Biomedical Engineering Reference
In-Depth Information
solve a local problem as quickly and as efficiently as possible.
Making niche tools, their file formats, and the data they generate generally accessible is a major step
in the evolution of standards. This phase represents an opportunity for larger academic or
commercial players to position their proprietary formats as standards. The advantage of making tools
and data openly available to a group of potential collaborators is that the best tools tend to attract
the greatest number of users. These users in turn perpetuate the tools and the data formats that
they support throughout the bioinformatics community, eventually making some tools de facto
standards, simply because they perform their functions very efficiently or effectively. The most
popular tools are often rewritten to enable sharing by supporting a uniform data format.
Data Uniformity
There are numerous reasons for developing data uniformity or a common file format for popular
applications. A common file format for applications reduces the cost of maintenance and data
archiving, minimizes the likelihood of data loss and results in more efficient use of software tools.
Another motivation for establishing data uniformity through standards is to improve the reliability of
searching the online bioinformatics databases. However, evolving to the data-uniformity stage of
standards requires more than simply publishing data format specifications; it requires active
cooperation among software and hardware developers.
Although cooperation may occur though a one-on-one relationship, in most cases there are either ad
hoc group collaborations or formal standards groups. In either case, politics and capital are typically
major deciding factors in which tools establish the standards. For example, a group of universities
collaborating on a project may informally agree on a particular hardware, operating system, and
application standard to facilitate sharing of data and applications. Similarly, a commercial venture
that has built its product around a particular file structure, for example, may stand to lose
considerable money if their format isn't selected as the industry standard.
The data uniformity stage of standards evolution is product- and industry-specific. For example, there
are competing standards for NMR data formats. Most of the more than 20 manufacturers of NMR
equipment support their own proprietary data format exclusively. Moreover, there may be several
different formats supported by different product lines from the same NMR manufacturer. For
example, there are the GE Omega, GN, and QE file formats, the Varian Gemini, XL, Unity, Inova, and
VXR formats, and the Nicolet 1180 and 1280 file formats.
While the NMR market has yet to crystallize around a single data format, the standards issue appears
much more certain in the area of protein structure data. The macromolecular crystallographic
information file (mmCIF) format has a good chance of becoming the industry standard, in part
because of a collaboration between the NIST and the RCSB. The two organizations are working to
develop data and data-exchange standards based on the mmCIF format and eXtensible Markup
Language (XML) over the Web.
Interoperability
The final stage of standards evolution—interoperability—is the ability of a device or application to
work seamlessly with tools and devices from multiple industries. True interoperability isn't limited to
bioinformatics, but extends to general-purpose tools, such as databases and spreadsheets, and to
other specialized areas, such as NMR equipment. Interoperability makes it possible for a Universal
Serial Bus (USB) printer to work with a Dell workstation running Linux or a Macintosh computer
running OS X, or for an NMR machine to output files directly to a format compatible with the PDB.
Ultimately, interoperability extends beyond bioinformatics and molecular biology, potentially to
encompass devices and software in every industry. As such, a bioinformatics application should be
able to share data and link seamlessly with applications used in other industries, including Microsoft's
suite of office products, Adobe's line of graphics creation and editing tools, and Oracle's suite of
database tools. Achieving true interoperability involves following industry standards for everything
Search WWH ::




Custom Search