Aromatic Metabolic Pathways

The limitation in genome analysis is not the availability of sequence data, but rather the interpretation of those data. Errors in current annotations are abundant. Since new annotations often rely upon the existing set of annotations, errors have proliferated and continue to proliferate. The situation is sufficiently severe that in many cases only experts familiar with particular pathways can recognize and sort out errors. A major problem has been the untidy and erratic nomenclature used to identify genes, e.g., (i) use of the same name for different genes, (ii) use of the same name for genes that, on the one hand, encode single-domain proteins, and, on the other hand, genes that encode multi-domain proteins (due to gene fusion), and (iii) use of different names in different organisms for genes encoding the same protein. It is absolutely critical (and surely inevitable) that a logical and consistent universal nomenclature be established.

AroPath is taking the initiative that this situation can best be addressed with a comprehensive, expert-assisted manual effort that is undertaken with a realistically manageable subsystem of metabolism. In our case this subsystem is the extensive network of aromatic metabolism. No matter how high the quality of an analysis is at a given time, it will become outdated rapidly as new genomes come on line. Therefore, our approach is to produce tools which are able to lock in the current advances in analysis as they come, which are freely available and interactive so that the previous work can be efficiently exploited, and which is amenable to progressive updating and refinement via curator approval at AroPath.

The left sidebar items indicate the general features and organization of AroPath that are currently in progress. A nearly completed section of AroPath is TyrPath, and TrpPath is partially completed. A sense of the analytical quality and the tools being created to maintain and refine a given section of AroPath can be obtained by visiting TyrPath and following the various links.

Jian Song and Roy Jensen welcome critical comments and suggestions.