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Posts: 66
Location:
Manchester
Registered:
October 2007
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Re: A Level 3 extension for Constraint Based models
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22 Mar '11 10:53
 
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> You mention that (e.g.) a ChEBI annotation could conflict with
> fba:chemicalEquation. The same annotation could conflict with fba:charge.
In principle yes. There also a possibility that these can be dealt with
in the Annotation proposal. Currently, the L2 attribute charge is used
in this way so we took the pragmatic route. Can chEBI represent these
two properties at different pH's for all the compounds in genome scale
models ... ?
No. ChEBI is too incomplete to represent everything. Also, relying on ChEBI means that the id must be looked-up somehow to extract the formula and charge. So I'm on favour of encoding this information explicitly.
However, as Brett points out, this could be done with Annotations if we introduced the predicates "charge" and "formula".
As far as potential inconsistencies go, this problem exists already. We could take a species that clearly is glucose and incorrectly annotate it to be some bonkers lipid. We could also annotate it to be a KEGG Pathway. These things aren't currently checked in any way, and I don't think that we need to start worrying about policing the use of annotations. If we did, it would be a job for software, not the core or fba extension itself.
Cheers,
Neil.
On 22 Mar 2011, at 15:56, "Brett G. Olivier" <brett.olivier@falw.vu.nl> wrote:
>> You mention that (e.g.) a ChEBI annotation could conflict with
>> fba:chemicalEquation. The same annotation could conflict with fba:charge.
>
> In principle yes. There also a possibility that these can be dealt with
> in the Annotation proposal. Currently, the L2 attribute charge is used
> in this way so we took the pragmatic route. Can chEBI represent these
> two properties at different pH's for all the compounds in genome scale
> models ... ?
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