Biomedical Engineering Reference
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that has made this process much more feasible is RDF (Resource
Description Framework), a simple language that allows the representation
of pairs of entities and the relationships between them (RDF triples).
These take the form of Subject-Predicate-Object. For example, we could
simply represent a fact about the author using the triple <David Wild><Is_
a><Author>. Each RDF triple can be considered as two nodes of a
network connected by an edge. In aggregate, the RDF triples describe a
network of entities and relationships between them.
18.2 The Semantic Web in drug discovery
The power of RDF lies in its simplicity, but also in the advent of three
other Semantic Web technologies which unleash its power: triple stores for
effi cient storage, access and searching of RDF; SPARQL, a language for
querying RDF stores, and ontologies for the standardization of the content
of RDF triples. More details on the RDF and semantic web approach are
discussed in Chapter 19, where Bildtsen and co-authors describe the
'Triple map' application, and how it is used for semantic searching and
knowledge collaboration in biomedical research. These technologies have
only recently reached a point of maturity where they are practically useful,
and in some ways the Semantic Web was over-hyped before it was mature
enough, leaving an impression in some quarters that it is not technically
up to the job of data integration. It is the opinion of the author that the
technologies have reached a point where they are not only technically
capable, but also are the only current technologies capable of tackling this
problem. Indeed, as the chapters by Bildtsen and colleagues (Chapter 19),
Harland and colleagues (Chapter 17) and Alquier (Chapter 16) show, this
technology is now gaining traction within industry.
Recently, there has been an escalation in activity in the application of
Semantic Web methods in drug discovery as a means of integration,
including the well-funded EU OpenPhacts project [4], the W3 Semantic
Web in Health Care and Life Sciences Interest Group [5], CSHALS [6] - a
conference on Semantics in Health Care and Life Sciences, and Linked
Open Drug Data (LODD) - a central repository for RDF related to drugs
[7]. More widely in the biological sciences, the Semantic Web is having
an impact through efforts such as Bio2RDF [8]. Bio2RDF covers a large
number of genetic, pathway, protein, and enzyme sets, but does not cover
chemical sets, except the KEGG ligand database. It thus overlaps with
Chem2Bio2RDF, but the key differentiator of the latter is that chemical
sets are mapped fully into genetic, protein, and pathway sets.
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