TAIR process terms-11/04/03

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Hi ,

I am attaching some process terms from TAIR. Please give me your feedback on this. Thanx Suparna

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/1285":https://sourceforge.net/p/geneontology/ontology-requests/1285

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Original comment by: smundodi

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Forgot to check the attach box. Ok, here it is now.

Original comment by: smundodi

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Please give me any feedback by friday11/07/03 because I plan on adding these terms to GO on monday am. Thanx

Suparna

Original comment by: smundodi

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- sucrose mediated signaling : that structure looks fine.

- cytokinin transport : you could add a bit more blurb about cytokinins to the def; eg. The directed movement of cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators, into, out of, within or between cells. (from the cytokinin metabolism def).

- response to phytotoxin : It looks as though phytotoxin can either mean 'toxin substance produced by a plant' or 'substance that is toxic to plants' (see www.onelook.com for a range of defs). In the def you've specified "a phytotoxin, a toxic chemical substance produced by microbes and is toxic to plants.", which is fine, but are all phytotoxins produced by microbes? Also, the second part of the sentence probably needs a "which" in it.

- mucilage utilization : what is your planned def for this term? IIRC there still hasn't been any decision made on the 'utilization' terms, so it might be an idea to propose a def to see another term name might be appropriate.

- microRNA synthesis : was this supposed to be microRNA biosynthesis? Could do with some more explanation of what microRNA is.

- polar nuclei fusion : could the def be reworded so that it refers more directly to the term? The same could be done with synergid cell death.

There are also some typos and errant capital letters in the defs but I presume they'll be ironed out before going into the ontologies!

Cheers, Amelia.

Original comment by: jenclark

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Hi Jen,

Thanx for looking into these. Will fix the typos when I add them to GO. My comments below.

-regarding phytotoxin, may be I can change the term to "response to microbial phytotoxin"? So if people come across other phytotoxins as you mentioned, they can add the others and define them accordingly.

utilization term-I would leave this out for now until the decision is made on this.

New definitions: microRNA synthesis ISA microRNA metabolism (NEW) ISA RNA metabolism GO:0016070 Def: The formation from simpler components of microRNA, which are a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity .

polar nuclei fusion PART OF female gametophyte development GO:0009553 Def: Polar nuclei refers to two nuclei, contained within the same cell, that are created from the mitotic division of the megaspore during angiosperm reproduction. Fusion of the polar nuclei, which takes place in the ovule, resulting in the fusion nucleus and giving rise to endosperm when fertilized.

If you have any better alternatives for these definitions, let me know. If you agree with what I suggested, I will add these terms to GO by the end of this week.

Suparna

Original comment by: smundodi

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Hi Suparna,

- 'response to microbial phytotoxin' is a good fix for the phytotoxin problem.

- microRNA synthesis (should it be biosynthesis or is synthesis correct?) - looks good.

- for the polar nuclei fusion def, perhaps if you swapped the sentences around thus: "The merging of the polar nuclei, the two nuclei contained within the same cell that are created from the mitotic division of the megaspore during angiosperm reproduction. Polar nuclear fusion takes place in the ovule, forming in the fusion nucleus and giving rise to the endosperm when fertilized."

That sounds fine otherwise! Amelia.

Original comment by: girlwithglasses

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added all the terms with definitions.

Original comment by: smundodi

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• status: open --> closed

Original comment by: smundodi