Utilization

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In component:

1. Chylomicron.

Chylomicrons are the largest lipoprotein complexes with the lowest protein-to-lipid ratio. They are present in the blood or lymph and transport exogenous (dietary) cholesterol, triacylglycerols and other lipids from the intestine to the liver or to the adipose tissue.

new term?

In process:

2. Citrate utilization.

Protein which allows the utilization of the 6-carbon tricarboxylic acid citrate as a sole source of carbon and energy.

new term?

3. Copulatory plug formation

Protein involded in the formation of the copulatory plug, a plug composed of a number of proteins which are secreted by the seminal vesicle under the influence of testosterone. Found in rodents.

new term?

4. Response to cycloheximide - new term?

Reported by: jl242

Original Ticket: "geneontology/ontology-requests/721":https://sourceforge.net/p/geneontology/ontology-requests/721

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I've added 'response to cycloheximide ; GO:0046898' under response to antibiotic.

No. 5 above should be cytochrome c-type biogenesis

Protein involved in the biogenesis of c-type cytochromes. Cytochromes c are electron transfer proteins having one or several heme c groups, bound to the protein by one, or more commonly two, thioether bonds involving sulphydryl groups of cysteine residues.

Original comment by: girlwithglasses

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1. Added 'chylomicron ; GO:0042627' as a part_of child of extracellular with defintion:

'A particle composed of a central core of triglycerides surrounded by a protein-phospholipid coating. Chylomicrons are found in blood or lymph and carry lipids from the intestines into other body tissues.'

2. Still working on this.

3. Added 'mating plug formation ; GO:0042628' as is_a child of post-mating behavior, synonym: 'copulatory plug formation' Defintion:

'The deposition of a plug of sperm or other gelatinous material into the opening of the vulva by a male at the termination of copulation. Probably acts to prevent subsequent matings by other males.'

5. Because cytochromes are basically modified proteins, we can't add cytochrome c-type biogenesis or biosynthesis - this will eventually be a case for slots. Instead, I would use instead 'cytochrome biogenesis' or 'cytochrome c-heme linkage' - probably the latter.

Original comment by: jl242

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• assigned_to: nobody --> jl242

Original comment by: jl242

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• summary: Terms for Swiss-Prot --> Utilization

Original comment by: girlwithglasses

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Re: utilization. There seems to be no standard way to define this term - it's just a process that 'uses' a substance in some way. My recommendation would be to obsolete all the utilization terms and replace them with more descriptive terms (eg. xxx catabolism, xxx transport, or whatever). Easy for me to say, I know, but at the moment, we have lots of different meanings for 'utilization' in the ontologies and nothing standardized.

Original comment by: girlwithglasses

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Some of the utilization terms represent MetaCyc pathways and can easily be renamed 'catabolism': GO:0019508 2,5-dihydroxypyridine utilization - MetaCyc:PWY-722 == maleamate p'way - 2,5-dihydroxypyridine catabolized to fumarate via maleamate GO:0019591 arabitol utilization GO:0019528 D-arabitol utilization - DARABITOLUTIL-PWY == D-arabitol degradation GO:0019590 L-arabitol utilization - LARABITOLUTIL-PWY == L-arabitol and xylitol degradation GO:0019697 L-xylitol utilization - LARABITOLUTIL-PWY == L-arabitol and xylitol degradation

All chemicals mentioned above will need metabolism terms adding.

GO:0019488 ribitol utilization - MC:RIBITOLUTIL-PWY == ribitol degradation to xylulose-5-P. Ribitol catabolism already exists so this term can be renamed 'ribitol catabolism to xylulose-5-phosphate'.

None of the above terms have any annotations.

-- 5 annotations to GO:0006008 glucose 1-phosphate utilization (all phosphoglucomutase) 11 annotations to GO:0006010 glucose 6-phosphate utilization (some phosphoglucomutases, some glucose-6-P dehydrogenases)

These two terms should be obsoleted. Phosphoglucomutase interconverts between gluc-1-P and gluc-6-P, so these annotations can be moved up to the parent terms. Gluc-6-P dehydrogenase is the first step of the Entner-Doudoroff p'way, so those annotations can go to gluc-6-P metabolism and the Entner-Doudoroff p'way term.

-- 7 annotations to GO:0019427 acetate utilization - all acetyl-CoA synthetase - ACETATEUTIL-PWY, HAMAP:MF_01123] The MetaCyc pathway refers to the interconversion of acetate, acetyl- CoA and acetylphosphate. Probably the best solution is to rename this term 'acetyl-CoA biosynthesis from acetate' (which can be either direct or via acetylphosphate).

that's some of the utilization terms dealt with!

Original comment by: girlwithglasses

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Some new terms added in the process ontology: glucose 6-phosphate metabolism, GO:0051156 arabitol catabolism, GO:0051157 L-arabitol catabolism, GO:0051158 D-arabitol catabolism, GO:0051159 L-xylitol catabolism, GO:0051160 arabitol metabolism, GO:0051161 L-arabitol metabolism, GO:0051162 D-arabitol metabolism, GO:0051163 L-xylitol metabolism, GO:0051164 2,5-dihydroxypyridine metabolism, GO:0051165 2,5-dihydroxypyridine catabolism, GO:0051166 xylulose 5-phosphate metabolism, GO:0051167

name changes: GO:0019427: name has changed from "acetate utilization" to "acetyl-CoA biosynthesis from acetate". GO:0019488: name has changed from "ribitol utilization" to "ribitol catabolism to xylulose 5-phosphate". GO:0019508: name has changed from "2,5-dihydroxypyridine utilization" to "2,5-dihydroxypyridine catabolism to fumarate". GO:0019528: name has changed from "D-arabitol utilization" to "D- arabitol catabolism to xylulose 5-phosphate". GO:0019590: name has changed from "L-arabitol utilization" to "L- arabitol catabolism to xylulose 5-phosphate". GO:0019697: name has changed from "L-xylitol utilization" to "L-xylitol catabolism to xylulose 5-phosphate".

'arabitol utilization' will need to be obsoleted.

Original comment by: girlwithglasses

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Several of the other utilization terms look like they've just been used as 'metabolism' terms, so they could be obsoleted and annotations directed to the parent metabolism term:

6 annotations to GO:0006791 sulfur utilization MIPS:01.02.01 nitrogen and sulfur utilization ==> sulfur metabolism ; GO:0006790

0 annotations to GO:0006794 phosphorus utilization MIPS:01.04.01 phosphate utilization ==> phosphorus metabolism ; GO:0006793

17 annotations to GO:0019740 nitrogen utilization ==>nitrogen metabolism ; GO:0006807

39 annotations to GO:0006808 regulation of N utilization lots of 'nitrogen regulation proteins' annotated to this term. Prob need to create new 'regulation of nitrogen metabolism' terms..

1 annotation to GO:0007587 sugar utilization InterPro:IPR003469, Pfam:PF02435 - glycosylhydrolase (hydrolyse the glycosidic bond between carbohydrates, or between a carbohydrate and a non-carbohydrate moiety) The parent term is 'digestion', so I would guess this term was supposed to mean sugar breakdown or possibly organismal carbohydrate metabolism. ==>carbohydrate metabolism ; GO:0005975 (sugar metabolism can be added if necessary)

10 annotations to GO:0015976 carbon utilization GenProtEC: 1.1 carbon compound utilization MIPS: 01.05.01 C-compound and carbohydrate utilization ==>This has been used for annotating carbonic anhydrases (involved in recycling carbon dioxide); the children are either to do with carbon fixing or organic compound metabolism. Propose new term 'organic compound metabolism'.

11 annotations to GO:0015977 carbon utilization by fixation of carbon dioxide ==>this would probably be best renamed 'carbon fixation' or 'carbon dioxide fixation', since all the children are examples of carbon fixing possible def: The conversion of inorganic carbon, usually atmospheric carbon dioxide, to organic carbon compounds, such as carbohydrates.

2 annotations to GO:0015978 carbon utilization by utilization of organic compounds ==>This term really just means metabolism of organic (or carbon- containing) compounds. Add new term 'organic compound metabolism'?

1 annotation to GO:0009758 carbohydrate utilization def: Series of processes that involve carbohydrate sensing, carbohydrate transportation and carbohydrate metabolism which lead to the utilization of carbohydrates. ==> It's really carbohydrate metabolism ; GO:0005976, carbohydrate transport ; GO:0008643, detection of carbohydrate stimulus ; GO:

9730. There isn't a single term which can really be used to encompass all these concepts (although the new metabolism def may well cover this a little better) so just suggest obsoleting it.

Original comment by: girlwithglasses

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• assigned_to: jl242 --> girlwithglasses

Original comment by: jl242

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Hi,

This item has been open for a long time. Please comment to let us know whether you would like it to remain assigned to you, or would prefer it to be reassigned. (You don't necessarily have to work on it immediately if you keep it; we just need to know whether it's still on your list.)

Thanks, Midori & David Ontology development group managers

Original comment by: mah11

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Original comment by: mah11

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MAH & DPH to work on this and SF 1052024 together https://sourceforge.net/tracker/index.php?func=detail&aid=1052024&group\_id=36855&atid=440764

Original comment by: mah11

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• assigned_to: nobody --> gomidori

Original comment by: mah11

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Now fixed! Details in log file for go/ontology/editors/gene_ontology_write.obo revision 1.1076 and on wiki at http://wiki.geneontology.org/index.php/Utilization.

Original comment by: mah11

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• status: open --> closed-fixed

Original comment by: mah11