propanediol utilization

[gocentral]

Hello,

I would like to request a new term.

term: 'propanediol utilization' def: The use of propanediol in metabolic reactions to produce useful compounds for the cell. parent: GO:0019751 'polyol metabolism' type: process

I couldn't find any other "utilization" term with a definition, so I made this one up - its not very good.

Thanks, Michelle

Reported by: mlgwinn

Original Ticket: "geneontology/ontology-requests/1866":https://sourceforge.net/p/geneontology/ontology-requests/1866

[gocentral]

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Hi Michelle,

I've added this term with a def similar to the only other defined utilization term, and I've opened a sourceforge item for discussion of a better standard def. [ 1004636 ] utilization standard def

< id: GO:0048504 < name: propanediol utilization < namespace: process < def: "Processes that involve propanediol sensing\, propanediol transportation and propanediol metabolism\, and lead to the utilization of propanediol." [TIGR:mlg] < is_a: GO:0019751

Do you have a reference for propanediol? The only dictionary reference I can find is really vague and claims it's to do with antifreeze.

Thanks,

Jen

Original comment by: jenclark

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Original comment by: jenclark

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Original comment by: girlwithglasses

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I don't think this term should have been added - it needs to be given some more thought. There is already an item open about terms with utilization in the term string, as they all seem to mean something different and the whole concept is ambiguous.

Original comment by: girlwithglasses

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Oh right. Thanks for telling me. Shall I remove it again?

Jen

Original comment by: jenclark

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Yes, looking at that other item it sounds as if the term should be a bit different. I will obsolete that one and start again.

Jen

Original comment by: jenclark

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I have obsoleted that term and will leave this item to wait for a conclusion to the discussion in [ 710180 ] Utilization

> id: GO:0048504 > name: propanediol utilization > namespace: process > def: "OBSOLETE. Processes that involve propanediol sensing\, propanediol transportation and propanediol metabolism\, and lead to the utilization of propan ediol." [TIGR:mlg] > comment: This term was made obsolete because it is an inaccurate representation of the intended concept. To update annotations\, consider the children of the molecular function term 'metabolism ; GO:0008152.' > is_obsolete: true

Jen

Original comment by: jenclark

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This term was actually removed entirely, because the file was reverted in cvs to the point before the term was put in in the first place.

Jen

Original comment by: jenclark

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Hi, OK, how about we change it to "propanediol catabolism". I guess we would then need a "propanediol metabolism" which would be its parent and the parent of the new metabolism term would be "polyol metabolism" GO:0019751. A second parent of "propanediol catabolism" would be "polyol catabolism".

I realize that the "utilization" issue is not resolved, but this should bypass that. In fact in the paper I read on this, "degradation" and "utilization" are both used so we'll go with "degradation".

Here is the reference for the paper: PMID:10498708

The new defintion could be "The breakdown into simpler components of propanediol."

Would this work?

Michelle

Michelle

Original comment by: mlgwinn

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Hi Michelle,

That sounds good to me. I'll check with Amelia before implementing it.

Jen

Original comment by: jenclark

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Jen,

Propanediol metabolism and catabolism terms would be fine. Michelle's
suggested parentage is good too.

A.

Original comment by: jenclark

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Hi Michelle,

I also have to find a definition of propanediol to add to the term definitions. How does this seem?

Propanediol, C3H8O2, a colorless viscous practically odorless liquid, miscible with water, acetone, and chloroform; and soluble in ether. synonym: propylene glycol metabolism (or catabolism) http://cerhr.niehs.nih.gov http://toxnet.nlm.nih.gov

Jen

Original comment by: jenclark

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Original comment by: jenclark

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That sounds fine to me.

Thanks, Michelle

Original comment by: mlgwinn

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Hi Jen,

Is this term ready to go in now?

Thanks, Michelle

Original comment by: mlgwinn

[gocentral]

• status: open --> closed-accepted

Original comment by: girlwithglasses

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Terms added: propanediol metabolism, GO:0051143 propanediol catabolism, GO:0051144

Original comment by: girlwithglasses

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Original comment by: girlwithglasses