Database Reference
In-Depth Information
3R su s
We use a small Antarctic data set to demonstrate the graph construction and
visualisation tools in the context of an exploratory scientific investigation.
Australia has an on-going research programme into the environmental im-
pacts of human occupation in Antarctica (see
http://www.aad.gov.au/
default.asp?casid=13955
). A recent component of this programme was an
investigation into the relationships between benthic species assemblages and
pollution near Australia's Casey station [25]. Marine sediment samples were
collected from two sites in Brown Bay, which is adjacent to a disused rubbish tip
and is known to have high levels of many contaminants. Samples were collected
at approximately 30 m and 150 m from the tip. Control samples were collected
from two sites in nearby, uncontaminated O'Brien Bay. Four replicate samples
were collected from two plots at each site, giving a total of 32 samples. Sediment
samples were collected by divers using plastic corers and analysed for fauna (gen-
erally identified to species or genus level) and heavy metal concentrations (Pb,
Cd, Zn, As, Cr, Cu, Fe, Ni, Ag, Sn, Sb). These metals are found in man-made
products (e.g. batteries and steel alloys) and can be used as indicators of anthro-
pogenic contamination. Details of the experimental methods are given in [25].
This data set has a very simple structure, comprising a total of 14 variables:
site name
,
species id
,
species abundance
, and measured concentrations of
the 11 metals listed above. Site latitude and longitude were not recorded but
the
site name
string provides information to the site/plot/replicate level (see
Fig. 1 caption). All of the above information appears in one database table. The
species id
identifier links to the AADC's central biodiversity database, which
provides additional information about each species (although we do not use this
additional information in the example presented here). Standard practice would
normally also see a separate table for the sample site details, but in this case
there are only a small number of sample sites that are specific to this data set.
Fig. 1.
A graph of Antarctic marine sample sites, linked by their species attribute
data. Sites can be separated into two clusters on the basis of their species, indicating
two distinct types of species assemblage. The white node is the “focus” node (see
text); other colours indicate the number of distinct species within a site, ranging from
grey (low) to black (high). Sites from contaminated Brown Bay (
right cluster
)haveless
species (less diversity) than sites from uncontaminated O'Brien Bay (
left cluster
). Node
labels are of the form
X
B
y
S
s
P
pr
and denote the position of the sample in the nested
experimental hierarchy. BB
y
denotes samples from one of two locations in Brown Bay
and OB
y
denotes O'Brien Bay;
s
denotes the site number within location;
p
denotes
the plot number within site; and
r
denotes the core replicate number within plot.
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