Biomedical Engineering Reference
In-Depth Information
converted to XML, and with the Gene Ontology [15]. A more detailed
account of the integration is given elsewhere [16]. Unfortunately, the
Gold Book turned out to have too broad a scope and too narrow coverage
to be particularly useful for this work. Initially attempts were made to
markup text with all of the entries in the Gold Book, but too many of
them, such as
cis
- and
trans
-, were about nomenclature and parts of
names, so only hand-picked selections from the resource were used.
Named reactions and analytical methods were additional obvious
areas to select for the further development of ontologies applicable to
chemistry publishing. RXNO [17] represents named reactions, for
example the Diels-Alder reaction, which are particularly easy to identify
and a method was established to determine under which classifi cation a
reaction falls. The Chemical Methods Ontology (CMO) [18] was initially
based on the 600 or so terms contained within the IUPAC Orange Book
[19] and then extended based on our experience with text-mining. It now
contains well over 2500 terms and covers physical chemistry as well as
analytical chemistry. RXNO and CMO have been provided as open
source and are available from Google Code where we have trackers and
mailing lists [17] [18]. When ChemSpider was acquired in 2009 (
vide
infra
), a number of processes were changed to make use of many of the
tools and interfaces available within the system. The processes associated
with (1), (2) and (3) listed above have been changed but (4), the method
by which non-structural chemical and biomedical terms are found in the
text, remains the same. At present we utilize OSCAR3, a greatly improved
version of OPSIN [11] and ACD/Labs' commercial name to structure
software [20]. The large assortment of batch scripts and XSLT transforms
has now been replaced by a single program, written in C#, for bulk
markup of documents, and it memorizes the results of the name to
structure transformations. The key difference for structure rendering is
that ChemSpider stores the 2D layouts in addition to the InChIs in the
database and as a result the rendering process is now a lot simpler.
The ChemSpider image renderer is also used in place of the original
CDK, providing signifi cant improvements in structure handling and
aesthetics. The original RSC Publishing SQL Server database serving the
Prospect Project has now been replaced by integration with ChemSpider,
meaning that substructure searching is now available as well as cross-
referencing to journal information from other publishers that has been
deposited in ChemSpider.
New approaches are being investigated to enhance the semantic
markup of RSC publications and to roll out new capabilities as
appropriate. These now include the delivery of our semantically enriched
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