TAIR process terms -February, 2006

[gocentral]

Hi,

Here is a new set of process terms I would like to add to the process ontology. Development terms are submitted as new item for the sake of convenience. Your feedback is appreciated.

Thanx

Suparna

1.tricyclic triterpenoid biosynthesis ISA triterpenoid biosynthesis GO:0016104 Def: The formation from simpler components of tricyclic triterpenoid compounds,terpenoids with 6 isoprene units and 3 carbon rings. Ref: TAIR:ct

2.medium-chain fatty acid metabolism ISA fatty acid metabolism GO:0006631 Def: The chemical reactions involving fatty acids with a chain length of 8 carbons to 11 carbons. Ref: TAIR:tb

3.phytate biosynthesis ISA biosynthesis GO:0009058 Def: The formation from simpler components of phytic acid,phytate/hexakisphosphate inositol, a regulator of intracellular signaling, a highly abundant animal anti-nutrient and a phosphate and mineral storage compound in plant seeds. Ref: PMID:16107538

4.SCF complex assembly ISA protein complex assembly GO:0006461 Def: The aggregation and bonding together of a set of components to form the SKP1-Cullin/Cdc53-F-box protein ubiquitin ligase (SCF) complex. Ref: TAIR:pz

5.response to vitamin B1 ISA response to nutrient GO:0007584 Def: A change in state or activity of a cell or an organism (in terms of movement,secretion, enzyme production, gene expression, etc.) as a result of a vitamin B1 stimulus. Ref: TAIR:pz

6.RNA interference, production of ta-siRNAs ISA RNA interference, production of siRNA GO:0030422 Def: Cleavage of double-stranded RNA to form trans- acting small interfering RNA molecules (siRNAs) of 21- 23 nucleotides. ta-siRNAs arise from PolII genes and function like miRNAs to guide cleavage of target mRNAs. Ref: TAIR:tb PMID:16129836

[Ps: ta-siRNAs are one of several classes of siRNAs that form through distinct characterized pathways. This is why I decided to have a separate term instead of the parent, more generic siRNAs one.]

7.brassinosteroid homeostasis ISA homeostasis GO:0042592 Def: Any of the processes involved in the maintenance of an internal equilibrium of brassinosteroids within an organism or cell. Ref: PMID: 15908602

8.response to selenium ion ISA response to metal ion
GO:0010038 Def: A change in state or activity of a cell or an organism (in terms of movement,secretion, enzyme production, gene expression, etc.) as a result of a stimulus from selenium ion. Ref: TAIR:mg

9.photosystem II oxygen evolving complex assembly ISA photosystem II assembly GO:0010207 Def: Formation of the oxygen evolving complex (OEC) of photosystem II on thylakoid membrane. In plants, the photosystem II OEC consists of three extrinsic nuclear-encoded polypeptides: PsbO, PsbP and PsbQ; and protects the CaMn4 cluster bound to D1 and CP43 proteins. Ref: PMID:16282331 Exact Synonym: OEC (PSII) ASSEMBLY

10.regulation of chlorophyll catabolism ISA chlorophyll catabolism GO:0015996 Def: Any process that modulates the frequency, rate or extent of the breakdown into simpler components of chlorophyll. Ref: PMID:16361392

11.response to silver ion ISA response to metal ion
GO:0010038 Def: A change in state or activity of a cell or an organism (in terms of movement,secretion, enzyme production, gene expression, etc.) as a result of a silver ion stimulus. Ref: PMID: 16367966

12.detoxification of copper ion ISA response to copper ion GO:0046688 ISA response to toxin GO:0009636 Def: The processes that reduce or remove the toxicity of copper ion. These include transport of copper away from sensitive areas and to compartments or complexes whose purpose is sequestration of copper ion. Ref: PMID: 16367966

13.hydrotropism ISA tropism GO:0009606 Def: Growth or movement in a sessile organism toward or away from water, as of the roots of a plant. Ref: ISBN:0-395-82517-2

14.NAD(P)H dehydrogenase complex assembly (NEW) ISA protein complex assembly GO:0006461 Def: The formation of NAD(P)H dehydrogenase complex, which is involved in electron transport from an unidentified electron donor, possibly NAD(P)H or ferredoxin(Fd) to the plastoquinone pool. Ref: TAIR:sm

Reported by: smundodi

Original Ticket: "geneontology/ontology-requests/3220":https://sourceforge.net/p/geneontology/ontology-requests/3220

[gocentral]

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=436423

2. We have GO:0051791 : medium-chain fatty acid metabolism (may have been added since this item was opened).

3. Ask Nick Stover to take a look (tho I didn't actually spot any problems).

The rest look fine to me.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=614564

Added all the terms here. Never received any feedback from Nick Stover and hence went ahead and added the term as it is represented above.

Suparna

Original comment by: smundodi

[gocentral]

• status: open --> closed

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=614564

Added all the terms here. Never received any feedback from Nick Stover and hence went ahead and added the term as it is represented above.

Suparna

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=473890

Hi,

I just checked with Nick and he says that the term is fine.

However, especially after some of the discussion at the recent GO meeting, I think when someone has specifically been mentioned for getting feedback, it's not necessarily appropriate to proceed without making another effort to get their comments. Nick happened to be out of town that week.

-Karen

Original comment by: krchristie

[gocentral]

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Hi,

In response to Karen's email regarding contacting Nick Stover, I had written to Nick soon after I got a comment from Midori suggesting to ask his advice. I never heard back from him and I resent the email and no luck. I am not sure how much more should I be trying...I don't think he was gone since february.

Suparna

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=473796

Hi Suparna,

What are the IDs of the terms you added? I need them for the monthly reports. :)

Thanks! Amelia.

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=614564

Hi Amelia,

Here are the terms. Thanx

GO:0010263 SM tricyclic triterpenoid biosynthesis GO:0010264 SM phytate biosynthesis GO:0010265 SM SCF complex assembly GO:0010266 SM response to vitamin B1 GO:0010267 SM RNA interference, production of ta- siRNAs GO:0010268 SM brassinosteroid homeostasis GO:0010269 SM response to selenium ion GO:0010270 SM photosystem II oxygen evolving complex assembly GO:0010271 SM regulation of chlorophyll catabolism GO:0010272 SM response to silver ion GO:0010273 SM detoxification of copper ion GO:0010274 SM hydrotropism GO:0010275 SM NAD(P)H dehydrogenase complex assembly

Original comment by: smundodi

[gocentral]

Logged In: YES user_id=473796

Thank you kindly!

Original comment by: girlwithglasses

[gocentral]

• milestone: --> TAIR
• status: closed --> closed-accepted

Original comment by: girlwithglasses

[gocentral]

Logged In: YES user_id=473890

When I checked with Nick about this, he said he hadn't ever gotten an email about this, so perhaps they went astray or there was an error in his address or something.

In any case, this highlights one of the main reasons why I think each separate term should get its own SF item. That way people can read the summary email or list on the web page and see which items affect areas they are interested in.

-Karen

Original comment by: krchristie