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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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seed growth not an organ growth #10215

Closed gocentral closed 9 years ago

gocentral commented 11 years ago

Seed growth (GO:0080112) is_a organ growth (GO:0035265), but seed is not an organ in the PO. In PO, seed (PO:0009010) is_a multi-tissue plant structure (PO:0025496). Seeds are not traditionally considered plant organs.

Multi-tissue plant structure follows the proposed new term in CARO2, but you may want to wait until CARO2 is released before you adopt this for GO.

Reported by: rlwalls2008

Original Ticket: geneontology/ontology-requests/10012

gocentral commented 11 years ago

Original comment by: tberardini

gocentral commented 11 years ago

growth subclasses have a bit of a mix and match feel:

..is_a GO:0040007 ! growth *** ...is_a GO:0003241 ! growth involved in heart morphogenesis ...is_a GO:0007117 ! budding cell bud growth ...is_a GO:0016049 ! cell growth ...is_a GO:0030447 ! filamentous growth ...is_a GO:0035264 ! multicellular organism growth ...is_a GO:0035265 ! organ growth ...is_a GO:0044110 ! growth involved in symbiotic interaction ...is_a GO:0048589 ! developmental growth ...is_a GO:0055017 ! cardiac muscle tissue growth ...is_a GO:0080189 ! primary growth ...is_a GO:0080190 ! lateral growth

I don't think GO will ever materialize growth/dev classes for many upper CARO classes. But it would be good to tame the beast here. And I think "organ" is a bit useless, no one agrees what an organ is, the CARO1 attempt to define organ was not successful.

You could go with:

structure DisjointUnion cell part, cell, gross structure

(not sure about the naming)

as soon as you start splitting gross structure it starts getting hard

Original comment by: cmungall

gocentral commented 11 years ago

Seed growth: The increase in size or mass of a seed. Seed is a propagating organ formed in the reproductive cycle of gymnosperms and angiosperms, derived from the ovule and enclosing an embryo.

Will need to modify the definition as well if seed != organ. Probably not the entire PO def but a derivative of it instead. I'll move 'seed growth' up one level to be a direct child of 'growth.

PO def: A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).

Original comment by: tberardini

gocentral commented 11 years ago

It may be of limited relevance to GO users, but seeds also occured in extinct seed plants that are neither gymnosperms or angiosperms (e.g., seed ferns). You could say they are found in spermatophytes.

Original comment by: rlwalls2008

gocentral commented 11 years ago

Moved parentage and modified definition to read: The increase in size or mass of a seed. A seed is a propagating organ formed in the reproductive cycle of a spermatophyte, derived from the ovule and enclosing an embryo.

Original comment by: tberardini

gocentral commented 11 years ago

Original comment by: tberardini