Biology Reference
In-Depth Information
Cellular
Component
COG Class
Category
localized in
participates in
Biological
Process
Molecular
Function
is a
has function
binds to
COG
Class
is a
Operator
interacts with
related to
Transcription
Factor
is a
part of
part of
interacts with
binds to
Protein
Promoter
Protein
Complex
upstream of
regulated by
interacts with
upstream of
encoded by
CDS
interacts with
is a
Shim
transcribes to
Compound
upstream of
RBS
upstream of
RNA
Enzyme
part of
produced by
consumed by
Operon
min/max expressed in
catalysed by
classified as
MicroArray
Experiment
terminates
Reaction
Enzyme
Classification
is gene of
member of
Terminator
Feed Forward
Loop
catalysed by
Pathway
Kegg Orthologs
Enzyme
Kegg Orthologs
Protein
is a
encoded by
Kegg Orthologs
Gene
FIGURE 2.14
Graphical depiction of the ontology underlying BacillOndex, a semantically annotated Bacillus
subtilis
-specific knowledge base constructed using the Ondex data integration system.
working microbiologists is the GO
6
(
Ashburner
et al.
, 2000
), which provides a con-
trolled vocabulary for the
biological process
,
cellular component
and
molecular
function
of genes from a wide range of species.
In a biological context, text mining has perhaps been most widely applied in the
field of systems biology, whose practitioners endeavour to understand biological sys-
tems in context, by integrating
in vivo
experiments with computational modelling
and theory in an iterative manner.
7
In order to achieve this aim, the integration of
large amounts of data is necessary, particularly when constructing simulateable
models of biological systems, which generally require extensive parameterisation.
Biologically reasonable values for model parameters are hard to find (
Gutenkunst
et al.
, 2007
), and must often be extracted from published literature, rather than from
databases. As an alternative to dedicating weeks of valuable postgraduate student
7
Definition adapted from
http://www.bbsrc.ac.uk/web/FILES/Publications/systems_biology.pdf
.
