Biology Reference
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refine their search queries, manage complex ontogenies, and cluster
biological entities in a meaningful manner that can shed light onto
novel systems associations [90].
Recently, a novel text-mining approach, called Systems Literature
Analysis [91], was adopted in an effort to retrieve from bibliographical
databases global pathway associations of complement proteins. [92].
Biovista's BioLab Experiment Assistant (BEA
TM
) tool, which supports
literature analysis and hypothesis generation, was used in this study as
a literature mining platform. This survey documented a broad range of
biological processes that are modulated by complement proteins and
presents for the first time an integrated map of complement-mediated
networks that incorporates well over 85 diverse biological pathways.
The use of this novel mining platform has expanded the comple-
ment ontology beyond its ~35 designated components by identifying
putative protein-protein interactions involving novel, noncomplement
ligands. Furthermore, unusual associations of complement with signal-
ing cascades and cellular networks that affect both inflammatory and
noninflammatory processes were revealed through text-based correla-
tions of complement genes and multiple pathways [92]. Integrating
complement within a unified “systems” framework underscores the
concept that innate immunity goes well beyond the maintenance of
host defense, extending previously underappreciated links to critical
developmental, homeostatic, and metabolic processes.
Complement essentially serves as a paradigm of how a defined
knowledge space can be manipulated in a cross-disciplinary fashion,
and thus be expanded by integrating both experimental and textual
information dispersed across the databases.
PERSPECTIVES
In recent years, it has become evident that “cutting edge” biomedical
research cannot be conducted with the exclusive use of traditional
experimental approaches. The enormous amount of raw data accumu-
lating in nucleotide and protein databases has urged the contemporary
scientist to adopt a more global and cross-disciplinary approach to
“old” scientific questions. Resolving the fine structure and biochemical
properties of proteins may still contribute to addressing functions that
underlie complex processes, provided that these research components
are placed into a wider context of interacting systems and pathways.
In this respect, the investigation of complement structure/function
relationships and protein-protein interactions that underlie critical bio-
logical processes is now being integrated in a systems-wide context that
requires the cooperative application of different disciplines, resources,
and experimental platforms. Using a combination of biophysical and
computational approaches, together with high-throughput screening
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