[MOBY-l] New MOBY application: "BioGraphNet: a distributed forum for heterogeneous biological networks"
fgibbons at hms.harvard.edu
Thu May 20 11:23:57 EDT 2004
Hey fellow MOBYers,
Below is an abstract I've submitted for BOSC (Bioinformatics Open Source
Conference) and BioPathways, satellite conferences of ISMC/ECCB in Glasgow,
Scotland this year. BioGraphNet is our 'sandbox' within the BioMOBY
'playground', in which we're looking at ways to share and view biological
At this point, Gabriel Berriz and I have a working prototype: a registered
object for describing fairly generic pairwise interactions, half a dozen
working services, and an application that runs in a web-browser to allow
end-users to play with the interaction data. A key element of this is that
anyone can make their data available at any time, and it will be discovered
and included in the webpage displayed to users (bench biologists). There's
no installation, no updating of databases. I'd appreciate your giving it a
try (http://llama.med.harvard.edu/cgi/BioTrawler) and letting us know what
you think. We're looking for feedback on a number of levels:
* Does the overall idea, (being able to view an interactive graphical
display of your chosen data sources for your favorite genes), seem useful
to you? What pitfalls do you see in the near or distant future?
* So far we've got correlated expression, synthetic lethality, homology,
transcription-factor/target (known and predicted), as well as experimental
protein-protein interaction results. What kinds of data would make it more
* Do you have some data you'd like to share? We've developed tools to
facilitate making data available as a MOBY service: drop a text file in the
right place, enter the textual description of your service - BOOM, it's
registered and available to the world. One goal of this project is to make
it easy for people with data to put it out there.
* Anything else that strikes you....
We're really keen to get input on this, just reply to me:
mailto:fgibbons at hms.harvard.edu
I'm looking forward to seeing some of you again in Glasgow!
TITLE: BioGraphNet, a distributed forum for heterogeneous biological networks.
AUTHORS: Francis D. Gibbons, Gabriel F. Berriz, and Frederick P. Roth
Dept. of Biological Chemistry and Molecular Pharmacology, 250 Longwood
Ave., Harvard Medical School, Boston MA 02115, USA
Biological network information is increasingly abundant. The combination
of biological networks may be viewed as a multicolor graph, with each color
representing a different gene-gene or protein-protein relationship, e.g.,
protein interaction, sequence homology, correlated expression,
transcriptional regulation, genetic interaction (sensu synthetic
lethality), or metabolic relationship. Relationship types may be further
stratified by type of evidence supporting the relationship, by
directionality or by confidence measure. Furthermore, each organism has
its own collection of networks. Although this information's complexity
argues for its maintenance by distributed groups, much of its value is
derived through network integration.
BioMOBY has established a 'playground' for distributed services. We have
developed a 'sandbox' within BioMOBY called BioGraphNet. BioGraphNet is a
common standard and collection of services for sharing distributed network
information. We now serve several network data types, and encourage others
to participate, using the common standard objects we have registered in
As an example application illustrating the use of BioGraphNet, we provide
BioTrawler, a web-based biological network browser that dynamically
discovers suitable distributed data sources within BioGraphNet, integrates
those selected by the end-user 'just in time', and visualizes the graph
neighboring a user-defined set of genes. Graph layout is handled by the
open-source GraphViz package (modified to handle multiple edges between a
pair of nodes). BioTrawler also exports graph representations in several
commonly used formats (GIF by default, but also Pajek, Cytoscape, and PDF).
The combination of BioMOBY and BioGraphNet represents a distributed network
annotation system analogous to the Distributed Annotation System (DAS) for
sharing genome annotation.
The object descriptions and service interfaces are already available to all
BioMOBY users. We plan to release BioTrawler under the Artistic License.
PhD, Computational Biologist,
Harvard Medical School BCMP/SGM-322, 250 Longwood Ave, Boston MA 02115, USA.
Tel: 617-432-3555 Fax:
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