Biology Reference
In-Depth Information
the provenance of DNA samples. For instance, their Minimum Informa-
tion about a Genome Sequence (MIGS) creates standards for reporting
the geographic location at which a sample was collected, the time, the
habitat (including temperature, light, pressure, pH, etc.), health of the
organism, sequencing method, assembly method, extraction methods,
standard operating procedures, and a range of other factors (all with as-
sociated standard vocabularies).
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To produce the information to meet
such a standard, biologists would need to follow specifi c procedures and
methods for gathering and processing DNA samples. That would mean
measuring temperature and pH, using a particular assembly method,
creating standard operating procedures, and so on. The standardization
of language enforces particular ways of working and doing.
In attempting to standardize language, the GO is also fl attening biol-
ogy. It takes the multiplicity and complexity of biological language and
renders it into a data structure. The GO shows how bioinformatics de-
pends on the standardization and data-ization of biological objects. But
the structure that the GO creates does not affect only computers; it also
affects how biologists think about biological objects and what they do
with them. A standardization of terms contributes to a standardization
of biological practice and biological knowledge. Like other technologies
of virtualization, ontologies make biology more compatible with com-
puting by reducing it to standard forms that can be coded, digitized, and
shared through electronic networks.
Virtual Spaces
What happens to data once they enter the virtual realm? How do they
get manipulated there? This section tracks how data are moved around
in the performance of bioinformatic knowledge making. The fl attening
and virtualization of samples and language into data allow the orga-
nization of data in space to become a kind of knowledge production.
The value of bioinformatic work consists of this careful spatial ordering
according to the structures of databases, data formats, and ontologies.
Formatting, managing, and curating data are ways of arranging them
into knowledge.
What do the virtual spaces of bioinformatics look like? In the most
literal sense, they are text on a computer screen. Most bioinformatics
begins with a “Unix shell”—a command prompt at which the bioinfor-
matician can enter commands in order to navigate around. In the fi rst
instance, one might only need to navigate around the fi les stored on
one's own computer using such commands as “cd” (change directory)
