MODELS & DATABASES

MODELS

This website contains models and databases that we have developed or co-developed and links to other websites with models and databases. 

The downloadable materials included on this website are provided to interested parties at no cost; however, to download any material you need to first request a password by sending an e-mail with your name and affiliation and download of interest to Jon Arnot.The registration information also provides us with contact information so that we can send notifications for model updates.

The models are updated occasionally to address potential errors and “bugs in the code” and to reflect scientific advancements. The most recent versions of the models and databases are most relevant since they include updates and possibly corrections to previous versions. Users are strongly encouraged to read the associated papers listed with the models and the “help” and “about” information accompanying the models (when included) before using them.

Limitations of liability and disclaimer of warranty
ARC Arnot Research & Consulting Inc. and all associated collaborators do not guarantee, warrant, or make any representations, either expressed or implied, regarding the use, or the results of the use of the materials provided with regards to reliability, accuracy, correctness, or otherwise. There are no warranty rights granted to users of the models or databases provided.

Users assume the entire risk as to the results and performance of the models and databases. ARC Arnot Research & Consulting Inc. and all associated collaborators are not liable under any circumstances, for any damages whatsoever, arising out of the use, or the inability to use, the models and databases provided, even if advised of the possibility of such damages.

jon@arnotresearch.com

RAIDAR (Risk Assessment, Identification And Ranking ) model
RAIDAR is an evaluative, regional-scale, mass balance model for screening level exposure and risk assessment. The model simulates chemical fate and transport in the environment, bioaccumulation in a range of species, food web bioaccumulation, far-field exposures to humans and representative ecological species, and effects (risk).  The general intent of the model is to screen and prioritize large numbers of chemicals based on hazard, exposure and risk assessment objectives for more comprehensive, higher-tiered assessments. The model has been used for high-throughput risk assessments for Environment Canada to address legislation outlined under the Canadian Environmental Protection Act 1999. Full details of the model are available in the following publications:

– Arnot JA, Mackay D, Parkerton TF, Zaleski RT, Warren CS. 2010. Multimedia modelling of human exposure to chemical substances: the roles of biomagnification and biotransformation. Environ Toxicol Chem 29(1): 45-55.

– Arnot JA, Mackay D. 2008. Policies for chemical hazard and risk priority setting: Can persistence, bioaccumulation, toxicity and quantity information be combined? Environ Sci Technol 42: 4648-4654.

– Arnot JA, Mackay D, Webster E, Southwood J. 2006. Screening level risk assessment model for chemical fate and effects in the environment. Environ Sci Technol 40: 2316-2323. 

The RAIDAR model is currently being revised to:

Simulate fate, bioaccumulation and exposure for ionogenic organic chemicals:
– Arnot JA, Armitage JM, Reid L, Wania F, Mackay D. 2012. Simulating ionogenic chemical fate, bioaccumulation and exposure with RAIDAR. SETAC Conference, November May 20-24, Berlin, Germany.

Calculate Trophic Magnification Factors (TMFs) in various food webs:
– Arnot JA, Burkhard L, Reid L. 2011. Applying multimedia models to calculate trophic magnification factors (TMFs): exploring basic assumptions and the role of the physical environment. SETAC Conference, May 15-19, Milan, Italy.
– Arnot JA, Burkhard L, Reid L. 2010. Exploring the use of multimedia fate and bioaccumulation models to calculate trophic magnification factors (TMFs). SETAC Conference, November 7-11, Portland, OR.

RAIDAR Ver.2.00 (Released March 2012)

RAIDAR Ver.2.01 (Released July 2012 to address a minor display error in Ver.2.00)

FHX (Far-field Human eXposure) model
FHX is an evaluative, regional-scale, mass balance model for screening level far-field human exposure assessment. The general objective of the FHX model is to provide information on far-field human exposures to chemicals by linking information on physical-chemical properties and chemical emissions to the environment with simulations for chemical fate in the physical environment (air, water, soil and sediment), food web bioaccumulation (including aquatic and agricultural food chains), and multimedia contact rates (inhalation of outdoor air, ingestion of drinking water and foodstuffs) for different human age classes representing the Canadian population.

The FHX model was co-developed with scientists at Health Canada and is currently parameterized using Health Canada Exposure Factor Data (ca. 1998) for seven age classes. The model calculates chemical intake rates and intake fractions.

Full details of the model are available in the following publications:

-Arnot JA, Mackay D, Sutcliffe R, Lo B. 2010. Estimating farfield organic chemical exposures, intake rates and intake fractions to human age classes. Environ Modell Softw 25:1166-1175.

Versions for Download: FHX Ver.1.11 (Released March 2012)

Download FHX Ver.1.11 

For earlier versions of the FHX model, please go the Canadian Centre for Environmental Modelling and Chemistry (CEMC) website 
or 
contact Jon Arnot

FHX-CAN (Far-field Human eXposure in Canada) model

FHX-CAN is an evaluative, regional-scale, mass balance model for screening level far-field human exposure assessments in selected regional areas of Canada. The general objective of the FHX-CAN model is to provide information on far-field human exposures to chemicals by linking information on physical-chemical properties and chemical emissions to the environment with simulations for chemical fate in the physical environment (air, water, soil and sediment), food web bioaccumulation (including aquatic and agricultural food chains), and multimedia contact rates (inhalation of outdoor air, ingestion of drinking water and foodstuffs) for seven human age classes in five specific Canadian regions. The model calculates chemical intake rates and intake fractions.

The FHX-CAN model was developed for Health Canada and is based on the FHX model and includes regional environments from the ChemCAN model.

Most details of the model are available in the following publications:

– Arnot JA, Mackay D, Sutcliffe R, Lo B. 2010. Estimating farfield organic chemical exposures, intake rates and intake fractions to human age classes. Environ Modell Softw 25:1166-1175.

– Webster E, Mackay D, Di Guardo A, Kane D, Woodfine D. 2004. Regional differences in chemical fate model outcome. Chemosphere 55: 1361-1376. 

Versions for Download:

FHX-CAN Ver.1.11 (Released March 2012)

Download FHX-CAN Ver.1.11 

AQUAWEB (Aquatic Food Web) model

AQUAWEB is a site-specific bioaccumulation model for aquatic food webs and provides estimates of chemical concentrations in organisms of aquatic food webs from chemical concentrations in the water and the sediment. The model is presented in rate constant format for assessing the bioaccumulation of non-ionic hydrophobic organic chemicals at steady-state.

For zooplankton, aquatic invertebrates and fish the model calculates rates of chemical uptake from the water and the diet and rates of chemical elimination to the water, feces and the “pseudo-loss” mechanism of growth dilution. Metabolic biotransformation rate data can also be included as a mechanism of chemical elimination (see database and the BCFBAF module of US EPA EPI Suite™). AQUAWEB is a modification of a previous food web model (Gobas 1993). The models are intended to estimate chemical concentrations and associated bioconcentration factors (BCF), bioaccumulation factors (BAF) and biota-sediment accumulation factors (BSAF) of non-ionic hydrophobic organic chemicals. The models are useful for assessing exposure and risks of chemicals in the water and sediment to organisms in aquatic ecosystems and higher trophic level organisms that eat aquatic species such as birds and mammals, including humans. 

Both the Gobas 1993 and Arnot and Gobas 2004 models have been evaluated using empirical data from three different freshwater ecosystems involving 1,019 observations for 35 species and 64 chemicals and are coded in one Microsoft Excel™ workbook. The AQUAWEB model also forms the basis of the U.S. Environmental Protection Agency’s KABAM model used primarily for pesticide assessments. 

Full details of the 2004 model are available in the following publication:

– Arnot JA, Gobas FAPC. 2004. A food web bioaccumulation model for organic chemicals in aquatic ecosystems. Environ Toxicol Chem 23(10): 2343–2355.

Versions for Download: For earlier versions of the AQUAWEB model please contact Jon Arnot.

AQUAWEB Ver.1.3

Download AQUAWEB 

Screening-level BCF and BAF models

This model provides screening-level estimates of the bioaccumulation factor (BAF) for generic fish species in lower, middle and upper trophic levels of aquatic food webs. The model also provides screening-level estimates of the bioconcentration factor (BCF) for water exposures only (i.e., in laboratory bioconcentration tests). The models require only the octanol-water partition coefficient (KOW) of the chemical and the metabolic biotransformation rate constant as input parameters (see database and the BCFBAF module of U. S. EPA’s EPI Suite™).

The BAF models are derived from the parameterization and calibration of a mechanistic bioaccumulation model to a large database of evaluated measured BAFs. The measured BAFs are for chemicals that are poorly metabolized and are grouped into lower, middle and upper trophic levels of fish species. The model is calibrated to each trophic level of measured BAF values thus providing estimates that are in general agreement with measured BAFs, thus capturing the overall food web biomagnification potential of chemicals in aquatic food webs for screening assessments. 

The model is intended to estimate BCFs and BAFs for non-ionic organic chemicals only. Thus it provides generic estimates in absence of site-specific measurements or estimates. The model can be used to predict dietary concentrations for higher trophic level predators (e.g., birds and mammals) including human exposure concentrations from fish in their diet. A previous version of the model has been used to categorize chemicals for their potential to bioaccumulate in aquatic food webs for Environment Canada to address legislation outlined under the Canadian Environmental Protection Act 1999. The model is coded in a Microsoft Excel™ workbook. 

General information on the model is available in the following publication:

– Arnot JA, Gobas FAPC. 2003. A generic QSAR for assessing the bioaccumulation potential of organic chemicals in aquatic food webs. QSAR Comb Sci 22(3): 337-345.

Versions for Download: 

BCFBAF Ver1.2 model (Spreadsheet Model)
Download BCFBAF VER1.2

OR available in U. S. EPA’s EPI Suite 

San Francisco Bay Food Web Bioaccumulation model

This model was developed to assess the effects of PCBs in wildlife and fishermen in San Francisco Bay and to identify potential risk management actions. The objective of this model is to estimate the concentrations of PCBs in a set of key species that reside in the Bay as a result of PCB concentrations in sediments and water in the Bay. 

The species that are the main focus of the study are the double-crested cormorant (Phalacrocorax auritus), the Forster’s tern (Sterna Forsteri), and the harbor seal (Phoca vitulina richardsi), as well as three fish species that are frequently caught by fishermen in the Bay, i.e. shiner surfperch (Cymatogaster aggregata), jacksmelt (Atherinopsis californiensis) and white croaker (Genyonemus lineatus). The fish species are important end-points of the model because of their role in passing PCBs to fishermen. Double-crested cormorants, Forster’s terns and harbor seals are included in the model because they have been identified as sensitive receptors of PCBs. 

The model can be used to determine what concentrations of PCBs in the water and sediments of the Bay need to be reached to achieve an adequate margin of safety in wildlife and humans exposed to PCBs in the Bay area. This information can be used as part of a Total Maximum Daily Loading (TMDL) characterization to formulate remedial actions to achieve desired water quality goals.

The model is in the form of a Microsoft Excel™ workbook. 

General information on the model is available in the following publication:

– Gobas FAPC, Arnot JA. 2010. Food web bioaccumulation model for polychlorinated biphenyls in San Francisco Bay, California, USA. Environ Toxicol Chem 29:1385-1395.


For more information on this model please contact Jon Arnot or Frank Gobas.

Contact Jon Arnot 

Fish biotransformation rate constant (or half-life) QSARs

The fish biotransformation rate constant (kM) database – July 2008 has so far been used to develop two QSARs that can be used to predict screening-level kM estimates from chemical structure (i.e., SMILES notation). The predictions can be used for screening level bioaccumulation hazard assessments, exposure and risk assessments, comparisons with other in vivo and in vitro estimates, and as a contribution to testing strategies that reduce animal usage. 

The first “kM-QSAR” is included in the BCFBAF module of the U. S. EPA’s EPI Suite™ software package and details about this QSAR are provided in the following publication:

– Arnot JA, Meylan W, Tunkel J, Howard PH, Mackay D, Bonnell M, Boethling RS. 2009. A quantitative structure-activity relationship for predicting metabolic biotransformation rates for organic chemicals in fish. Environ Toxicol Chem 28(6): 1168-1177. 

Versions for Download: 

Download Here – U. S. EPA’s EPI Suite™ 

The second “kM-QSAR” has recently been developed using the Iterative Fragment Selection QSAR method developed by Trevor Brown. 
Details about this QSAR are provided in the following publication:

– Brown TN, Arnot JA, Wania F. 2012. Iterative fragment selection: A group contribution approach to predicting fish 
biotransformation half-lives. In press Environ Sci Technol DOI: 10.1021/es301182a 

Download – IFS_Fish_HLQSAR 

The IFS Fish HLQSAR Ver1.0 model is also available for download at Frank Wania’s web page 

Thank you for your interest in these models. 
For more information about these models and databases please contact Jon Arnot.

Request Permissions

DATABASES

The Excel spreadsheet models and databases are expected to work using Microsoft Office or other similar programs (Note: Visual Basic for Applications support is often required).

Limitations of liability and disclaimer of warranty
ARC Arnot Research & Consulting Inc. and all associated collaborators do not guarantee, warrant, or make any representations, either expressed or implied, regarding the use, or the results of the use of the materials provided with regards to reliability, accuracy, correctness, or otherwise. There are no warranty rights granted to users of the models or databases provided.

Users assume the entire risk as to the results and performance of the models and databases. ARC Arnot Research & Consulting Inc. and all associated collaborators are not liable under any circumstances, for any damages whatsoever, arising out of the use, or the inability to use, the models and databases provided, even if advised of the possibility of such damages.

jon@arnotresearch.com

BCF and BAF database

This database is the result of a review of 392 scientific papers and publicly available bioaccumulation data sources and includes 5,317 BCFs and 1,656 BAFs measured for 842 organic chemicals in 219 aquatic species. The data were subject to a data quality evaluation and scoring method. 

Details about the database and the data quality assessment method are available in the following publication: 

– Arnot JA, Gobas FAPC. 2006. A review of bioconcentration factor (BCF) and bioaccumulation factor (BAF) assessments for organic chemicals in aquatic organisms. Environ Rev 14: 257-297. 

Versions for Download: >

Download Here – BCF and BAF database – 2006 

Fish biotransformation rate constant (kM) database

Fish biotransformation rate constant (kM) database

More than 5,400 bioaccumulation measurements in fish for more than 1,000 organic chemicals were critically reviewed to compile a database of 1,535 kM estimates for 702 organic chemicals. Biotransformation rates range over six orders of magnitude across a diverse domain of chemical classes and structures. Screening-level uncertainty analyses provide guidance for the selection and interpretation of kM values.

Details about the database are available in the following publication:

– Arnot JA, Mackay D, Parkerton TF, Bonnell M. 2008. A database of fish biotransformation rates for organic chemicals. Environ Toxicol Chem 27(11): 2263-2270.

Versions for Download:

Download Here – kMdatabase 

Thank you for your interest in these databases. 
For more information about these databases please contact Jon Arnot.

Request Permissions