Biomedical Engineering Reference
In-Depth Information
Figure 24.1
Screenshot of GitHub Webpage providing code review functionality. The
comments show a reviewer question regarding a parameter description missing in the
JavaDoc (see http://github.com/bioclipse/bioclipse.cheminformatics/commit/3ce78ba ).
in these information resources is derived from experimental data. For example,
force fi elds, which are used to calculate energies for molecular conformations,
are based on common patterns, such as average bond lengths, the angles
between two bonds that have one atom in common, and so on.
The collaborative building of knowledge bases is now well established, with
popular examples in chemistry, including compound databases like PubChem
[21] and ChemSpider [22], where people can deposit chemical structures.
Social sites to share open data include the NMRShiftDB [23] (licensed under
a GNU FDL license), ChemPedia [24] (available under a CC0 license), and
the Blue Obelisk Data Repository, which is a collaborative project initiated
by a number of cheminformatics tools [25], including Kalzium [26] (see Fig.
24.2), the Chemistry Development Kit (CDK), and others. However, it should
be noted that these collaborative, open-data resources are small in size and
the collaborating community is not, as yet, of critical mass.
In contrast, Wikipedia has an active development community and collabo-
ration within the WikiProject Chemistry [27]. This project has many contribu-
tors and keeps track of the chemistry-related pages in Wikipedia and has
frequent discussions on how to improve the chemistry on these pages.
Collaboration is organized via a project wiki page that can be edited by all
contributors (see Fig. 24.3 ).
The toxicology community has bootstrapped a community effort to share
knowledge around the OpenTox Open Standard [28]. OpenTox provides an
interoperable standard for the support of predictive toxicology, including data
management, and the specifi cation of algorithms, modeling, validation, and
reporting. OpenTox takes advantage of other open standards for data repre-
sentation, interfaces, vocabularies, and ontologies: Functionality is provided as
RESTful services [29], and replies are provided in various formats, including
the resource description framework [30], the underlying technology of the
Semantic Web [31] .
Search WWH ::
Custom Search