Created "OMP:0000311 amino acid biosyntheis phenotype" a child of "OMP:0000310 small molecule biosynthesis phenotype" (a child of "OMP:0000309 biosynthetic phenotype" which also now is parent to "OMP:0000306 macromolecular biosynthesis phenotype"). The question I have is this: what is "extracellular accumulation"? Does this mean something is taken up from the outside? Does this mean that it is not secreted? Do these have to actually do with biosynthesis? I suggest we do a live discussion of this term.
Marcus
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During some metabolic processes, metabolites are exported outside the cell as a way to store the substance for later and subsequently imported as needed. For instance, E.coli will export acetate into the media during times when other preferred nutrients are available and will then take the acetate back up later as other carbon sources get depleted.
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Suggested revision of definition for OMP:0000252 A metabolic phenotype that deals with the intracellular or extracellular accumulation of small molecules, which may be intermediates or end products of metabolism.
The following child terms are needed:
extracellular accumulation of metabolite
intracellular accumulation of metabolite
altered accumulation of metabolite
decreased accumulation of metabolite
abolished accumulation of metabolite
increased accumulation of metabolite
Note: The chemical that is accumulated will be indicated in the annotation extension field using the CHEBI id.
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Suvi, I discovered another term in the ontology OMP:0000192 chemical production phenotype that seems to refer to the same sort of phenotypes as OMP:0000252. Maybe we will have time in the group call next week to discuss whether these are duplicate terms or if there are separate phenotypes.
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Created "OMP:0000311 amino acid biosyntheis phenotype" a child of "OMP:0000310 small molecule biosynthesis phenotype" (a child of "OMP:0000309 biosynthetic phenotype" which also now is parent to "OMP:0000306 macromolecular biosynthesis phenotype"). The question I have is this: what is "extracellular accumulation"? Does this mean something is taken up from the outside? Does this mean that it is not secreted? Do these have to actually do with biosynthesis? I suggest we do a live discussion of this term.
Marcus
During some metabolic processes, metabolites are exported outside the cell as a way to store the substance for later and subsequently imported as needed. For instance, E.coli will export acetate into the media during times when other preferred nutrients are available and will then take the acetate back up later as other carbon sources get depleted.
Suggested revision of definition for OMP:0000252 A metabolic phenotype that deals with the intracellular or extracellular accumulation of small molecules, which may be intermediates or end products of metabolism.
The following child terms are needed:
extracellular accumulation of metabolite
Note: The chemical that is accumulated will be indicated in the annotation extension field using the CHEBI id.
Suvi, I discovered another term in the ontology OMP:0000192 chemical production phenotype that seems to refer to the same sort of phenotypes as OMP:0000252. Maybe we will have time in the group call next week to discuss whether these are duplicate terms or if there are separate phenotypes.