Computational tools and Interoperability in Comparative ... - CBS

Interoperability
Figure 4.1: Screen shot of NCBI Entrez Genome projects web page
Services, an interoperble life science community may not be far away. When connected,
the communities will be able to exchange not only data but many services such as tools
for predicting protein function, performing sequence alignments, or gene finding.
4.2 Interoperability
”The term ’interoperability’ is defined as the ability ... information, by IEEE (http...)”.
The term ’interoperability’ is defined as the ability of two or more systems to exchange
and make use of information (IEEE, http://www.ieee.org). Whether systems can be
said to be ’interoperable’ depends on how one interprets ’make use of’. Consider the list of
full prokaryotic genome sequences, maintained by NCBI at http://www.ncbi.nlm.nih.
gov/genomes/lproks.cgi, as shown in figure figure 4.1.
To automatically retrieve this list, one may write a parser to transform the HTML
into a computer-readable text. Apart from being overly sensitive to changes in the HTML
document, such a parser will lack the knowledge behind the data since the format is not
typed nor structured. It is only when interpreted by an internet browser and presented
graphically to a human, that this information makes any sense. Both recipient and receiver
must in other words have knowledge about the information that is exchanged, before these
can be said to be interoperable. The are two aspects of interoperability: First, there must
exist agreement on the format by which data is exchanged. Whether this is structured
XML or any arbitrary format, the server must return the format expected by the client
upon a request. Second, the description and understanding of the content of the data being
exchanged is a requirement when building client-side code and objects in Web Services.
Without the knowledge of exact data types, the programming environment (e.g. C, Java,
Perl) fails to declare the objects with proper variable types.
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