Biology Reference
In-Depth Information
constructed network that is built using local materials and using local
methods; it is highly heterogeneous but can include a large amount of
data because it does not need to be rigorously maintained or policed.
Centralized solutions, on the other hand, aim to bring all the data
into a common format at a single location—software is written to trans-
late data from various formats and deposit and maintain them in a
master database. These are the most ubiquitous and fastest-growing
solutions to the problems of sharing biological data. These centralized
solutions, called “ontologies,” manifest a philosophy opposite to that of
a DAS, as they tend to be top-down and heavily managed. Ontology is
the branch of philosophy that deals with what things exist in the world:
it is “the science of what is, of the kinds, structures of objects, proper-
ties, events, processes, and relations in every area of reality. . . . Ontology
seeks to provide a defi nitive and exhaustive classifi cation of entities in
all spheres of being.”
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For computer scientists, predominantly those
concerned with information management and artifi cial intelligence,
“ontology” has a slightly different meaning:
a dictionary of terms formulated in a canonical syntax and with
commonly accepted defi nitions designed to yield a lexical or
taxonomical framework for knowledge-representation which
can be shared by different information systems communities.
More ambitiously, an ontology is a formal theory within which
not only defi nitions but also a supporting framework of axioms
is included.
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Why would computer scientists care about making such dictionar-
ies? If computers are to be able to reason with information, the lan-
guage used to communicate such information to the machines must be
standardized. Several ambitious attempts have been made to build ex-
haustive vocabularies for large-scale business enterprises. In 1981, the
fi rm Ontek began developing “white collar robots” that would be able
to reason in fi elds such as aerospace and defense:
A team of philosophers (including David W. Smith and Peter
Simons) collaborated with software engineers in constructing
the system PACIS (for Platform for the Automated Construc-
tion of Intelligent Systems), which is designed to implement a
comprehensive theory of entities, ranging from the very con-
crete (aircraft, their structures, and the processes involved
in designing and developing them) to the somewhat abstract
