Biomedical Engineering Reference
In-Depth Information
be noted that the Application Programming Interfaces (APIs) are free to
access but are not open source. PubMed (through Entrez) [34] has both
SOAP and RESTful APIs. The Entrez API is both extensive and robust,
providing access to most of the NCBI/NLM [35] electronic databases.
Google now provides RESTful APIs and has deprecated the SOAP
services that it once supported. This probably refl ects the trend to support
only lightweight protocols for modern web applications. All of these
APIs are called in a similar way: a list of approved synonyms associated
with a particular ChemSpider record is listed, sorted by 'relevance'
(which is calculated based on the length of the synonym as well as its
clarity), then used to call against the API. The result (whether SOAP,
XML or HTML) is then processed by an 'adapter', transformed into an
intermediate XML representation and passed through XSLT to produce
the fi nal HTML shown in the ChemSpider records.
The value of analytical data is as reference data for comparing against
other lab-generated data. Acquisition of a spectrum and comparison
against a validated reference spectrum speeds up the process of sample
verifi cation without the arduous process of full data analysis. As a result
of this general utility, ChemSpider has provided the ability to upload
spectral data of various forms against a chemical record such that an
individual chemical can have an aggregated set of analytical data to
assist in structure verifi cation. As a result of contributions from
scientists supporting the vision of ChemSpider as a valuable centralizing
community-based resource for chemical data for chemists, over 2000
spectra have been added to ChemSpider in the past 2 years with additional
data being added regularly. These data include infrared, Raman, mass
spectrometric and NMR spectra, with the majority being 1H and 13C
spectra. Spectral data can be submitted in JCAMP format [36] and
displayed in an open source interactive applet, JSpecView [37], allowing
zooming and expansion. JSpecView is open source but the code seems to
lack a clearly defi ned architecture and boundaries. JSpecView has been
modifi ed to visualize range selection (inverting a region's color while
dragging a mouse cursor). One of the main problems faced with
supporting JSpecView is that it understands only one of the many fl avors
of JCAMP produced by spectroscopy vendors. This is not the fault of
JSpecView but rather the poor adherence to the offi cial JCAMP standard
by the spectroscopy vendors. An alternative spectral display interface is
the ChemDoodle spectral web component [38], which is a 'Spectrum
Canvas' and renders a JCAMP spectrum in a web page along with
controls to interact with it - for example to zoom in on a particular area
of interest. However, it relies on HTML5, which limits its usage to
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