Abstract
Many databases propose their own structure and format to provide data describing biological processes. This heterogeneity contributes to the difficulty of large systematic and automatic functional comparisons. To overcome these problems, we have used the Bio formal description scheme which allows multi-level representations of biological process information. Applied to the description of the tricarboxylic acid cycle (TCA), we show that Bio allows the formal integration of functional information existing in current databases and make them available for further automated analysis. In addition such a formal TCA cycle process description leads to a more accurate biological process annotation which takes in account the biological context. This enables us to perform an automated comparison of the TCA cycles for seven different species based on processes rather than protein sequences. From current databases, Bio is able to unravel information that are already known by the biologists but are not available for automated analysis tools and simulation software, because of the lack of formal process descriptions. This use of the Bio description scheme to describe the TCA cycle was a key step of the MitoScop project that aims to describe and simulate mitochondrial metabolism in silico.
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Abbreviations
- α-KDH:
-
α-ketoglutarate dehydrogenase
- BAs:
-
biological activities
- BEAs:
-
basic elements of action
- BFs:
-
biological functionalities
- BRs:
-
biological roles
- FADH2:
-
reduced flavin adenine dinucleotide
- GO:
-
Gene Ontology
- NADH:
-
reduced nicotinamide adenine dinucleotide
- PDH:
-
pyruvate dehydrogenase
- SMILES:
-
simplified molecular input line entry system
- SMIRKS:
-
SMIles ReaKtion Specification
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Mazière, P., Parisey, N., Beurton-Aimar, M. et al. Formal TCA cycle description based on elementary actions. J Biosci 32, 145–155 (2007). https://doi.org/10.1007/s12038-007-0013-4
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DOI: https://doi.org/10.1007/s12038-007-0013-4