Knowledge Management Tools

Part of genomics’ success has resulted from genes being annotated with structured vocabularies like the Gene Ontology. Unknown functions of genes can often be predicted by comparing their sequences to similar sequences of genes whose expression profiles have been annotated with functional/structural information. Similarly, metabolic pathways can be predicted from annotated enzymes.   Even with these advances, the unprecedented amount of information derived from the new genomics technologies is still outpacing our ability to transform that same information into actionable knowledge. While these advances increase our knowledge about genes and the structures/functions/systems they give rise to, knowledge about how systems interact to impact health/nutritional status has yet to be codified into formalized ontologies or databases.  Access to tools that allow researchers to mine this information is similarly daunting, with steep learning curves both for choosing available tools, as well as learning how to use them.

Presented here is a demonstration of the International Milk Genomics Consortium’s state-of-the-art Web Portal where leading international experts in nutrition, genomics, bioinformatics and lactation can contribute/review ongoing research.  Emphasis will be placed on demonstrating how the Portal can unite scientists from across the milk research spectrum to identify subsets of mammalian genomes responsible for milk creation and digestion; and to distinguish the actions and nutritional benefits by which mammalian milk genes and their products evolved.

The Portal guides expert and novice users by automatically displaying relationships between publicly available databases and ontologies.  By mapping these resources into a visual framework where researchers can navigate within a milk-and-health oriented *-omic information space, (while sharing, annotating, commenting, and contributing any particular concept relevant to their scientific pursuit); researchers can focus on translating biological information into health knowledge.

We know that milk evolved to nourish growing mammals.  The survival of mammalian offspring consuming milk exerted strong Darwinian selective pressure on the evolution of the lactation process. This evolutionary pressure led to genes, their products, proteins, peptides, complex lipids and oligosaccharides coming together as a complex, multi-component food system.  Thus, mammalian genomes are repositories of perhaps the most valuable resource for understanding the molecular basis of diets for improved health: lactation. Yet, only a fraction of milk's biological value is known.  The Portal provides a collaborative, networked environment where researchers can begin assembling sophisticated annotations of these biological systems and components with information about health.

Proof-of-principle for health-based annotation already exists, but is based on disease annotations involving SNPs, nutrient deficiencies, or exposure to toxins. Annotating genes, their products, nutrients, and/or metabolites with health information is much more difficult to conceive. Among the difficulties in developing “health” ontologies, versus “disease” ontologies, is that terms that would distinguish health by absolute scientific criteria are not defined.

Finally, also presented here then, is a brief deconstruction of health as a concept, its components, its causal relationships, and a suggested framework for the development of health/nutrition ontologies. Widespread adoption of such ontologies could provide a formalized conduit through which newly discovered biological knowledge can be translated into evidence-based clinical practice.  Of course, the ultimate goal is to translate this knowledge of milk, and its properties, into improved health through diets for humans.