What is FIG?
FIG is a nonprofit organization devoted to providing support for those analyzing genomes.
Sequencing of genomes is laying the foundation for advances in science
that will dramatically reshape our society. These advances will
initially occur in medicine, agriculture, and chemical production, but
in the long term the impact will be pervasive. The computer revolution
started by impacting payrolls, but eventually allowed man to travel to
the moon. Similarly, the biological revolution is beginning by
reshaping the life sciences, but this will surely not be the the whole
story or even the most significant outcome.
The interpretation of genomes will constitute the most exciting and
most significant science of the century. By rapidly advancing our
understanding of life, how it arose, and how it continues to change,
we will acquire the tools that will allow us to better understand and
improve our existence. Understanding will begin with relatively imple
forms of life -- unicellular organisms. While the central mechanisms
of life are shared by both these organisms and the most complex
animals and plants, they also contain a remarkable diversity. They
have an immense amount to teach us about life itself, and we will need
to master these lessons before full understanding of complex genomes
will be achievable.
The Fellowship for Interpretation of Genomes will focus on organizing
the data needed to support interpretation of genomes, providing the
infrastructure needed by the world community in its efforts to achieve
understanding. In addition, we will ourselves pick specific, critical
problems and attempt to actively participate in the unravelling of the
secrets within these amazing entities. It is only by merging the work
of building infrastructure with the applications that use it that we
will more deeply understand what is needed at each step.
FIG was started in May, 2003. The founders were Michael Fonstein,
Yakov Kogan, Andrei Osterman, Ross Overbeek, and Veronika Vonstein. An
early position paper began with the following comments:
The FIG Architecture: the SEEDWe begin with the "seed" of FIG. The SEED contains the essential,basic elements that are needed to sustain a scalable integration ofthousands of genomes. The later parts of this document will attempt tooffer precise notions of what makes up the seed of FIG. I will coverthe basic types of objects, make comments on what extensions will beneeded to support hundreds of thousands of genomes, and offer animplementation plan.However, before we go into such detail, some broad notions should bediscussed. The idea of integrating hundreds of thousands of genomesneeds some clarification. Indeed, what is meant by integrating a bunchof genomes, no matter what the number. In my mind, the notion ofintegration is essentially "maintenance of notions of neighborhood,allowing forms of access that can be used to easily exploreconnections and comparisons between data from numerous genomes". Thismay be viewed as a complicated way to say "a framework to supportcomparative analysis".
To be more precise:
Genes from a single genomes are often "functionally related" in that
the participate in implementing a single pathway or subsystem. For any
single gene, the "functional neighborhood" of that gene is the set of
genes that are functionally related to the gene. To support access
relating to this notion of neighborhood requires an encoding of the
cellular machinery (e.g., pathways). Genes that occur close to each
other on a chromosome may be thought of as "postionally related". The
set of genes that are positionally related to a given gene amounts to
the "positional neighborhood" of the gene. One of the huge payouts of
integrations to data has been based on a correlation between the
neighborhoods imposed by "functionally related" and "positionally
related" in the case of prokaryotic genomes. Genes from one or more
genomes that share a common ancestor are called "homologous". Homology
induces yet another notion of neigborhood. One can build more
restricted neighborhoods upon this basic concept. Thus, we tend to
think of a protein family as a set of homologous genes that have a
common function (an imprecise notion, we grant). Maintenance of
protein families will, of course, be an absolutely essential part of
effectively integrating many thousands of genomes. Sets of very
closely related genomes may be viewed as a neighborhood (i.e., the
neighborhood of a genome becomes a set of closely related
genomes). One can layer a notion of "variation", including SNPs, on
the notion of closely related genomes, and then whole frameworks for
exploring minor variations become possible. The power in an
integration arises from mixing the different notions of
neighborhood. The tools for supporting effective use of a variety of
comparative notions constitute the computational framework for
comparative analysis, which is often abbreviated to the notion of
"integration".
FIG offers the key services required to architect and implement a
comparative framwork for interpreting genomes.
The Fellowship for Interpretation of Genomes is a 501 (c) (3) organization.
