Biology Reference
In-Depth Information
(business processes and organizations, their structures, and the
strategies involved in creating them) to the exceedingly abstract
formal structures which bring all of these diverse components
together.
14
This was an attempt to create a “theory of the world” that could be used
by computers. In biology, the problem is not only getting computers
to work with biological data, but also getting biologists to work with
one another. Biological ontologies are supposed to solve the “data silo”
problem by creating
controlled vocabularies
for the sharing of biologi-
cal information.
In the late 1990s, as the number of organisms with completely se-
quenced genomes grew, several senior scientists in charge of managing
the genome databases for these organisms began to realize the need for
a shared language. In particular, they needed a way of talking about
the functions of genes, the central objects of biological interest. Several
efforts had been made to create functional classifi cation systems, but
these “were limited because they were not shared between organisms.”
15
Suzanna Lewis, who was in charge of FlyBase (the genome database for
Drosophila
fruit fl ies), reported on some of her emails from 1998:
Our correspondence that spring contained many messages such
as these: “I'm interested in defi ning a vocabulary that is used
between the model organism databases. These databases must
work together to produce a controlled vocabulary” (personal
communication); and “It would be desirable if the whole ge-
nome community was using one role/process scheme. It seems
to me that your list and the TIGR [The Institute for Genome
Research] are similar enough that generation of a common list
is conceivable (personal communication).
16
In July 1998, at the Intelligent Systems for Molecular Biology (ISMB)
conference in Montreal, Michael Ashburner suggested a simple, hierar-
chical, controlled vocabulary for gene function. His paper, “On the Rep-
resentation of 'Gene Function' in Databases,” was not well received—
most participants considered it naïve. Afterward, however, in the hotel
bar, Lewis (representing FlyBase) met with Steve Chervitz (representing
the yeast database, Saccharomyces Genome Database) and Judith Blake
(Mouse Genome Informatics) and agreed to a common scheme for de-
scribing the functions of genes.
17
This collaboration became the Gene
Ontology (GO) Consortium.
