Supplemental Material for Subsystems Paper
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):
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.
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.
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.
The third stage involves determination of the evolutionary history of
the genes within the 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.
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.
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.