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panicle vs inflorescence #419

Closed planteome-user closed 9 years ago

planteome-user commented 12 years ago

PO has one term:

PO:0009049 ! inflorescence [SYNONYM: "Asteraceae floret" (narrow)] [SYNONYM: "capitulum" (narrow)] [SYNONYM: "catkin" (narrow)] [SYNONYM: "corymb" (narrow)] [SYNONYM: "cyme" (narrow)] [SYNONYM: "dichasium" (narrow)] [SYNONYM: "drepanium" (narrow)] [SYNONYM: "helicoid cyme" (narrow)] [SYNONYM: "inflorescencia (Spanish)" (exact)] [SYNONYM: "monochasium" (narrow)] [SYNONYM: "panicle" (narrow)] [SYNONYM: "raceme" (narrow)] [SYNONYM: "rhipidium" (narrow)] [SYNONYM: "scorpioid cyme" (narrow)] [SYNONYM: "Sorghum cob" (narrow)] [SYNONYM: "Triticeae spike" (narrow)] [SYNONYM: "umbel" (narrow)] [SYNONYM: "verticillaster" (narrow)]

TO distinguishes between them:

TO:0000014 ! panicle weight TO:0000040 ! panicle length TO:0000152 ! panicle number TO:0000201 ! panicle color TO:0000271 ! inflorescence length TO:0000547 ! primary branch number TO:0000581 ! inflorescence color TO:0000582 ! inflorescence number TO:0000583 ! inflorescence weight TO:0006028 ! inflorescence bract number TO:0011003 ! inflorescence axis color TO:0011004 ! inflorescence branch color

Reported by: cmungall

Original Ticket: obo/plant-ontology-po-term-requests/419

planteome-user commented 12 years ago

I am not sure what is wanted here. However, floret is not a synonym of inflorescence. I am not sure that verticillaster is a synonym of inflorescence.

Original comment by: dws409

planteome-user commented 12 years ago

I suppose that is because TO was created with grasses in mind, so it has some terms that are specific to grasses. For at least the past year, Dennis and I have been talking about creating an extension of the PO that describes the different inflorescence types, but who knows when it will be done! I think for the time being, it is okay to just keep inflorescence in PO, with synonym panicle. If you want to build xrefs into TO, they should link to PO:0009049 for all of the above, except maybe TO:0000547 ! primary branch number - not sure if that is referring to a branch (PO:0025073) or an inflorescence branch (PO:0009081).

Dennis is correct that "Asteraceae floret" should be removed as a synonym of inflorescence. It refers to a single flower, and we already have terms for it (disk flower and ray flower).

According to Bell and Bryan, a verticillaster is a type of pleiochasial cyme in which the branches are arranged in whorls, so it is okay to leave it here as a synonym. Beentje defines it as two opposing cymes on a stem, which is a different meaning, but does not negate our using it as a synonym for inflorescence.

Original comment by: rlwalls2008

planteome-user commented 12 years ago

I have tried to make it generic 'inflorescence...' in TO because the TO was used specifically for annotating rice and other crop/-plant traits. This was required to map the traits to ontology. However, it does have mapping to the PO term 'inflorescence' because 'panicle' is the narrow synonym. I think this is appropriate. At some point I TO will reflect the same approach as PO by being generic and all the species specific terms becoming synonyms with some exceptions.

Original comment by: jaiswalp