0000029 tip-organizer of the migratory slug
DDANAT:0000042 upper cup region of the early culminant
DDANAT:0000044 prespore/base region of the early culminant
DDANAT:0000049 prestalk A region of the mid culminant
DDANAT:0000062 apical disc of the late culminant
DDANAT:0000067 outer basal disc of the late culminant
DDANAT:0000078 surface sheath of the late culminant
DDANAT:0000405 prespore cell
DDANAT:0000012 fruiting body ('sorocarp' is synonym)
DDANAT:0010001 Dictyostelium discoideum anatomical structure

https://github.com/dictyBase/migration-data/blob/master/ontologies/dicty_anatomy.obo

[raymond91125]

Is DDANAT_0010082 whole organism the proper grouping term equivalent to gross anatomical part in animals or plants? The goal is to have a grouping term for all multicellular body parts and to use it in the logical definition so that each specific body part development can be automatically inferred to be a subclass of gross anatomical part development.

[raymond91125]

DDANAT:0000405 prespore cell

Gross anatomical part is about multicellular structures thus a cell is not a gross anatomical part. I have not checked the others.

[pfey03]

I know, it was just a selection

[raymond91125]

+[Term]
+id: GO:0160108
+name: animal gross anatomical part developmental process
+namespace: biological_process
+def: "Any developmental process whose specific outcome is the progression of a gross anatomical part of an animal from an initial immature state, to a later, more mature state." [GOC:pg]
+synonym: "animal development" RELATED []
+is_a: GO:0032502 ! developmental process
+property_value: term_tracker_item "#26121" xsd:anyURI
+created_by: rynl
+creation_date: 2023-09-18T20:43:55Z
+
+[Term]
+id: GO:0160109
+name: plant gross anatomical part developmental process
+namespace: biological_process
+def: "Any developmental process whose specific outcome is the progression of a gross anatomical part of a plant from an initial immature state, to a later, more mature state." [GOC:pg]
+synonym: "plant development" RELATED []
+is_a: GO:0032502 ! developmental process
+property_value: term_tracker_item "#26121" xsd:anyURI
+created_by: rynl
+creation_date: 2023-09-18T20:55:06Z

[raymond91125]

• copying animal gross anatomical part developmental processes under GO:0160108
• copying plant gross anatomical part developmental processes under GO:0160109