Bioverse Version 1.0

[Jason McDermott]

We've released version 1.0 of the Bioverse
(http://bioverse.compbio.washington.edu), our attempt to develop a
framework to integrate single molecule data with genomic/proteomic
data.  This is still an experimental release, but before we proceed
with the next one, we wanted to solicit feedback on features and bugs
(some of which we're already working on) and any other comments that
would help improve this resource.

One of the things possible in this release is the ability to
interactively browse contextual and similarity networks.  The
contextual maps are based on using interaction information that's out
there (from 2-hybrid experiments, PDB complexes, literature, etc.) and
mapping it to related sequences. The contextual maps potential enable
us to understand pathways and systems (please note that these URLs are
long and so if your e-mail reader wraps things around, it may not
work):

http://bioverse.compbio.washington.edu/homo-sapiens/explore/interaction/display?
network=18&lod=6
http://bioverse.compbio.washington.edu/salmonella-typhimurium/explore/interactio
n/display?network=7&lod=4&mode=_clique
http://bioverse.compbio.washington.edu/clostridium-perfringens/explore/interacti
on/display?network=1&lod=4
http://bioverse.compbio.washington.edu/pseudomonas-aeruginosa/explore/interaction/display?network=3&lod=5
http://bioverse.compbio.washington.edu/oryza-sativa/explore/interaction/display?network=30&lod=6

and both the contextual and similarity maps enable us to do better
annotation than before. Take a look at:

http://bioverse.compbio.washington.edu/salmonella-typhimurium/explore/interaction/display?network=5&lod=4
http://bioverse.compbio.washington.edu/pseudomonas-aeruginosa/explore/interaction/display?network=11&lod=2
http://bioverse.compbio.washington.edu/homo-sapiens/explore/similarity/display?network=63&lod=6
http://bioverse.compbio.washington.edu/yersinia-pestis/explore/interaction/display?network=1&lod=6
http://bioverse.compbio.washington.edu/oryza-sativa/explore/interaction/display?network=25&lod=6

There's a protein in the maps above that's annotated as "no function
found". Even though the red and yellow are low-confidence hits, you
can clearly see how an annotation can be made for the "no function
found" protein. The type of annotation will differ based on whether
you're looking at a contextual or similarity network. This visual
method of annotation works for the smaller networks, but we will use
graph theory approaches along with neural networks to do this in an
automated fashion.

Some of this can be used to identify putative drug targets:

http://bioverse.compbio.washington.edu/salmonella-typhimurium/explore/interaction/display?network=7&lod=4&mode=_clique
http://bioverse.compbio.washington.edu/escherichia-coli/explore/interaction/display?network=3&lod=5

We are in the process of developing a highly flexible, interactive and
manipulatable client-based three-dimensional viewer that can be used
to include information from other organisms and select and deselect
edges using arbitrary specifications.

Like we say above, all feedback would be greatly appreciated so we can
make this resource as useful as possible. Thanks!

The Bioverse Team
Jason McDermott, administrator