Thursday, March 29, 2007

Intro to RDF biomedical specifications

Many of us in the healthcare and life sciences spend a non-significant portion of our professional lives preparing data that will be entered into large databases.

Sometimes databases disappoint us. For a variety of reasons, we can never seem to merge our data with data produced by colleagues who have used a different database. Often, databases within a single institution are incompatible. The solution, we are told, is data standards. If we could mutually decide what data we need to store and how the stored data should be structured, then our databases would be compatible. Our trust in the wisdome of standards has fueled thousands of standards initiatives in the healthcare field.

The problem is that compliance with standards is often very low, and standards themselves can be flawed. As technologies change, standards do not always keep apace. This often results in obsolete standards or standards with multiple versions with idiosyncratic implementations.

RDF (Resource Description Framework) is a formal method for describing specified data objects with paired metadata and data and is prepared in XML syntax. In the next few blogs, I will try to show that RDF-specified data provides some of the functionality of standards. In addition, RDF-specifications greatly expand our ability to understand information. In my opinion, all life science professionals can benefit from understanding the basics of RDF.

-Jules Berman tags: biomedical, data standards, metadata, rdf, specifications
Science is not a collection of facts. Science is what facts teach us; what we can learn about our universe, and ourselves, by deductive thinking. From observations of the night sky, made without the aid of telescopes, we can deduce that the universe is expanding, that the universe is not infinitely old, and why black holes exist. Without resorting to experimentation or mathematical analysis, we can deduce that gravity is a curvature in space-time, that the particles that compose light have no mass, that there is a theoretical limit to the number of different elements in the universe, and that the earth is billions of years old. Likewise, simple observations on animals tell us much about the migration of continents, the evolutionary relationships among classes of animals, why the nuclei of cells contain our genetic material, why certain animals are long-lived, why the gestation period of humans is 9 months, and why some diseases are rare and other diseases are common. In “Armchair Science”, the reader is confronted with 129 scientific mysteries, in cosmology, particle physics, chemistry, biology, and medicine. Beginning with simple observations, step-by-step analyses guide the reader toward solutions that are sometimes startling, and always entertaining. “Armchair Science” is written for general readers who are curious about science, and who want to sharpen their deductive skills.