POC meeting, Webex Conference Call; Date: Tuesday Jan 3rd, 2012 10am (PST)

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-20-11?

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PSDS Revisions: Whole plant development stages

Review of PO terms for gametophyte/sporophyte dormant stage

These were accepted at the POC Conf. Call 12-13-11, but we are waiting for the revisions from GO to complete them.

sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in an multicellular organism dormancy process (GO:xxxx). link to dev

comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure. Dormancy may be preceded by the senescence of plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials and by the formation of dormant buds. The end of dormancy in a sporophyte is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Resurrection plants are in a dormant stage when they become dessicated.

gametophyte dormant stage (PO:0025342): A gametophyte development stage during which a gametophyte participates in a organism dormancy process (GO:xxxx). link to dev

comment: Multicellular organism dormancy is a suspension of most physiological activity and growth that can be reactivated. This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage may be a response to environmental conditions such as seasonality or extreme heat, drought, or cold. Examples of a gametophyte dormant stage are a moss that has undergone dessication (a resurrection plant) or the female gametophyte of Ginkgo, which is dormant before fertilization. (need to check on details of Ginkgo)

Note: We can put the general term for dormancy process (GO:0022611) in the comment until a new term for organism dormancy is added.

Updates to GO terms for Dormancy Process terms:

Link to discussion on GO SF Tracker

GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.

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. (They also have a term for seed dormancy.)

proposed new definition for dormancy process: A developmental process in which a dormant state is induced, maintained or broken.

Comment: A dormant state is characterized by a suspension of most physiological activity, and in plants, a suspension of growth.

Should say dormancy, instead of dormant state.

New comment: Dormancy is a suspension of most physiological activity and growth that can be reactivated.

Will check with animal people at GO to see if comment applies only to plants and if there are other comments needed for animals.

Dormancy is defined in the comment; is different from dormancy process; sometimes called a dormant state. Need to check with GO 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 (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.

proposed new definition for seed dormancy: A dormancy process that has as participant a seed.

comment: Seed dormancy is characterized by a suspension of physiological activity that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.

should be called seed dormancy process.

Should say dormancy, instead of dormant state.

New 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.

organism dormancy (new term): A dormancy process that has as participant a whole organism.

Comment: A dormant state in an organism is characterized by a suspension of most physiological activity. In plants, organism dormancy is marked by a suspension of growth and generally involves the formation of dormant buds. These may be above ground (in woody plants), at ground level (in herbaceous plants), or underground (in plants with tubers, bulbs, corms, or perennating rhizomes). Organism dormancy in plants may be preceded by the senescence of other 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. Organism dormancy in plants is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, although environmental stimuli may not be necessary for the onset of dormancy.

should be called "multicellular organism dormancy process

New 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.

We may also want to request GO terms like bud dormancy process and spore dormancy process.

Existing synonyms

Are these actually appropriate as synonyms for sporophyte dormant stage (PO:0007132, was dormancy), which was a subtype of whole plant growth stage?

Seems like they should be synonyms of seed dormant stage, but we do not have a term for that, which is why they probably got stuck here.

10.05-seed dormant in barley

10.05-seed dormant in oat

10.05-seed dormant in Triticeae

10.05-seed dormant in wheat

10.06-viable seed germination in barley

10.06-viable seed germination in oat

10.06-viable seed germination in Triticeae

10.06-viable seed germination in wheat

10.07-seed not dormant in barley

10.07-seed not dormant in oat

10.07-seed not dormant in Triticeae

10.07-seed not dormant in wheat

They all come from GRO.

review of definitions for embryo stage and plant embryo

embryo stage

We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed embryo stage and made is_a sporophyte vegetative stage.

proposed def.:

embryo stage (PO:0007631): A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.

Comment: An embryo stage generally starts after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it begins after the division of a single cell that is not a zygote. The end of an embryo stage varies among taxa.

plant embryo

Now that we have a working term for embryo stage, we can define plant embryo in terms of the stage.

existing def. plant embryo (PO:0009009): A whole plant in the early part of a sporophytic phase after the first cell division.

proposed def. plant embryo (PO:0009009): A whole plant that participates in the embryo stage (PO:0025369).

comment (basically the same as existing comment): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.

-change from participates_in sporophyte development stage to participates_in embryo stage

We had a discussion a few weeks ago whether is better to define stages in terms of structures or structures in terms of stages. We agreed that in general, it is better to define stages in terms of structures. This works well for terms like trichome development stage which have a trichome as a primary participant. However, in the case of embryo stage (and other whole plant growth stages), the primary participant is a whole plant that is undergoing certain processes, and the stage is a more fundamental term that defines what those processes are. It would be circular to define the embryo stage as a stage that has as participant an embryo, then define the embryo as a whole plant during a certain time. Better to define the embryo stage as a stage that has as participant a whole plant that is undergoing certain processes (in this case, everything between first cell division and the other events that mark the end of embryo stage).

We agreed that in the case of embryo and zygote (and probably other whole plant stages), it is better to define the stage first, then define the whole plant as participating in that stage.

zygote stage

We already have a term "A zygotic stage" (PO:0001097), is_a embryo stage. This was renamed zygote stage and made is_a sporophyte development stage.

current def. zygote stage (PO:0001097): One cell stage that results from fertilization.

proposed def. zygote stage: A sporophyte development stage that occurs during the interval between syngamy and the first cell division.

Comment: Succeeds syngamy and precedes the embyro stage.

As with the embryo stage/embryo, RW thinks it would be better to define the stage, then define a zygote as a whole plant that participates the zygote stage, rather than the other way around.

We had some discussion of whether it was better to name this plant zygote or zygote. Zygotes in plants are the same thing as zygotes in animals, so why call them something different? Reason to name it plant zygote is to disambiguate it from terms that are named zygote in other ontologies.

RW after meeting: Embryo stage and zygote stage be probably be plant embryo stage and plant zygote stage too.

gametophyte/sporophyte senescent stage

Senescence and aging in GO

PO has the following terms: sporophyte senescent stage (PO:0007017), gametophyte senescent stage (PO:0025343), H anther senescence (PO:0001036), and 4 leaf senescence stage (PO:0001054), plus 6 ripening (PO:0007010). Rather than writing out the definition senescence in every term, we would like to be able to refer to a GO biological process term.

Go had the general term:

senescence GO:0010149: OBSOLETE. A preprogrammed process associated with the dismantling of an anatomical structure and an overall decline in metabolism. This may include the breakdown of organelles, membranes and other cellular components. An example of this process is found in Arabidopsis thaliana, when older leaves or floral organs are shed.

but, as their comment says: "This term was made obsolete because its name is ambiguous and it is covered by the two more specific terms: 'organ senescence ; GO:0010260' and 'cell aging ; GO:0007569'."

The POC needs a term for whole organism senescence, and we feel that the existing definitions of aging is not appropriate for plants, or even for GO:cell aging and GO:cellular senescence.

Revisions to existing GO terms

GO tree view:

aging

>cell aging

>>cellular senescence

>multicellular organismal aging

>organ senescence

>>leaf senescence

See References/notes, below, for source of definitions.

aging (GO:0007568)

current definition: The inherent decline over time, from the optimal fertility and viability of early maturity, that may precede death and may be preceded by other indications, such as sterility.

proposed definition: A developmental process that is a deterioration and loss of function over time.

Comment: Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death (GO:0016265) and may succeed developmental maturation (GO:0021700). May be preceded by other indications, such as sterility in animals. (RW: Isn't sterility part of aging? GO has a term for aging-dependend sterility, synonym of chromatin silencing at silent mating-type cassette.)

Note: GO:biological process already states that this applies is "pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms", and GO:developmental process states that it is a "progression of an integrated living unit... over time from an initial condition to a later condition".

We only had time for a quick discussion of senescence. Will go over it more next week.

We agreed that comment about sterility should probably come out.