Georgopoulos,P.G.(200): A multiscale
approach for assessing the interactions of environmental and biological
systems in a holistic health risk assessment framework. Water
Air Soil Pollut: Focus, 8, 3-21.
『ホリスティック(全体論的)健康リスク評価枠組みにおける環境系と生物系の相互作用を評価するための多規模アプローチ』
『Abstract
Advances in computing processing power and in availability of
environmental and biological data have allowed the development
and application of comprehensive modeling systems that utilize
a holistic, integrated, approach for assessing the interactions
of environmental and biological systems across multiple scales
of spatiotemporal extent and biological organization. This approach
allows mechanism-based environmental health risk assessments in
a person-oriented framework, which accounts for simultaneous exposures
to contaminants from multiple media, routes, and pathways. The
conceptual basis and example applications of the Modeling
ENvironment for TOtal Risk (MENTOR), and
the DOse-Response Information ANalysis
system (DORIAN) are presented.
Keywords: Comprehensive modeling systems; DORIAN; MENTOR; Environmental
health; Risk assessments; Exposures to mixtures』
1. Introduction: The evolution of environmental risk assessment
2. The modeling environment for total risk studies (MENTOR)
3. The dose-response information analysis system (DORIAN)
4. Examples: Selected case studies
5. Conclusions
Acknowledgments
Appendix
References
Appendix
Table 2 A representative subset of databases (with website
reference) that are available for providing data for use in MENTOR
applications (see http://www.ebKB.org
for a more extensive list)
Table 3 A representative subset of databases (with website
reference) that are available for providing data for use in DORIAN
applications (see http://www.ebKB.org
for a more extensive list)
- Biological Databases
Genomics/transcriptomics
ArrayExpress (Public repository for microarray data; EMBL-EBI) http://www.ebi.ac.uk/arrayexpress/
ArrayTrack (Public bioinformatics resource for DNA microarray
and systems biology; US FDA) http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/
Chemical Effects in Biological Systems (CEBS; NIH) http://cebs.niehs.nih.gov
CIBEX − Center for Information Biology gene EXpression database
(Gene expression database system; DDBJ) http://cibex.nig.ac.jp/index.jsp
Database of Transcribed Sequences (DoTS; A human transcript index;
University of PA) http://www.allgenes.org
dbSNP (Database of Single Nucleotide Polymorphisms; NCBI-NIH) http://www.ncbi.nlm.nih.gov/SNP/
dbZach (Toxicogenomic database; Michigan State University) http://dbzach.fst.msu.edu
EDGE − Environment, Drugs and Gene Expression (rResource for
toxicology-related gene expression information; University of
Wisconsin ? Madison) http://edge.oncology.wisc.edu
EMBL Nucleotide Sequence Database (EMBL-EBI) http://www.ebi.ac.uk/embl/Documentation/
Entrez Gene (Searchable database of genes; NCBI-NIH) http://www.ncbi.nih.gov/entrez/query.fcgi?db=gene
Gene Expression Omnibus (Gene expression repository; NCBI-NIH) http://www.ncbi.nlm.nih.gov/geo/
Gene Finder (Search genes based on search criteria; NCI) http://cgap.nci.nih.gov/Genes/GeneFinder
GeneLoc (Integrated map for each human chromosome; Weizmann Institute
of Science) http://bioinfo2.weizmann.ac.il/geneloc/index.shtml
Genomatix Suite (transcription factors, pathways; Genomatix Software
GmbH) http://www.genomatix.de/
Human Genome Browser (database of the human genome; UC Santa
Cruz) http://genome.ucsc.edu/cgi-bin/hgGateway
Human Genome Database (GDB; RTI) http://www.gdb.org/
DrugMatrix (toxicogenomics and pharmacology; Iconix) http://www.iconixpharm.com/
KEGG genes database (collection of gene catalogs for genomes;
Kyoto University) http://www.genome.jp/kegg/genes.html
Marker Maps (Mapping data of genetic markers; CHLC-NIH) http://gai.nci.nih.gov/html-chlc/ChlcMaps.html
NCBI Nucleotide Sequence Database (NCBI-NIH) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide
PharmGKB − (Knowledge base for relationships among drugs, diseases,
and genes; Stanford University) http://pharmgkb.org
SymAtlas (Experimental gene functionalization datasets; GNF) http://symatlas.gnf.org/SymAtlas/
Tox-MIAMExpress (links biological endpoint data with gene expression
data; EBI) http://www.ebi.ac.uk/tox-miamexpress/
TransFac (database on eukaryotic transcription factors, their
genomic binding sites and DNA-binding profiles; Biobase) http://www.gene-regulation.com/pub/databases.html#transfac
TransPath (data visualization and modeling and for the analysis
of gene expression data; Biobase) http://www.gene-regulation.com/pub/databases.html#transpath
Bioinformatics
Biological Biochemical Image Database (Biological pathways, macromolecular
structures, gene families, and cellular relationships; NIH) http://bbid.grc.nia.nih.gov/
BioModels (Database of annotated published biological models;
EMBL-EBI) http://www.ebi.ac.uk/biomodels/
Comparative Toxicogenomics Database (Interactions between chemicals
and genes/proteins in organisms; Mount Desert Island Biological
Laboratory) http://ctd.mdibl.org/
ExPASy − Expert Protein Analysis System ? Sequence Retrieval
System (Network browser for databanks in molecular biology; SIB)
http://www.expasy.org/cgi-bin/search-biochem-index
Integr8 (Database of complete genomes and proteomes; EMBL-EBI) http://www.ebi.ac.uk/integr8/EBI-Integr8-HomePage.do
OmicBrowse (Integrative databases of the multi-dimensional “omic
space”; RIKEN) http://omicspace.riken.jp/gps/index.html
Structural Biology Software Database (University of Illinois) http://www.ks.uiuc.edu/Development/biosoftdb/
TIGR gene index (Analysis of transcribed sequences for various
organisms; TIGR) http://www.tigr.org/tdb/tgi
Cheminformatics
Cambridge Structural Database (Small molecule crystal structures;
CCDC) http://www.ccdc.cam.ac.uk/products/csd/
ChEBI ? Chemical Entities of Biological Interest (Dictionary
of small chemical compounds and molecular entities; EMBL-EBI) http://www.ebi.ac.uk/chebi/
ChemBank (Data from small molecules; Harvard University) http://chembank.broad.harvard.edu/
ChemIDplus (Structure and nomenclature information of chemicals
cited in NLM databases; NLM) http://chem.sis.nlm.nih.gov/chemidplus/
KEGG LIGAND Database (Databases of chemical substances and reactions
relevant to biological systems; Kyoto University) http://www.genome.ad.jp/ligand/
Klotho: Biochemical Compounds Declarative Database (University
of Missouri) http://www.biocheminfo.org/klotho/
NCI DIS 3D (3-D structures of over 400,000 pharmaceutical drugs;
NIH-NCI) http://dtp.nci.nih.gov/docs/3d_database/dis3d.html
Nucleic Acid Database (3-D structural information about nucleic
acids; Rutgers University) http://ndbserver.rutgers.edu/
PubChem (Biological activities of small molecules; NCBI-NIH) http://pubchem.ncbi.nlm.nih.gov/
Structure-Activity Relationships (SAR) Toxicity Database (International
Life Sciences Institute) http://rsi.ilsi.org/devtoxsar.htm
Cytomics
Apoptosis-DB (The Burnham Institute) http://www.apoptosis-db.org
Dynamic Signaling Maps (Hippron Physiomics Inc.) http://www.hippron.com/hippron/index.html
GenAge Database (genes related to senescence:; FUNDP) http://genomics.senescence.info/genes/index.html
PathArt (mammalian signaling and disease pathways; Jubilant Biosys) http://jubilantbiosys.com/ppa.htm
ResNet Pathway Database (eukaryotic molecular interactions; Ariadne
Genomics) http://www.ariadnegenomics.com/products/resnet/
SPAD − Signaling Pathway Database (genetic information and signal
transduction systems; Kyushu University) http://www.grt.kyushu-u.ac.jp/spad/index.html
Metabonomics
BOND − Biomolecular Object Network Databank (Thomson Corporation) http://www.unleashedinformatics.com/index.php?pg=products
BRITE− Biomolecular Relations in Information Transmission Expression
(mapping of genomic and molecular data; Kyoto University) http://www.genome.jp/brite/
Case Pathways Database System (biological pathways data and visualization
tools; Case Western Reserve University) http://nashua.cwru.edu/PathwaysWeb/
CGAP − Cancer Genome Anatomy Program (Pathways Search Portal;
NIH-NCI) http://cgap.nci.nih.gov/Pathways/
ExPASy − Expert Protein Analysis System (Biochemical Pathways;
SIB) http://www.expasy.org/cgi-bin/search-biochem-index
HumanCyc (metabolic pathways and genome; SRI International) http://humancyc.org/
IPA − Ingenuity Pathways Analysis (Ingenuity Systems) http://www.ingenuity.com/products/pathways_analysis.html
KEGG − Kyoto Encyclopedia of Genes and Genomes (manually drawn
pathway maps; Kyoto University) http://www.genome.jp/kegg/
MetaCyc (experimentally-determined metabolic pathways; SRI International) http://www.metacyc.org/
Pathway Database (metabolic pathways; Protein Lounge) http://www.proteinlounge.com/pathway_home.asp
Pathway Interaction Database (PID; NIH) http://pid.nci.nih.gov/
Reactome (core pathways and reactions; CSHL/EBI) http://www.reactome.org/
Proteomics
AMDIS − Automated MS Deconvolution and Identification System
(mass spectral reference library; USEPA, NIH, NIST) http://www.nist.gov/srd/nist1a.htm
BOND − Biomolecular Object Network Databank (Thomson Corporation) http://www.unleashedinformatics.com/index.php?pg=products
Blocks (multiply aligned ungapped segments corresponding to the
most highly conserved regions of proteins; Fred Hutchinson Cancer
Research Center) http://blocks.fhcrc.org/
BMRB − BioMagResBank (NMR spectra on proteins, peptides, and
nucleic acids; University of Wisconsin − Madison) http://www.bmrb.wisc.edu/
BRENDA − Enzyme Database (Cologne University) http://www.brenda.uni-koeln.de/
CluSTr (hierarchy of cluster of related proteins; EMBL-EBI) http://www.ebi.ac.uk/clustr/
Database of Macromolecular Movement (conformational changes in
proteins; Yale University) http://molmovdb.mbb.yale.edu/molmovdb/
DIP − Database of Interacting Proteins (experimentally determined
interactions between proteins; UCLA) http://dip.doe-mbi.ucla.edu/
Enzyme Structures Database (known enzyme structures in PDB; EBI) http://www.ebi.ac.uk/thornton-srv/databases/enzymes/
IMGT/3Dstructure-DB (protein structure query; IMGT) http://imgt3d.igh.cnrs.fr/
InterPro/InterProScan (database of protein families, domains
and functional sites; EMBL-EBI) http://www.ebi.ac.uk/InterProScan/
iProClass (databases for protein families, functions and pathways,
interactions, structures and structural classifications, genes
and genomes, ontologies, literature, and taxonomy; GU-PIR) http://pir.georgetown.edu/iproclass/
Markers List (protein markers; Lacroix) http://www.geocities.com/m.lacroix/marqueurs/lismark.htm
PDB − Protein Data Bank (RCSB) http://www.rcsb.org/pdb/home/home.do
PFD − Protein Folding Database (biophysical data from experimental
protein folding studies; Victorian Bioinformatics Consortium) http://pfd.med.monash.edu.au/cgi-bin/WebObjects/pfd
PRINTS (protein fingerprints; University of Manchester) http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
PROSITE (protein families and domains; SIB ExPASy) http://us.expasy.org/prosite/
Protein Database (protein sequences; NIH NCBI) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
Protein Sequence Database (GU-PIR) http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
Proteome Bioknowledge Library (protein interactions; Incyte) https://www.proteome.com/control/tools/proteome
Topology of Protein Structure (University of Glasgow) http://www.tops.leeds.ac.uk/
UniProt − Universal Protein Resource (protein sequence and function;
SIB) http://www.expasy.uniprot.org/index.shtml
UniProtKB − Universal Protein Resource Knowledgebase (protein
function, classification, and cross-reference; SIB) http://www.expasy.org/cgi-bin/sprot-search-ful
Physiomics
Blood/Brain-Barrier Information (University of Arizona) http://users.ahsc.arizona.edu/davis/bbb.htm
Cardiac Anatomical Database (Johns Hopkins) http://www.ccbm.jhu.edu/software/card.php
ERED − Environmental Residue-Effects Database (biological effects
and tissue concentrations measurements; US Army Core of Engineers,
USEPA) http://el.erdc.usace.army.mil/ered/
Glandular Organ Development Database (complete info from macroscopic
level description to genetics; Hunter and Davies) http://www.ana.ed.ac.uk/anatomy/database/orghome.html
Human Anatomy Online (animation/graphics; Intellimed) http://www.innerbody.com/index.html
ICRP − International Commission on Radiological Protection (reference
anatomical and physiological values for occupational settings;
ICRP) http://www.icrp.org/
JavaMan (computer model of human physiology; University of Adelaide) http://www.health.adelaide.edu.au/paed-anaes/javaman/
LONI Atlases (brain structure and function; UCLA) http://www.loni.ucla.edu/Atlases/
Neurodatabase (database of neurophysiology; Cornell University) http://neurodatabase.org/dataserver/
NHANES − National Health and Nutrition Examination Survey (CDC) http://www.cdc.gov/nchs/nhanes.htm
P3M − Physiological Parameters for PBPK Modeling (The Lifeline
Group) http://www.thelifelinegroup.org/p3m
Pathophysiology of the Digestive System (Colorado State University) http://arbl.cvmbs.colostate.edu/hbooks/pathphys/digestion/
Pathophysiology of the Endocrine System (Colorado State University) http://arbl.cvmbs.colostate.edu/hbooks/pathphys/endocrine/
PBPK parameter database (anatomical, physiological, biochemical,
and physicochemical data; Health and Safety Laboratory) http://www.hsl.gov.uk/capabilities/pbpk_database.htm
Primate Info Net (anatomy and physiology of tissues and organ
systems; University of Wisconsin − Madison) http://pin.primate.wisc.edu/aboutp/anat/index.html
Visible Human Project (3D representations of normal anatomy and
physiology; NIH) http://www.nlm.nih.gov/research/visible/visible_human.html
Whole Brain Atlas (Harvard University) http://www.med.harvard.edu/AANLIB/home.html
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