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The lack of simple localization cues in genomic sequence data and annotations however leads to missing compartmentalization information for eukaryotes in automatically generated databases, such as the Pathway-Genome Databases (PGDBs) of the SRI Pathway Tools software that drives much biochemical knowledge representation on the internet.
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Others, such as inconsistent irreversibility constraints, stoichiometry errors, compound names, compartmentalization errors or missing transporters, required sequential tracing through the model to identify breakpoints and careful evaluation of the possible causes.
However, examples of this compartmentalization strategy are still missing for prokaryotes, although complex cellular architectures are also widespread among this group of organisms.
Unfortunately, sub-cellular compartmentalization information is generally missing from genome annotation data.
Thus, even if compartmentalization knowledge could be mapped to a representation system, this knowledge would necessarily be missing without manual curation.
= missing miss.
Focus on compartmentalization.
Compartmentalization of digestion.
Martin, W. Evolutionary origins of metabolic compartmentalization in eukaryotes.
But in recent decades such compartmentalization has disintegrated.
Caschera, F. & Noireaux, V. Compartmentalization of an all-E.
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