Biomedical Engineering Reference
In-Depth Information
The Bioclipse Graphical User Interface for uploading
data to OpenTox. Sharing new toxicological data about
molecular structures can be done by uploading the
data to an OpenTox server. This Bioclipse dialog shows
a selected MDL SD fi le with ten neurotoxins
(neurotoxins.sdf) being shared on the Ambit2 server,
the OpenTox server to upload to, providing a title for
the data set, and the CC0 waiver (see main text).
Clicking the Finish button will upload the structures
and open a web browser window in Bioclipse with the
resulting online data set (see Figure 2.3)
Figure 2.2
the Bioclipse dialog for uploading a small data set with ten neurotoxin
structures to an OpenTox server. This dialog asks to which OpenTox
server the structures should be uploaded (the Ambit2 server is selected,
http://apps.ideaconsult.net:8080/ambit2
/), a title under which this data
set will be available (
'Ten neurotoxins found in Wikipedia'
), and the data
license under which the data will be available to others (the Creative
Commons Zero license in this case [23]).
At a scripting level, this dialog makes use of the createDataSet(service,
molecules), setDatasetLicense(datasetURI, licenseURI), and set
DatasetTitle(datasetURI, title) commands, as listed in Table 2.1. The
latter two methods use the data set's Universal Resource Identifi er
(URI) returned by the fi rst method. The dialog, however, opens the
data set's web page in a browser window in Bioclipse (see Figure 2.3)
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