142
D. L. Svoboda et al.
enables a toxicologist to formulate a comprehensive picture of toxicity with greater
efficiency than traditional methods.
Keywords ToxFX · DrugMatrix · Signature · Toxicogenomics · Database ·
National Toxicology Program · In vivo · In vitro
Abbreviations
API
Application Program Interface
BDE
Brominated Diphenyl Ethers
CEBS Chemical Effects in Biological Systems
FDA
US Food and Drug Administration
GD
Gestation Day
GUI
Graphical User Interface
NIEHS National Institute of Environmental Health Sciences
NTP
National Toxicology Program
PND
Postnatal Day
8.1 Introduction and History
The power of transcriptomics for understanding biology relates to the technology’s
ability to provide a researcher not only the ability to view an entire landscape of
molecular alterations but to perform high-dimensional relational analysis that can
quantify relative similarities of different biological states. Consistent with this idea,
at the inception of the toxicogenomics methodology, it was apparent that in order
to achieve contextualization of the complex findings, anchoring of the studies to
reference data sets of traditional toxicity metrics would be needed. This realization
led to the creation of Iconix Biosciences in the early 2000s [1]. Their mission was
to generate a toxicologist friendly resource that integrated pathology, clinical chemistry, and transcriptomics metric all derived from a large set of comprehensive, welldocumented short-term in vivo rat toxicity studies [2]. To further broaden the context
of the information, targeted high throughput screening assays were performed, rat
specific annotated pathways were generated, signatures of pathology were derived
from the data, copious pharmacology curation was performed, and toxicologically
relevant ontologies were built and curated on several hundred chemicals and drugs.
To integrate and provide ease of access to toxicologists, all this information was
organized in a relational database, and a sophisticated java-based web application
was constructed. A web-browser-based GUI provided simple, end-user query access
to the data. It enabled uploading and integration of end-user data, together with
data visualization, to identify deeper patterns in the data. This application named
DrugMatrix. Due to its robustness of design and detailed consideration of the target
D. L. Svoboda et al.
enables a toxicologist to formulate a comprehensive picture of toxicity with greater
efficiency than traditional methods.
Keywords ToxFX · DrugMatrix · Signature · Toxicogenomics · Database ·
National Toxicology Program · In vivo · In vitro
Abbreviations
API
Application Program Interface
BDE
Brominated Diphenyl Ethers
CEBS Chemical Effects in Biological Systems
FDA
US Food and Drug Administration
GD
Gestation Day
GUI
Graphical User Interface
NIEHS National Institute of Environmental Health Sciences
NTP
National Toxicology Program
PND
Postnatal Day
8.1 Introduction and History
The power of transcriptomics for understanding biology relates to the technology’s
ability to provide a researcher not only the ability to view an entire landscape of
molecular alterations but to perform high-dimensional relational analysis that can
quantify relative similarities of different biological states. Consistent with this idea,
at the inception of the toxicogenomics methodology, it was apparent that in order
to achieve contextualization of the complex findings, anchoring of the studies to
reference data sets of traditional toxicity metrics would be needed. This realization
led to the creation of Iconix Biosciences in the early 2000s [1]. Their mission was
to generate a toxicologist friendly resource that integrated pathology, clinical chemistry, and transcriptomics metric all derived from a large set of comprehensive, welldocumented short-term in vivo rat toxicity studies [2]. To further broaden the context
of the information, targeted high throughput screening assays were performed, rat
specific annotated pathways were generated, signatures of pathology were derived
from the data, copious pharmacology curation was performed, and toxicologically
relevant ontologies were built and curated on several hundred chemicals and drugs.
To integrate and provide ease of access to toxicologists, all this information was
organized in a relational database, and a sophisticated java-based web application
was constructed. A web-browser-based GUI provided simple, end-user query access
to the data. It enabled uploading and integration of end-user data, together with
data visualization, to identify deeper patterns in the data. This application named
DrugMatrix. Due to its robustness of design and detailed consideration of the target