An article on Blueprint in BioscienceWorld. Some key clips:
In fields ranging from medicine and biotechnology to agriculture and
the environment, the genomics revolution of the past decade is slowly
giving way to a systems-wide approach to solving biological questions,
as scientists are reminded that living organisms are comprised of more
than just their genes. Although invaluable, initiatives like the Human
Genome Project provide researchers with a parts list of life, but don’t
offer much information about how these parts assemble to create cells,
tissues and organisms.
Proteome projects have gone a long way toward filling in the gaps,
offering scientists information about protein content, numbers and
modifications. But in general, even these efforts can only provide a
snapshot of what is going on within a cell or organ, and do not always
tell researchers how these component parts interact to form complexes
and pathways critical to the function of life. More recently, however,
academic, government and commercial groups worldwide are addressing
this problem, finding ways to pull together biomolecular interaction
and pathway data from various sources into central repositories against
which researchers can test their hypotheses and probe for new insights.....
....Several groups, both commercial and academic, have undertaken a
systematic analysis of how biologically important molecules interact
both in the cell and in the lab....
....The largest of these databases, however, can be found in Canada at the
Blueprint Initiative (Blueprint), a research program of the Samuel
Lunenfeld Research Institute (SLRI) in Toronto, Ont.’s Mount Sinai
Hospital. Led by Christopher Hogue, PhD, Blueprint’s goal is to provide
researchers worldwide with free access to the information and tools
they need to improve their understanding of basic biology and human
health. To achieve this, they develop, host and maintain public
databases and bioinformatics software tools.
The central pillar of Blueprint’s efforts is the Biomolecular
Interaction Network Database (BIND), which captures data generated by
expensive research efforts in a computationally accessible format. BIND
records — which span molecular interactions, small-molecule chemical
reactions and genetic interaction networks — allow researchers to
identify macromolecular complexes, metabolic pathways and potential
clues to drug targets and leads. BIND is populated with interaction
data directly deposited by researchers or extracted from peer-reviewed
literature and a variety of genomic, proteomic, pathway and
disease-specific databases, which Blueprint curates and validates using
rigorous bioinformatics standards.
Currently, BIND houses more than 120,000 records of paired interactions
and complexes involving biopolymers (e.g., proteins, DNA and RNA) and
small molecules (e.g., lipids, nucleotides, sugars and ions). Using any
of more than 20 different search functions available through BIND’s Web
interface, researchers can identify interacting molecules on the basis
of their sequences, gene names, publication record and species origin,
to name a few, and examine how these interactions interplay with larger
molecular networks using BIND’s Interaction Viewer. Alternatively, new
features allow researchers to search relatively broad terms, such as
cancer, and pinpoint molecules of particular interest based on
characteristics such as subcellular co-localization, biological
function and binding partners...
....In August 2004, Blueprint’s Singapore node, Blueprint Asia, initiated a
collaboration with the Novartis Institute for Tropical Diseases
(Singapore, Singapore) (NITD) to assemble and curate known protein
interactions relevant to the biology of dengue virus.
“By examining information about dengue virus alongside other data in
the BIND repository, NITD scientists will gain a better understanding
of the dengue life cycle and of complex interactions with host proteins
leading to dengue hemorrhagic fever,” says Brian Yates, managing
director of Blueprint Asia. “This information can then be used to
develop drugs or vaccines to fight the disease.”
The collaboration is also expected to help NITD researchers identify
gaps in their information base, which could lead to the exploration of
new research avenues.
Almost regardless of the source, however, these interaction databases
and bioinformatics tools offer researchers insights into the function
of the cell and thereby offer the hope of turning molecular parts lists
provided by genome initiatives into blueprints of life.
It remains one of the great coincidences in scientific history that the one person Wallace should choose to approach to share his ideas on natural selection was the only other scientist who separately had come to the same conclusions - Charles Darwin.
