dormancy process (GO:0022611) and new subtypes

[gocentral]

GO has terms for dormancy process and seed dormancy. The PO curators would like to request revisions to these terms, plus new terms for whole organism dormancy process, and bud dormancy process. It might be useful to add a term for spore dormancy process as well. The PO is creating/revising terms for dormant stages, and would like to refer to these GO processes.

DORMANCY PROCESS: Current definition of dormancy process (GO:0022611): The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity.

Proposed new definition for dormancy process (GO:0022611): A developmental process in which dormancy is induced, maintained or broken. Comment: Dormancy is a suspension of most physiological activity and growth that can be reactivated.

This definition works for plants. Someone at the GO will need to check if there are other comments needed for animals.

As it stands now, dormancy is defined in the comment. Dormancy (sometimes called a dormant state) is different from dormancy process. GO curators will need to decide if they want to define dormancy as a separate term, of just keep it in the definition of dormancy process, as we have here.

SEED DORMANCY PROCESS: Current definition of seed dormancy (GO:0010162): The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated.

This should be renamed "seed dormancy process".

Proposed new definition for seed dormancy process (GO:0010162): A dormancy process that has as participant a seed. Comment: Seed dormancy is a suspension of physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.

You could add an xref: seed dormancy process (GO:0010162) has_participant seed (PO:0009010). Only_in_taxon Spermatophyta

MULTICELLULAR ORGANISM DORMANCY PROCESS: Proposed definition, multicellular organism dormancy process (new term): A dormancy process that has as participant a whole organism. Comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. In plants, multicellular organism dormancy may involve the formation of dormant buds and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of organism dormancy in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. May be a response to environmental conditions such as seasonality or extreme heat, drought, or cold.

Other comments could be added for animals, if desired.

BUD DORMANCY PROCESS: Proposed definition, bud dormancy process (new term): A dormancy process that has as participant a bud. Comment: Bud dormancy is a suspension of most physiological activity and growth in a bud that can be reactivated. In plants, bud dormancy may precede multicellular organism (whole plant) dormancy. The end of bud dormancy is marked by the resumed growth of a bud. May be a response to environmental conditions such as seasonality or extreme heat, drought, or cold.

You could add an xref: bud dormancy process (GO:0010162) has_participant bud (PO:0000055).

Reported by: rlwalls2008

Original Ticket: geneontology/ontology-requests/9064

[gocentral]

As references for these terms, you could site POC:curators for all of them, and the reference below for multicellular organism dormancy process and bud dormancy process.

http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.15.060164.001153 Vegis; Dormancy in Higher Plants ARPP 1964 PO_REF:00009

Original comment by: rlwalls2008

[gocentral]

Hi Ramona,

Thanks for all the information.

I'm afraid I don't fully understand the need for a new term "multicellular organism dormancy process". dormancy process (GO:0022611), as a direct child of "developmental process", covers "an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism", including multicellular organisms. Do we really need to create "multicellular organism dormancy process" as a child of dormancy process (GO:0022611), and then rearrange the child terms of dormancy process (GO:0022611)? Personally, I'd favor not creating the new term, but I'd include some of the information you provide in a comment to the def. of dormancy process. Here's my suggestion: [my questions to you and/or the other editors are in square brackets]

GO:0022611 dormancy process: Edit def. as follows: A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. [I think that this def would work for animals as well. Does anyone disagree on this?] Add definition comment: In plants and animals, dormancy may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. In plants, dormancy may involve the formation of dormant buds, and may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system [in] herbaceous perennials. The end of dormancy [or "exit from dormancy", to parallel the symbiont terms] in vascular plants is marked by resumed growth of buds and/or growth of vascular cambium. [Would anyone add specific comments about animals?] Dbxrefs: GOC:PO_curators [to be added to the curators' initials file], http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.15.060164.001153, PO_REF:00009 [how should I enter this? I haven't found any other PO_REF in GO or in the GO>references file.]

GO:0010162 seed dormancy: Rename as "seed dormancy process". Edit def. as follows: A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a seed. Seed dormancy is a suspension of [most??] physiological activity and growth in a seed, including the embryo contained therein, that can be reactivated. It often requires special conditions for reactivation, such as specific temperature, scarification, or leeching of inhibitors. Add related synonym: seed dormancy Dbxrefs as above [Ramona notes: "You could add an xref: seed dormancy process (GO:0010162) has_participant seed (PO:0009010)." Do we already use has_participant in contexts other than chemicals? I couldn't find any example in the obo file.] [Ramona notes: "Only_in_taxon Spermatophyta" This is already implemented.]

I would add the new term: GO:NEW bud dormancy process [To make it clear that this term refers to plant buds only, and to avoid confusion with other buds i.e. those resulting from asexual reproduction, I'd add a taxon constraint. Plant experts, please advise if this should be to Viridiplantae, Embryophyta or Spermatophyta.]
Def: A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken in a bud. Bud dormancy is a suspension of most physiological activity and growth that can be reactivated. It may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. The end of bud dormancy [or "exit from bud dormancy"] is marked by the resumed growth of the bud. Comment: Bud dormancy may precede dormancy of the whole plant. [Ramona notes: "You could add an xref: bud dormancy process (GO:0010162) has_participant bud (PO:0000055)." Do we already use has_participant in contexts other than chemicals?]

BTW, to do too: GO:0042751 estivation add exact synonym: aestivation

I will point the other GO editors to this discussion. Thanks and happy holidays! Paola

Original comment by: paolaroncaglia

[gocentral]

• assigned_to: nobody --> paolaroncaglia

Original comment by: paolaroncaglia

[gocentral]

Our reasoning behind suggesting a new term for multicellular organism dormancy process was that dormancy process was the general term, and other terms, like bud dormancy process, seed dormancy process, or organism dormancy process were all special cases. This follows from how the PO is organized, where whole plant, bud, and seed are all subtypes of plant structure. However, I think we can work with the new definition you have proposed for dormancy process, without adding a new term for multicellular organism dormancy process. I would ask that you add "multicellular organism dormancy process" as a narrow synonym of dormancy process in that case. I am fine with changing "end of dormancy" to "exit from dormancy" and, yes, please insert the word "in" as you have suggested.

New definition of seed dormancy process is good. It should say "suspension of MOST physiological activity" as you suggested.

New definition of bud dormancy process is good. Again, "exit from dormancy" is fine. I think the taxon restriction should be for Embryophyta, but I will check into whether or not the term bud is used for green algae.

In PO, we tend to be more minimal with our definitions, and put more in the comments, but I don't mind that you prefer to have more of the info in the definition. I think that is actually useful in some cases, like for applications that only display definitions, and not comments.

PO has begun using participates_in and has_participant as links between plant anatomical entities and plant structure development stage. My understanding is they are appropriate for linking occurants to continuants or vice versa. If GO starts to add has_participant relations to PO, there are probably a lot more that could be put it.

Thanks for responding so quickly!

Original comment by: rlwalls2008

[gocentral]

Thank you, Ramona. I'm on Christmas leave until the New Year, so I'll implement the changes when I'm back at work (your synonym included). Feel free to comment if/when you find out about the taxon rule, and let's see if we get any more comments from other editors.

Season's greetings, Paola

Original comment by: paolaroncaglia

[gocentral]

Paola,

This looks really good. A few comments:

(1) leeching -> leaching (2) In GO,we do not currently use has_participant outside of the go_xp_chebi.obo file, I think. (3) I don't think we need '"multicellular organism dormancy process" for reasons that Paola described very well. The string is fine as a narrow synonym, if needed.

Happy holidays!

Tanya

Original comment by: tberardini

[gocentral]

I just noticed one thing I would change with in the definitions of seed dormancy process and bud dormancy process. The first line of the definitions should read "A dormancy process in which..." instead of "A developmental process in which...". Dormancy process is more appropriate as the genus in the definition, because is the parent term.

PO_REF is a set of wiki pages we set up to reference old journal articles that do not have a Pubmed or Jstor ID. See http://wiki.plantontology.org:8080/index.php/PO\_references.

Here is the text for our dbxref file: abbreviation: PO_REF database: Plant Ontology custom references object: Reference identifier example_id: PO_REF:00001 generic url: http://wiki.plantontology.org:8080/index.php/PO\_references url_syntax: http://wiki.plantontology.org:8080/index.php/PO\_REF:\[example\_id] url_example: http://wiki.plantontology.org:8080/index.php/PO\_REF:00001

This probably should be added to GO's dbxref file, if you are going to cite PO_REF in GO. Alternatively, you could add the article to the GO reference collections (http://www.geneontology.org/cgi-bin/references.cgi).

Original comment by: rlwalls2008

[gocentral]

Thanks, Ramona. I've added GOC:PO_curators in the GO.curator_dbxrefs file, and PO_REF in the GO.xrf_abbs file.

Let me know when you find out about the most appropriate taxon restriction for the new term "bud dormancy process" (or do you confirm Embryophyta?). I'll take care of the new terms soon -

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Thanks Paola! I talked to an algae expert yesterday, and he said they do use the term bud in a similar sense to how the PO defines it, so the taxon restrictions should actually be for Viridiplantae.

Original comment by: rlwalls2008

[gocentral]

Hi Ramona, these are done as per discussion below:

Edited GO:0022611 dormancy process, GO:0010162 seed dormancy, GO:2000033 regulation of seed dormancy, GO:0042751 estivation; added new term GO:0097207 bud dormancy process.

I'll add the taxon constraint as soon as the new term is live in the ontology.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> open-accepted

Original comment by: paolaroncaglia

[gocentral]

At the POC conference call yesterday, some additional issues about dormancy process came up:

1. Should GO add a term for spore dormancy process? This was discussed some under https://sourceforge.net/tracker/index.php?func=detail&aid=2946506&group\_id=36855&atid=440764. We expect that there will be times when people will need to describe spore dormancy processes in plants, but not sure if you want to include this under the generic "dormancy process", as you did for whole organism dormancy. If so, then perhaps spore dormancy process should be a narrow synonym of dormancy process as well.

2. More specific subtypes for dormancy process: We were concerned that the term dormancy process is so general, that no one should really be annotating to it. We think it would be good to create specific subtypes like induction of dormancy, maintenance of dormancy, and release of dormancy. Similar subtypes already exist for seed dormancy [see maintenance of seed dormancy (GO:0010231) and release of seed from dormancy (GO:0048838)], and the definitions could be similar. Of course, there are also many more specific biological processes that could go under each of these, as the need arises.

On a related note, acquisition of desiccation tolerance (GO:0048700), is defined as "The process in which a seed acquires tolerance to severe drying, before entering into a dry, either dormant or quiescent state." It is part of both seed dormancy process and dormancy process. I think based on the definition it should only be part of seed dormancy process, in which case it will be inferred to be part of dormancy process anyway. It should also have a more specific name like "acquisition of desiccation tolerance in a seed". Other things (like whole plants or individual leaves) can also acquire dessication tolerance, and not only as part of dormancy, so if you want, you could also make a more general term called acquisition of desiccation tolerance.

Original comment by: rlwalls2008

[gocentral]

Hi Ramona,

I've added a taxon constraint to GO:0097207 bud dormancy process (only in Viridiplantae).

I'll look into your latest comment shortly.

Thanks, Paola

Original comment by: paolaroncaglia

[gocentral]

Hi Ramona, in response to your points below, I'd suggest the following:

1) I'll add "spore dormancy process" as a narrow synonym of GO:0022611 dormancy process. Should the POC feel the need for a separate new term for "spore dormancy process" later on, you may then request this along with suggestions for definition and references.

2) I would add the following new term: entry into dormancy, maintenance of dormancy, and release from dormancy, see details below:

a) GO:NEW entry into dormancy [I'd opt for this name, instead of "induction of dormancy", to parallel "entry into diapause". The only "induction" terms I see in GO are subtypes of positive regulation and/or synonyms of activation, and I'm not sure that's what you're looking for, but let me know otherwise. I'll keep induction of dormancy as a synonym.] is_a GO:0032502 developmental process part_of GO:0022611 dormancy process Def: A developmental process in which dormancy (sometimes called a dormant state) is induced. Dormancy is a suspension of most physiological activity and growth that can be reactivated. [Would you want to expand on that, and/or suggest a plant-specific definition comment?] Dbxrefs: GOC:PO_curators, PO_REF:00009 Narrow synonym: induction of dormancy

b) GO:NEW maintenance of dormancy is_a GO:0032502 developmental process part_of GO:0022611 dormancy process Def: A developmental process in which dormancy (sometimes called a dormant state) is maintained. Dormancy is a suspension of most physiological activity and growth that can be reactivated. [Would you want to expand on that, and/or suggest a plant-specific definition comment?] Dbxrefs: GOC:PO_curators, PO_REF:00009

c) GO:NEW release from dormancy is_a GO:0032502 developmental process part_of GO:0022611 dormancy process Def: A developmental process in which dormancy (sometimes called a dormant state) is broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated. [Would you want to expand on that, and/or suggest a plant-specific definition comment?] Dbxrefs: GOC:PO_curators, PO_REF:00009

If placements and definitions for these terms are approved, I'll re-position some of the existing terms accordingly (e.g. maintenance of seed dormancy would become is_a GO:NEW maintenance of dormancy). Let me know what you think.

3) Wrt GO:0048700 acquisition of desiccation tolerance: I'd rename it "acquisition of desiccation tolerance in seed", and make it a child of a new term "acquisition of desiccation tolerance", as follows:

GO:NEW acquisition of desiccation tolerance is_a dormancy process Def: The process in which tolerance to severe drying is acquired, before entering into a dry, either dormant or quiescent state. Dbxrefs: GOC:PO_curators, PO_REF:00009

GO:0048700 acquisition of desiccation tolerance in seed is_a GO:NEW acquisition of desiccation tolerance [and, therefore, child of dormancy process] is_a GO:0003006 developmental process involved in reproduction part_of GO:0010162 seed dormancy process Def: left as is Dbxrefs: GOC:PO_curators, PO_REF:00009

Would you agree with this?

Best, Paola

Original comment by: paolaroncaglia

[gocentral]

Most of what you suggested is great. I just have a few comments/suggestions.

Rather than making entry into dormancy, maintenance of dormancy, and release from dormancy part_of dormancy process, I would make them is_a dormancy process. The definition of dormancy process is "A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. " Since entry into dormancy is a developmental process in which dormancy is induced, it is logically a subtype of dormancy process. The same goes for the other two. If GO had a term for "dormancy" (rather than dormancy process), then entry into dormancy would be part_of dormancy.

It is easy to confuse dormancy (=dormant state) with dormancy process, which is the reason we felt it was important to append "process" to all of the term names. The existing definitions described the processes, not the states.

This same reasoning applies to maintenance of seed dormancy and release of seed dormancy -- they should be subtypes of seed dormancy process, not part_of. This may be problematic, because maintenance of seed dormancy would be both is_a seed dormancy process and is_a maintenance of dormancy process, plus its existing is_a parent, response to abscisic acid stimulus. Having multiple parent terms is not desirable, but it is the only logical solution based on the definitions.

Regarding the references:

PO_REF:00009 should not be used as a reference for acquisition of desiccation tolerance or acquisition of desiccation tolerance in seed.

You could use ISBN: 978-1-4051-3983-0 (Annual Plant Reviews, Volume 27, Seed Development, Dormancy and Germination) for acquisition of desiccation tolerance in seed and other seed dormancy related terms.

I will look for an appropriate reference for the general term acquisition of desiccation tolerance.

Original comment by: rlwalls2008

[gocentral]

Note for self: also see this related SF item: https://sourceforge.net/tracker/?func=detail&aid=3071821&group\_id=36855&atid=440764

Original comment by: paolaroncaglia

[gocentral]

• status: open-accepted --> open

Original comment by: paolaroncaglia

[gocentral]

Hi Ramona,

Apologies this took so long, but the 'dormancy process' ontiology node should now be all set. Here are my recent edits:

Added "spore dormancy process" as a narrow synonym of GO:0022611 dormancy process. [xrefs: GOC:PO_curators]

Added new terms:

1) GO:0097436 entry into dormancy is_a GO:0022611 dormancy process Def: The dormancy process that results in entry into dormancy. Dormancy (sometimes called a dormant state) is a suspension of most physiological activity and growth that can be reactivated. Dbxrefs: GOC:PO_curators, PO_REF:00009 Exact synonym: induction of dormancy

b) GO:0097437 maintenance of dormancy is_a dormancy process Def: The dormancy process that results in an organism remaining in dormancy. Dormancy (sometimes called a dormant state) is a suspension of most physiological activity and growth that can be reactivated. Dbxrefs: GOC:PO_curators, PO_REF:00009

c) GO:0097438 exit from dormancy is_a GO:0022611 dormancy process Def: The dormancy process that results in exit from dormancy. Dormancy (sometimes called a dormant state) is a suspension of most physiological activity and growth that can be reactivated. Dbxrefs: GOC:PO_curators, PO_REF:00009 Exact synonym: release from dormancy

Re-positioned some of the existing terms accordingly (e.g. maintenance of seed dormancy has become is_a GO:NEW maintenance of dormancy and is_a seed dormancy process)

Renamed GO:0048700 acquisition of desiccation tolerance as "acquisition of desiccation tolerance in seed", and made it is_a child of a new term "acquisition of desiccation tolerance", as follows:

GO:0097439 acquisition of desiccation tolerance is_a dormancy process Def: The process in which tolerance to severe drying is acquired, before entering into a dry, either dormant or quiescent state. Dbxrefs: GOC:PO_curators

GO:0048700 acquisition of desiccation tolerance in seed is_a GO:0097439 acquisition of desiccation tolerance is_a GO:0003006 developmental process involved in reproduction part_of GO:0010162 seed dormancy process Def: left as is Dbxrefs: GOC:PO_curators, ISBN:9781405139830

Added dbxref ISBN:9781405139830 to GO:0010162 seed dormancy process and its children.

I think this should cover everything, if not feel free to re-open this item.

Thanks! Paola

Original comment by: paolaroncaglia

[gocentral]

• status: open --> closed-accepted

Original comment by: paolaroncaglia

[gocentral]

• Group: TAIR --> Plant Ontology

Original comment by: cooperl09