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.