Biomedical Engineering Reference
In-Depth Information
ChEBI
Bio2RDF
ChEBI ID
ChEBI ID
Chemical
blogspace
R.O.N
InChl
ChemSpider
ChemSpider
ID
InChl
DBPedia
Figure 24.5 The rdf.openmolecules.net website operates as a hub in the Semantic Web
for small molecules by using the InChI to create unique molecular URIs to provide a
referenceable RDF resource for any compound.
used to identify information in a database. Common URIs include Web
addresses, such as http://www.chemspider.com/. The URI specifi cation is an
open standard that formalizes the structure of identifi ers: an identifi er consists
of a scheme (http), followed by a : and then an authority prefi xed with // (//
www.pharmbio.org) and fi nally a path (/). An example of a URI that does not
contain an authority is the URI used in Web pages to link to an e-mail address,
such as mailto:cdk-users@lists.sf.net, where the scheme is mailto, and the path
is the e-mail address. Other URIs include the life science identifi er (LSID)
[52]. For example, The LSID for the 1AFT protein in the PDB database is
urn:lsid:pdb.org:pdb:1aft. The urn scheme in the LSID refers to the uniform
resource name (URN) specifi cation, which is based on the URI but aimed at
being location independent [53].
Using these URIs, it is possible to create a linked open-data network, linking
together different databases on the Semantic Web. A subsection of this linked
data network is created by the website http://rdf.openmolecules.net/, which
takes advantage of the International Chemical Indentifi er (InChI) to create a
network for small molecules. Figure 24.5 shows how this is used to create links
to the Chemical Entities of Biological Interest (ChEBI) [54], ChemSpider,
NMRShiftDB [55], and other resources [56]. By taking advantage of such
identifi ers, the various participants can easily collaborate but work quite inde-
pendently at the same time. Other large initiatives in this area include the
Semantic Web for Health Care and Life Sciences Interest Group of the World
Wide Web Consortium [57] , Bio2RDF [58] , and Chem2Bio2RDF [59] .
Userscripts also present an approach to linking resources with a very low
barrier to entry. The idea of a userscript was fi rst made available by the
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