Utilization

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Background

For many years, GO has had terms for '[compound or element] utilization' that have posed problems because they had vague or inconsintent definitions, or no definition at all. OVer the years some have been made obsolete, but we needed to clean up the remaining few. This page serves as a record of what we've done to fix them.

These are the last-closed of several SourceForge items; the comments contain quite a bit more of the discussions that led to the eventual fix.

Utilization
Utilization pathways
Utilization and assimilation

Content standards and edits

Standardized definitions and parentage

Standard definitions and parents are based on Michelle's and Chris' comments in the SourceForge items listed above. They use the "series of processes" phrase from Chris, but follow Michelle's drafts to describe the outcome of the utilization process.

generic "standard" definition:

  • A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary X sources, [optional words] and then activates genes to scavenge the last traces of the primary X source and to transport and metabolize [optional adjective] X sources [optional: such as Y or Z]. The utilization process begins when the cell or organism detects [the substance] levels, includes the activation of genes whose products detect, transport or metabolize [the substance], and ends when [the substance] is incorporated into the cell or organism's metabolism.

Parentage now reflects two major changes:

  • Moved utilization terms out from under any metabolism parents
  • Added has_part links to detection, metabolism, and transport terms

As of this writing (2010-03-08), the utilization terms are direct is_a children of biological process, and the biggest remaining question is whether they can have any more specific is_a parent.

Example stanzas

[Term]
id: GO:0009758
name: carbohydrate utilization
namespace: biological_process
def: "A series of processes that forms an integrated mechanism by which a cell or an organism 
detects the depletion of primary carbohydrate sources,usually glucose, and then activates genes 
to scavenge the last traces of the primary carbohydrate source and to transport and metabolize 
alternate carbohydrate  sources. The utilization process begins when the cell or organism detects 
carbohydrate levels, includes the activation of genes whose products detect, transport or 
metabolize carbohydrates, and ends when the carbohydrate is incorporated into the cell or 
organism's metabolism." [GOC:mah, GOC:mlg]
is_a: GO:0008150 ! biological_process
relationship: has_part GO:0005975 ! carbohydrate metabolic process
relationship: has_part GO:0008643 ! carbohydrate transport
relationship: has_part GO:0009730 ! detection of carbohydrate stimulus

[Term]
id: GO:0015976
name: carbon utilization
namespace: biological_process
alt_id: GO:0015978
def: "A series of processes that forms an integrated mechanism by which a cell or an organism 
detects the depletion of primary carbon sources and then activates genes to scavenge the last 
traces of the primary carbon source and to transport and metabolize alternative carbon source. 
The utilization process begins when the cell or organism detects carbon levels, includes the 
activation of genes whose products detect, transport or metabolize carbon-containing substances, 
and ends when carbon is incorporated into the cell or organism's metabolism." [GOC:mah]
subset: goslim_pir
subset: gosubset_prok
synonym: "carbon utilization by utilization of organic compounds" EXACT [GOC:mah]
synonym: "heterotrophy" EXACT []
xref: Wikipedia:Heterotroph
is_a: GO:0008150 ! biological_process
relationship: has_part GO:0008152 ! metabolic process
relationship: has_part GO:0071702 ! organic substance transport
relationship: has_part GO:0071703 ! detection of organic substance

Additional notes

  • A few utilization terms were merged into the corresponding metabolism or catabolism parent:
arabitol catabolic process GO:0051157
  [i] arabitol utilization GO:0019591 (this term had no annotations)

glucose 1-phosphate metabolic process GO:0019255
  [i] glucose 1-phosphate utilization GO:0006008

glucose 6-phosphate metabolic process GO:0051156
  [i] glucose 6-phosphate utilization GO:0006010
  • One thing not done: no terms were renamed. Large parts of the previous rounds of discussion focused on whether we should add one or more words to the 'utilization' term names so they won't be mistaken for metabolism terms, and if so, what to add. We unequivocally rejected 'pathway' and 'network' for good reasons, and didn't reach agreement on 'system'. In the end we decided to leave the names as they are, because the text definition and has_part relationships should provide strong indications of how the utilization terms differ from metabolism terms.
  • Added grouping terms for carbon compound transport and metabolism ('organic substance transport' and 'organic substance metabolic process' respectively). Note that ChEBI defines 'organic molecular entity' as 'A molecular entity that contains carbon', so we can say organic compound (or substance) = carbon compound (or carbon-containing substance) in GO and rearrange existing links accordingly. (I'll also make a note of this on the GOCHE page. -m)
  • Could add terms for phosphorus-containing substance transport & detection, sulfur-containing substance transport & detection, and nitrogen compound detection (but haven't yet).
  • Consider possibly merging 'sugar utilization' into 'carbohydrate utilization'.

Annotation recommendations

  • Genes that are activated in the presence of the 'utilized' substance, such as those whose products detect the substance in low concentrations, would be annotated with this term. Note that many would also have annotations with the "regular" metabolic terms