Supplemental Material for Subsystems Paper

Subsystem Examples

These subsystem examples represent relatively well curated subsystems, include powerpoint slides that anyone is welcome to use, and include links to the current form of the subsystem (as it resides on the University of Chicago SEED).

We think of subsystems as going through three stages of curation (see The Project to Annotate 1000 Genomes for a detailed description):

  1. The initial stage of the project will involve development of subsystems that will cover most of the conserved cellular machinery in prokaryotes (and all of the central metabolic machinery in eukaryotes). This work will be done largely by trained annotators who achieve a limited mastery of specific subsystems via review articles and detailed analysis of the collection of genomes.
  2. The second stage will involve the gradual refinement and enhancement of the original subsystem encodings by domain experts. Almost every subsystem spreadsheet makes it clear that numerous detailed questions remain to be answered.
  3. The third stage involves determination of the evolutionary history of the genes within the subsystem.
Most of these examples are more-or-less complete versions of stage 1 subsystems. In some cases, real domain experts have produced a stage 2 subsystem.

What is worth noting is the number of research conjectures that have been formulated in the process of developing this initial set. In a number of cases the results have not yet been published, and they await wet lab confirmation.

Release 1 Subsystems

This link will take you to a table of the subsystems that have been included in Release 1. For each subsystem, we include a link that will let you peruse it in its current form, as well as a link to show it in the exact form it had when it was released.

Downloading Release 1

You can download subsystems at any time by accessing the clearinghouse. When you take the above link, you will be accessing a clearinghouse of stored objects. Each object has a type. You will be accessing objects of type 1-subsystem, which are the subsystems as they appeared in the "frozen" release 1. If you wish to download current versions of the subsystems, you can use this link.