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spore and embryo dormant stages #426

Open planteome-user opened 12 years ago

planteome-user commented 12 years ago

At the POC meeting on 1-3-12, we discussed the need for new terms for spore dormant stage and embryo dormant stage. I suggest we add these new terms.

(see new tracker for plant spore stage: https://sourceforge.net/tracker/?func=detail&aid=3469811&group\_id=76834&atid=835555)

proposed definition, plant spore dormant stage: A gametophyte dormant stage during which a spore participates in a dormancy process. Comment: A dormancy process (GO:0022611) is 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.

is_a gametophyte dormant stage, has_participant spore

If we make plant spore stage XP of is_a gametophyte development stage and has_participant spore, this will be inferred to be is_a plant spore stage.

We should probably rename spore to plant spore.

proposed definition, plant embryo dormant stage: A sporophyte dormant stage during which a plant embryo participates in a dormancy process. Comment: A dormancy process (GO:0022611) is 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. In seed plants, a plant embryo dormant stage may be part of a seed dormant stage.

is_a sporophyte dormant stage, has_participant plant embryo

If we make plant embryo stage XP of is_a sporophyte development stage and has_participant plant embry, this will be inferred to be is_a plant embryo stage.

We should also add seed dormant stage (new term, see tracer) has_ part plant embryo dormant stage. Can't add the inverse part_of relation, because not all embryo dormancy occurs in seeds.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/426

planteome-user commented 12 years ago

New terms added: PO:0025376, plant spore dormant stage PO:0025377, plant embryo dormant stage

Original comment by: rlwalls2008

planteome-user commented 12 years ago

At the POC meeting on 1-17-12, we agreed to add these terms.

Original comment by: rlwalls2008

planteome-user commented 10 years ago

I suggest that plant embryo dormant stage be a subclass of mature plant embryo stage (PO:0001081).

See https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=3#ff84

Original comment by: rlwalls2008

planteome-user commented 10 years ago

New proposed definition:

plant embryo dormant stage (PO:0025377): A mature plant embryo stage (PO:0001081) during the interval between when a plant embryo (PO:0009009) begins a dormancy process (GO:0022611) and one of the following: the beginning of the seed germination stage (PO:0007057) in seed plants, formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes, or the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).

Comment: During a plant embryo dormant stage, a plant embryo participates in a dormancy process, but not all plant embryos have a dormant stage. A dormancy process (GO:0022611) is 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. In seed plants, a plant embryo dormant stage may be part of a seed dormant stage.

Note: plant embryo dormant stage is currently a subclass of sporophyte dormant stage, which is correct. We would need to add a logical definition to sporophtyte dormant stage (XP is_a sporophyte development stage XP participates in GO:dormancy processs) in order to infer that plant embryo dormant stage is_a sporophyte dormancy process if we used this new definition. As we can't do that just yet, I suggest leaving it with two is_a parents.

Original comment by: rlwalls2008

planteome-user commented 9 years ago

Agreed, makes sense.Will look at the definition.

Original comment by: cooperl09