Biology Reference
In-Depth Information
tem (DAS). As it was described in a seminar at the EBI, a DAS is like a
Web 2.0 “mashup,” like using Google to create a map of local pubs by
pulling in data from different sources. The idea is that the data remain
in various “native” formats in a large number of geographically dis-
persed repositories; the DAS server, however, knows how to talk to each
repository and extract data from it on the fl y. The EBI's main database,
known as Ensembl, works largely through a DAS. When a feature is
requested through the Ensembl website, the website creates a standard
URL that tells the DAS which information to retrieve; the DAS then
queries the remote database and sends back the relevant data in XML
format, which can be interpreted and displayed by the Ensembl website.
The Ensembl DAS does not aim to translate all the data into a common
language or format—instead, it can display data from multiple sources
side by side on a website. This method not only sidesteps problems of
translation, but also avoids (since data are requested in real time over
the web) time-consuming efforts to keep data up to date. The inventors
of the Ensembl DAS system were explicit with their intentions for the
kinds of biological work they hoped it would promote:
DAS distributes data sources across the Internet improving scal-
ability over monolithic systems. This distribution of data en-
courages a divide-and-conquer approach to annotation, where
experts provide and maintain their own annotations. It also per-
mits annotation providers to disagree about a particular region,
encouraging informative dissension and dialogue. The sepa-
ration of sequence and map information from annotation al-
lows them to be stored and represented in a variety of database
schema. A number of different database backend alternatives
could arise. The use of links as a method of referencing back to
the data provider's web pages provides even greater power of
expression and content control.
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The DAS is not only a technical solution but also a mode of political
organization for biology. The creators of the DAS imagined a democratic
biology in which the task of data management is shared and knowledge
is a product of debate and negotiation. The DAS does not allow bio-
logical data to travel anywhere—local databases must be compatible
with the XML standards that the DAS server uses. However, the DAS
attempts to be minimal in its approach, requiring a relatively small in-
vestment on the part of the local database. The DAS represents a simply
