Biomedical Engineering Reference
In-Depth Information
and between research communities and the industries that serve them. In the
life sciences, the Open Biological and Biomedical Ontologies “OBO Foundry”
(www.obofoundry.org) [3] is the clearinghouse for free and open collabora-
tions in developing interoperable ontologies. Ironically there is an ongoing
debate over how best to represent ontologies themselves in a computer-
readable manner, and the ontologies to be found on OBO Foundry are split
between using the .obo and .owl formats.
Once the terminology has been nailed down, there is still the question of
how data should be formatted. The use of a standardized data format (ideally
accompanied by a reference implementation of code for readers and writers
of the format) allows software developers to concentrate on novel algorithms
instead of the drudgery of input/output issues, especially when implemented
using standardized encoding rule sets such as XML (Extensible Markup
Language) or JSON (JavaScript Object Notation). This author is most familiar
with standards development in the area of proteomics-related mass spectrom-
etry in the form of the mzXML and newer mzML [4] XML formats and can
attest to the fact that these are long-term projects requiring serious effort from
academia and industry alike and requiring constant extension as technologies
evolve.
14.4.1
Some Notable Standards Efforts in Life Sciences
There are many complimentary and sometimes competing standards efforts
ongoing at any given time and many that have been superseded or simply
abandoned for lack of support or failure to keep up with rapidly evolving
technologies. Some major active and ongoing efforts include:
• Systems Biology Markup Language (SBML), a computer - readable format
for representing models of biological processes [5]. The project also
includes a variety of software projects supporting the use of the format.
• The mzML mass spectrometry data format from HUPO - PSI [6] and its
reference implementation in the ProteoWizard project [7], which con-
tains many excellent support tools for converting from proprietary mass
spectrometry vendor formats. Perhaps the greatest achievement of the
ProteoWizard team is securing the cooperation of the mass spectrometry
vendors in producing those converters, a political feat which previous
proteomics mass spectrometry standards efforts did not achieve and
which is a signal marker of the shifting attitudes toward openness in the
sciences in academia and industry alike.
• Also in the proteomics fi eld, HUPO-PSI is facilitating the development
of mzIdentML as a standard for protein identifi cation [8], along with the
closely related mzQuantML standard for protein quantitation [9], and
TraML [10] for the exchange and transmission of transition lists for
selected reaction monitoring (SRM) experiments. These are just a few
projects in this exceedingly active and successful group.
Search WWH ::
Custom Search