CompTox Chemicals Dashboard: Release Notes

• Latest Version 
• Latest Version: Known Issues
• Previous Versions

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Latest Version

Version 2.5 – November 05, 2024 

Feature Updates 

• Advanced Search > Molecular Formula Search has a new option, Formula Contains that has been made the default selection 
• Reply column has been added to the Comments page 
• Updated the Hazard and HTPP data and assay descriptions, respectively, to accordions to be more widely accessible 
• In the downloaded Batch Search file after MS-Ready SMILES are selected, MS-Ready mass and MS-Ready formulae are now included 

Data (Updated) 

• The hazard database is updated to ToxValDB v9.5, visualized on the Hazard and Executive Summary tabs. ToxValDB v9.5 represents a major restructuring compared to previous versions, please see the EPA CCTE Clowder repository for more detail. 
  • Executive Summary tab restructure due to updated ToxValDB 
    • Reproductive and Developmental Toxicology endpoints are now displayed together 
    • Subacute, endocrine system, and occupational exposure endpoints are no longer displayed 
  • Hazard subtab 
    • The scope of ToxValDB has been modified to focus curation efforts on human health-relevant toxicity information. Visit the ECOTOX Knowledgebase (ECOTOX, www.epa.gov/ecotox) to access ecological toxicity data from over 54,000 publications, including effects and endpoints measured and detailed metadata from each toxicity test on test compound, test organism, study design, test conditions, and statistical analysis.  
    • Revised classification schemes were developed for effect type supercategory, risk assessment class, study type, study duration class, and quality control. 
    • A new classification was added to indicate whether records were experimentally-derived, as opposed to cases where the numeric for the effect level is based on an analogue or surrogate chemical. 
    • Improvements to source document accessibility have been made via added columns of subsource URL and stored source record (links to associated documents in the EPA CCTE Clowder repository) 
  • Genotoxicity subtab 
    • Export option is now available 
    • 1 additional column (Genotox Call) has been added to the Summary table 
  • Skin/Eye subtab 
    • Two additional columns (GLP and Authority) have been added to the Hazard > Skin / Eye subtab, in addition to updating the source link. Please note that the GLP and Authority columns can be made visible through selection any column heading. 

      

    • New High Throughput Phenotypic Profiling (HTPP) data from multiple cell types are available via the Bioactivity > HTPP: Summary subtab. Updates also include two new columns (Seeding Density and Exposure Duration). Plot toggle buttons are available for Cell Type, Exposure Duration, and Seeding Density. Data visualizations have been updated to facilitate viewing of results in instances where a chemical has been tested in more than one combination of Cell Type, Exposure Duration and Seeding Density.
    • New Factotum/ChemExpoDB data (CPDat 4.0.0-alpha.3 - March 2024), visualized on the Exposure > Product & Use Categories, Chemical Weight Fraction, and Chemical Functional Use subtabs, as well as the homepage Products/Use Categories search.
    • Updated SeqAPASS data, visualized on the Bioactivity > ToxCast: Summary subtab, specifically the “SeqAPASS” column in data table.

Resolved Issues

• In the Executive Summary
  • the Regional Screening table is now visible
  • the IVIVE POD has been removed since no data source were available to populate it
• The Hazard data hoverover descriptions for various point-of-departure (PODs) values are updated.
• Genotoxicity aggregation for number of reports positive and negative are correct.
• The gene information for individual assays under Lists of Assays now point to multiple genes, when applicable.
• Comment status is now being correctly shown (e.g., “Resolved”)
• Batch Search
  • The MetFrag option has been removed, as it has not been active for several years
  • Safety Data option is now providing correct links to the GHS website
  • Integrated Source warnings in the FOUND_BY column within the downloaded batch search files have been removed

Known Issues

• ACD/Labs. OPERA, TEST and EPISuite chemical predictions have not been updated. Issues remain in regard to the display of certain OPERA calculation reports.
• Structure Substructure Search – Substructure searches fail to take explicitly defined stereochemistry into account.
• Hazard (information below pertains to known issues in ToxValDB v9.5; an updated version of ToxValDB that resolves these issues may become publicly available before the next CCD release, please see https://github.com/USEPA/toxvaldbmain for updates)
  • Missing Regional Screening Level (RSL) data: a subset of chemicals with RSL values are missing from the Executive Summary RSL Table and from the Hazard subtab
  • Records from HAWC Project are erroneously grouped in the source “EPA HAWC”. HAWC Project includes data from projects outside of EPA and is not an EPA-based product.
  • A subset of records is absent from the included ECHA IUCLID subsources: Immunogenicity, Carcinogenicity, Neurotoxicty, Developmental Toxicity Teratogenicity, Toxicity Reproduction, Repeated Dose Toxicity Oral
• The ability to perform InChIKey skeleton searches via the batch search, and download an associated export file (e.g., CSV, XLSX, etc.), is not working.

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox (incl. ACD Lab Names and MS-Ready, QSAR-Ready)	20240208_DSSTox	Feb-24	20240208_DSSTox
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
OPERA	v2.6	Apr-23	-
ACD Labs/PERCEPTA	-	-	-
Analytical QC for PFAS compounds	PMID: 36535553	Nov-22	Analytical QC for PFAS compounds
ACToR	-	-	ACToR
ToxValDB	v.9.5	August-24	ToxValDBv9.5 GitHub
ToxRefDB	v2.1	Aug-22	ToxRefDBv2.1
invitroDB /ToxCast	v4.1	Sept-23	invitroDBv4.1
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra ; res_htpp_u2os_toxcast	May-24	Metadata for the HTPP global- , category- , and feature-level mappings  HTPP U2OS Publication
AOP	-	Apr-23	AOP-wiki
SeqAPASS	SeqAPASS data version 8	Apr-24	SeqAPASS
Product & Use Categories	CPDat 4.0.0-alpha.3 (March 2024)	Mar-24	ChemExpo  CPDat Publication
Chemical Weight Fraction	CPDat 4.0.0-alpha.3 (March 2024)	Mar-24	ChemExpo  CPDat Publication
Collected Data on Functional Use	CPDat 4.0.0-alpha.3 (March 2024)	Mar-24	ChemExpo  CPDat Publication
Predicted Probability of Associated Functional Use	ccd_qsur_table_Sep-27-2023.csv	Sept-23	Publication data
Biomonitoring Data	NHANES-Parent-Chemical-Exposure-Inferences-2024-4-25.txt	Apr-24	R package "bayesmarker" Publication Publication2
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	flat file submitted by subject matter expert (new2020ProductionVolumeData_longform.xlsx)	Oct-22	CDR website
ADME > IVIVE	HTTK v2.3	Jan-24	HTTK invivoPKfit Concen. vs time

Previous Versions

Version 2.4.1 – April 2024

After the Version 2.4 release, we noticed a few issues, which are now fixed.

• ToxValDB Batch Search download was not working. It is now able to be downloaded.
• Broken images in tile view now shows, “No image found for this structure”
• The time stamps on chemical lists are updated

Please note that the release notes for Version 2.4 – April 2024 are still applicable.

Version 2.4 – April 2024

Feature Updates

• Enhanced batch search
  • New option “ToxRefDB Details” under Enhanced Data Sheets containing individual ToxRefDB data
  • Updated option “ToxCast Assays: AC50” under Enhanced Data Sheets containing active AC50 data instead of simply active/inactive.
• Utilizing publicAPIs for home page chemical searching, chemical lists, and presence in lists

Data (Updated)

• DSStox – updated chemical database, including ~17,000 new chemicals, release of newly curated data, new ACD/IUPAC and ACD/Index Names for tens of thousands of chemicals, fully regenerated MS-Ready and QSAR-Ready structures to address previously reported bug for multicomponent chemicals, newly generated ToxPrints across the entire dataset.
• Structure-substructure-similarity search database updated with new chemicals and reindexed. Improved formula searches in terms of include/exclude elements.
• ADME > IVIVE data table has been updated using the latest release of the HTTK R-package v2.3. Two additional data points have been added to this table.
  • Measured Volume of Distribution (in rats) and measured PK half-life (in rats) based on estimations from toxicokinetic concentration vs. time data contained in the CvTdb database, https://doi.org/10.1038/s41597-020-0455-1.
• Predicted Probability of Functional Use found under Exposure > Chemical Functional Use
• Biomonitoring data found under Exposure > Biomonitoring Data

Resolved Issues

• Re-enabled batch download MS-Ready and QSAR-Ready SMILES, and ToxPrint fingerprints, including correct data.
• Issues with InChIKey searching fixed by refresh of InChI data for all newly curated and new chemical data registrations
• “Presence of Lists” in both the Chemical Details page and in the batch search are up-to-date.
• Re-enabled ECHA links in the Links subtab
• Re-enabled Monoisotopic Mass Batch Search

Known Issues 

• ACD/Labs. OPERA, TEST and EPISuite chemical predictions have not been updated. Issues remain in regard to the display of certain OPERA calculation reports.
• Structure Substructure Search – Substructure searches fail to take explicitly defined stereochemistry into account.
• The Regional Screening table is not visible in the Executive Summary; however this and other hazard data are still available in the Hazard tab. This table will be available when ToxValDB is updated.
• The gene information for individual assays under Lists of Assays only contains a single gene, which is incomplete for assay endpoints annotated to > 1 gene in the ToxCast database, invitrodb. However, all genes associated with the assay endpoints are correctly linked in the ToxCast Summary tab (plot and table).
• The Hazard data hoverover descriptions for various point-of-departure (PODs) values as currently displayed may not be accurate for a subset of PODs. The subset are provided below (table) for reference and will be updated in the next release of ToxValDB and subsequently in CCD

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox (incl. ACD Lab Names and MS-Ready, QSAR-Ready)	20240208_DSSTox	Feb-24	20240208_DSSTox
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
OPERA	v2.6	Apr-23	-
ACD Labs/PERCEPTA	-	-	-
Analytical QC for PFAS compounds	PMID: 36535553	Nov-22	Analytical QC for PFAS compounds
ACToR	-	-	ACToR
ToxValDB	v.9.4	Apr-23	ToxValDBv9.4
ToxRefDB	v2.1	Aug-22	ToxRefDBv2.1
invitroDB /ToxCast	v4.1	Sept-23	invitroDBv4.1
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra	Jul-22	Metadata for the HTPP global- , category- , and feature-level mappings
AOP	-	Apr-23	AOP-wiki
Product & Use Categories	CPDat 4.0.0-alpha.2	Aug-23	ChemExpo  CPDat Publication
Chemical Weight Fraction	CPDat 4.0.0-alpha.2	Aug-23	ChemExpo  CPDat Publication
Collected Data on Functional Use	CPDat 4.0.0-alpha.2	Aug-23	ChemExpo  CPDat Publication
Predicted Probability of Associated Functional Use	ccd_qsur_table_Sep-27-2023.csv	Sept-23	Publication data
Biomonitoring Data	NHANES-Parent-Chemical-Exposure-Inferences-2024-4-25.txt	Apr-24	R package "bayesmarker" Publication Publication 2
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	flat file submitted by subject matter expert (new2020ProductionVolumeData_longform.xlsx)	Oct-22	CDR website
ADME > IVIVE	HTTK v2.3	Jan-24	HTTK invivoPKfit Concen. vs time

Version 2.3 – December 2023 

Feature Updates 

• ToxCast Summary tab is now a single tab that combines the previous ToxCast Summary and ToxCast Conc. Response tabs 
• Updating ToxCast Summary tab to use invitrodb v4.1 resulted in addition of columns to the ToxCast Summary table, including benchmark dose (BMD), benchmark response (BMR), and Continuous Hitcall. For more details on the updates to invitrodb v4+, please see https://doi.org/10.3389/ftox.2023.1275980 
• New EPA Health Assessment Workspace Collaborative (HAWC) tab. For more information about EPA HAWC, please see https://www.epa.gov/risk/health-assessment-workspace-collaborative-hawc  
• Enhanced home page chemical search 
  • Provides search suggestions when available 
  • Provides a table of chemicals when a single search yields more than one match (e.g., pfos). This is executed by hitting the keyboard “enter” button after typing the ambiguous term 
• Enhanced batch search 
  • New button “Replace Batch Search Chemical” under Display All Chemicals that converts CASRN, names, and InChiKey to DTXSIDs and de-duplicates and puts them back in the search box 
  • Downloaded file contains all of the user’s search terms 
• Enhanced HTTr Summary plots with toggles for cell type and exposure duration 

Data (Updated) 

• invitroDBv4.1, visible in the ToxCast Summary and Executive Summary tabs, as well as in the Batch Search 
• CPDat.4.0.0.alpha.2 (early release of the upcoming CPDat 4.0), visible in the Exposure tab, specifically the following sub-tabs: Product & Use Categories, Chemical Weight Fraction, and Chemical Functional Use. 
• OECD endorsed AOPs relevant to bioactivitie(s) visible in the ToxCast Summary and Executive Summary tabs 

Resolved Issues 

• Mixtures, Components, and Isotopomers are now showing results for chemicals. 
• Mol files are now available for chemicals with no mass (e.g., DTXSID3020041) under Chemical Details > Details > Intrinsic Properties 
• Batch search using MS-Ready Formula(e) > Display all chemicals is displaying the correct number of chemicals found 
• Batch Search > Display all chemicals the lefthand dropdown is now working  
• Batch download of OPERA includes the updated OPERAv2.6 data 
• Env. Fate/Transport parameters have been removed from the Physchem Prop. tab. 

Known Issues

• Temporarily disabled the ability to batch download MS-Ready and QSAR-Ready SMILES and ToxPrint fingerprints due to data error issues. These features will be re-enabled in the next update of the Dashboard. 
• TEST chemical predictions are not yet available for the newly added chemicals since the last time DSSTox was refreshed (CCDv2.1). 
• The Regional Screening table is not visible in the Executive Summary; however, this and other hazard data are still available in the Hazard tab. This table will be available when ToxValDB is updated. 
• OPERA v2.6 was released and incorporated into the Physchem Prop and Env. Fate/Transport tables; however, the reports need updating as some of the images are missing and nearest neighbors are in log value for several property values. COMPARA and CERAPP models have not been updated under the Bioactivity > ToxCast Models tab and still reflect the values from the original publications of these models. 
• InChIKey searching is incorrect. 
• Chemical lists under the "Presence in Lists" have been updated to include only public lists; however, some chemical lists are missing from the Presence in Lists. 
• The gene information for individual assays under Lists of Assays only contains a single gene, which is incomplete for assay endpoints annotated to > 1 gene in the ToxCast database, invitrodb v4.1. However, all genes associated with the assay endpoints are correctly linked in the ToxCast Summary tab (plot and table). 

  

• In the Bioactivity > ToxCast: Summary sub-tab, the Assay List is not filterable, but is sortable (see image right).
• The Hazard data hover-over descriptions for various point-of-departure (PODs) values as currently displayed may not be accurate for a subset of PODs. The subset are provided below (table) for reference and will be updated in the next release of ToxValDB and subsequently in CCD. 

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox (incl. ACD Lab Names and MS-Ready, QSAR-Ready)	prod_dsstox_01262023	Feb-22	v2000 v3000
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
OPERA	v2.6	Apr-23	-
ACD Labs/PERCEPTA	-	-	-
Analytical QC for PFAS compounds	PMID: 36535553	Nov-22	Analytical QC for PFAS compounds
ACToR	-	-	ACToR
ToxValDB	v.9.4	Apr-23	ToxValDBv9.4
invitroDB	v4.1	Sept-23	invitroDBv4.1
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra	Jul-22	Metadata for the HTPP global- , category- , and feature-level mappings
AOP	-	Apr-23	-
Product & Use Categories	CPDat 4.0.0-alpha.2	Aug-23	ChemExpo  CPDat Publication
Chemical Weight Fraction	CPDat 4.0.0-alpha.2	Aug-23	ChemExpo  CPDat Publication
Collected Data on Functional Use	CPDat 4.0.0-alpha.2	Aug-23	ChemExpo  CPDat Publication
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker" Publication
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	flat file submitted by subject matter expert (new2020ProductionVolumeData_longform.xlsx)	Oct-22	CDR website
HTTK	v2.2.1	Sep-22	HTTK

Version 2.2.1 – May 2023

• Data (Updated)
  • Hazard update - ToxValDBv9.4
  • Physchem property and environmental fate/transport data - OPERA v2.6) updated data
• Resolved Issues
  • ToxValDB batch download function has been restored
  • Chemical structure images in the predicted TEST reports are now visible
• Known Issues
  • TEST and EPISuite chemical predictions are not yet available for the newly added chemicals.
  • The Regional Screening table is not visible in the Executive Summary; however this and other hazard data are still available in the Hazard tab. We are working to get this back up shortly.
  • Chemical lists under the "Presence of Lists" include outdated lists names. These outdated lists do not contain chemicals and information. 
  • Mixtures, Components, and Isotopomers are not showing results for most chemicals.
  • OPERA v2.6 was released; however the reports need updating. COMPARA and CERAPP models have not been updated.
  • Batch download of QSAR-Ready structures may be corrupted with commas.
  • Batch download of OPERA is utilizing v2.2 and not the v2.6 found through chemical-specific searching.
  • InChIKey searching is incorrect.
  • Env. Fate/Transport parameters in the Physchem Prop. tab only contain OPERA predictions. Please use the Env. Fate/Transport tab for these predictions.
  • Some ToxPrints (<1%) are incorrect.

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox (incl. ACD Lab Names and MS-Ready, QSAR-Ready)	prod_dsstox_01262023	Feb-22	v2000 v3000
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
OPERA	v2.6	Apr-23	-
ACD Labs/PERCEPTA	-	-	-
Analytical QC for PFAS compounds	PMID: 36535553	Nov-22	Analytical QC for PFAS compounds
ACToR	-	-	ACToR
ToxValDB	v.9.4	Apr-23	ToxValDBv9.4
invitroDB	v3.5 (prod_internal_invitrodb_v3_5)	May-22	invitroDBv3.5
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra	Jul-22	Metadata for the HTPP global- , category- , and feature-level mappings
AOP	-	-
Product & Use Categories	prod_factotum_202009	Sep-20	Factotum
Chemical Weight Fraction	prod_factotum_202009	Sep-20	Factotum
Collected Data on Functional Use	functional_use_data_05242022	May-22	Factotum
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker" Publication
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	flat file submitted by subject matter expert (new2020ProductionVolumeData_longform.xlsx)	Oct-22	CDR website
HTTK	v2.2.1	Sep-22	HTTK

Version 2.2.0 – March 2023

• Feature Updates
  • Addition of an ACToR tab (under the single chemical search) containing legacy data previously available via the now discontinued ACToR web services, as well as removing the legacy links
  • Updated Hazard tab including new sub-tabs (Hazard, Cancer, Genotoxicity, and Skin/Eye), as well as added new executive summary links
  • New Search capability - Structure Substructure Searching, available under the “Search” tab
  • Migration of About, News, Help, Downloads, and Release Notes sub-tabs to an easier to navigate (and update) website
  • Addition of Analytical QC data for PFAS compounds in the HTTr and HTTP data tables
  • Updated information icon in the HTTr and HTPP sub-tabs to include a metadata link.
  • Added an information icon to the Abstract Sifter sub-tab, including a link to the enhanced excel version of Abstract Sifter (free download).
  • Batch Search data availability enhancements – ToxPrints are now available for download in Excel format. Chemical lists are now available for download in CSV and SDF formats.
• Data (New and Updated)
  • Hazard update - ToxValDBv9.3, including genotoxicity and skin/eye data
  • Physchem Prop - ACD Labs PERCEPTA updated prediction data
  • ACToR – legacy data added; however, the data were previously available using the now discontinued ACToR web services
  • Analytical QC available for ~200 perfluorinated chemicals in the HTTr and HTTP data tables. Note the QC data is interpreted at the chemical level and these data are also relevant for the specific ToxCast PFAS samples, but have not yet been integrated into the ToxCast data tables on CCD. A download of the PFAS QC data is available at http://doi.org/10.23645/epacomptox.22118099 .
• Resolved Issues
  • Disabled invalid links in Exposure tables
  • Removed duplicated ToxCast data in the ToxCast Summary tables
  • Re-enabled the download of gene symbols from the ToxCast Summary table, as well as enable gene information in the pop-up from the Details column
  • Fixed executive summary links
  • Search path has been updated. e.g., “searched by DTXSID, etc.”
  • Interchangeable apostrophes are allowed in the search
  • Batch Search by DSSTox Compound ID is working
  • Batch Search toxprint downloads are now available in both csv and xlsx formats
• Known Issues
  • Chemical structure images in the predicted TEST reports are missing
  • TEST, OPERA, EPISuite chemical predictions are not yet available for the newly added chemicals

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox (incl. ACD Lab Names and MS-Ready, QSAR-Ready)	prod_dsstox_01262023	Feb-22	v2000 v3000
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
ACD Labs/PERCEPTA	-	Feb-22	-
Analytical QC for PFAS compounds	PMID: 36535553	Nov-22	Analytical QC for PFAS compounds
ACToR	-	-	ACToR
ToxValDB	v.9.3 (res_toxval_v93)	Sep-22	ToxValDBv9.3
invitroDB	v3.5 (prod_internal_invitrodb_v3_5)	May-22	invitroDBv3.5
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra	Jul-22	Metadata for the HTPP global- , category- , and feature-level mappings
Product & Use Categories	prod_factotum_202009	Sep-20	Factotum
Chemical Weight Fraction	prod_factotum_202009	Sep-20	Factotum
Collected Data on Functional Use	functional_use_data_05242022	May-22	Factotum
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker" Publication
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	flat file submitted by subject matter expert (new2020ProductionVolumeData_longform.xlsx)	Oct-22	CDR website
HTTK	v2.2.1	Sep-22	HTTK

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Version 2.1.1 - Winter 2022

Feature Updates

• Updated help pages under About > Help
• Redesign of the left-hand navigation to simplify finding the chemistry-related data tabs. The update includes adding a Chemical Details tab, with the following previously named tabs as sub-tabs: Details, Synonym, Related Substances, and Similar Compounds.
• reCAPTCHA implemented to ensure continued functionality
• Ability to visualize structures in Batch Search
• Ability to filter out chemicals that are structures

Data

• Data update
  • Production Volume has been updated to the latest Chemical Data Reporting data (2020)
  • ADME > IVIVE table has been updated using the latest release of the HTTK R-package v2.2.1

Resolved Issues

• The Endocrine System link in the Executive Summary points to the correct data
• The Advanced Search Min/Max issue is fixed
• All columns in the HTTr tables are now sortable
• Cell Type data is now displayed properly in the HTPP tables
• Toxcast Conc. Response Data plots are now visible for all recently loaded data
• Updated Batch Search to ignore 00-00-0
• In Tile View, the ability to select chemicals from a list to send to batch search is restored
• Batch Search can now handle chemical names with periods properly
• “Searched by” text included correct information
• Histograms selection has been restored in Assay view

Known Issues

• ACD/Labs values for water solubility are listed incorrectly
• Chemical structure images in the predicted TEST reports are missing
• TEST, OPERA, Percepta/ACD Labs, EPISuite chemical predictions are not yet available for the newly added chemicals
• Analytical QC data have not yet been incorporated in the bioactivity data tables

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox	prod_dsstox_202202	Feb-22	-
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
ToxValDB	v.9.1.1	Apr-21	ToxValDB v9.1.1
invitroDB	v3.5 (prod_internal_invitrodb_v3_5)	May-22	invitroDBv3.5
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra	Jul-22	Metadata for the HTPP global- , category- , and feature-level mappings
Product & Use Categories	prod_factotum_202009	Sep-20	Factotum
Chemical Weight Fraction	prod_factotum_202009	Sep-20	Factotum
Collected Data on Functional Use	functional_use_data_05242022	May-22	Factotum
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker"  Publication
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	flat file submitted by subject matter expert (new2020ProductionVolumeData_longform.xlsx)	Oct-22	CDR website
HTTK	v2.2.1	Sep-22	HTTK

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Version 2.1 - Fall 2022

• Feature Updates
  • Added HTTr and HTPP data and visualizations - data from EPA's High Throughput Transcriptomics (HTTr) and High Throughput Phenotypic Profiling (HTPP) have been added in separate “HTTr: Summary” and “HTTP: Summary” tabs, under the “Bioactivity” main tab. Data can be visualized in plots, searched, and downloaded.
  • Extended ToxVal download available in batch search - A new “Enhanced Data Sheet ->ToxVal Details” in the batch search allows the user to download the ToxVal data values. The ability to populate a Yes/No column for ToxVal data from the batch search “Metadata->Include ToxVal Data Availability” is still available.
  • Extended chemical property download available in batch search - A new “Enhanced Data Sheet -> Chemical Properties Details” in the batch search allows the user to download the experimental and predicted chemical property values altogether.
  • Updated demographics exposure predictions under “Exposure -> Exposure Predictions” to include multiple predictors (e.g., Systematic Empirical Evaluation of Models (SEEM), Stochastic Human Exposure and Dose Simulation (SHEDS), USETox), and new generic predictions data table for predicted production volume, presence/absence on the Stockholm Convention list, and probability of type of exposure.
  • Updated “More” column in the Hazard data table to include more complete metadata.
  • Updated ADME>IVIVE data table to include multiple species (human and rat), multiple models (1 compartment, 3 compartment steady state, and physiologically based toxicokinetic (PBTK)), and multiple percentiles (50% and 95%)
  • Streamlined the About dropdown menu and the About page
• Data
  • Data update
    • DSSTOX (prod_dsstox_202202), including ~300,000 new chemicals, plus updated MS-Ready and QSAR-Ready structures, and ACD Names
    • invitroDBv3.5 (prod_internal_invitrodb_v3_5), including updates to the ToxCast bioactivity data
    • ChemExpoDB (prod_factotum_202009), visible from the Exposure tabs
  • New data
    • HTTr (ro_httr_20220120) and HTPP (res_htpp_u2os_apcra) added in new sub-tabs under the Bioactivity tab
    • Please note, this initial release of the HTPP visualization includes the dataset published in Nyffeler et al. 2020 (PMID: 31899216). Data on additional chemicals, including additional PFAS chemicals, will be made available in future releases.
  • Note, new chemicals have been added as this release has incorporated an update to the DSSTOX database. The current update includes MS-Ready and QSAR-Ready structures and ACD Names. Due to limited resources, an update to the chemical predictions (TEST, OPERA, Percepta/ACD Labs, EPISuite) have not been included at this time. Please stay tuned for a future release containing these data.
  • Note, analytical QC data have not yet been incorporated. There are columns in the HTTr and HTPP data tables as placeholders. Please stay tuned for a future release containing these data, specifically for PFAS compounds in the near future.
• Resolved Issues
  • Executive summary links work properly
  • Chemical list SDF download works
  • Chemicals with only DTXCID values are now visible
  • Broken image in chemical tile view is fixed
  • ToxPrint fingerprints (ChemoTyper) are now downloadable in standard CSV format
  • Link in downloadable data from the batch search using ToxVal Data Availability now works
  • Updated NIH NCATS Tox21 analytical QC link
• Known Issues
  • ACD/Labs values for water solubility are listed incorrectly
  • Chemical structure images in the predicted TEST reports are missing
  • TEST, OPERA, Percepta/ACD Labs, EPISuite chemical predictions are not yet available for the newly added chemicals
  • Production volume data are outdated. Until the updated data are available, please refer to: https://www.epa.gov/chemical-data-reporting/access-cdr-data
  • Analytical QC data have not yet been incorporated in the bioactivity data tables

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox	prod_dsstox_202202	Feb-22	-
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
ToxValDB	v.9.1.1	Apr-21	ToxValDB v9.1.1
invitroDB	v3.5 (prod_internal_invitrodb_v3_5)	May-22	invitroDBv3.5
HTTr	ro_httr_20220120	Jan-22	Metadata for the HTTr signature level pathway information
HTPP	res_htpp_u2os_acpra	Jul-22	Metadata for the HTPP global- , category- , and feature-level mappings
Product & Use Categories	prod_factotum_202009	Sep-20	Factotum
Chemical Weight Fraction	prod_factotum_202009	Sep-20	Factotum
Collected Data on Functional Use	functional_use_data_05242022	May-22	Factotum
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker"
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	-	-	CDR website
HTTK	v2.1.0	May-22	HTTK

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Version 2.0.2 - Summer 2022

• Resolved Issues
  • Removed duplicated records in chemical lists
  • OPERA model reports are now displaying correctly
  • Email addresses entered in the comments are now internally visible

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox	prod_dsstox_202202	Feb-22	-
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
ToxValDB	v.9.1.1	Apr-21	ToxValDB v9.1.1
invitroDB	v3.5 (prod_internal_invitrodb_v3_5)	May-22	invitroDBv3.5
Product & Use Categories	prod_factotum_202009	Sep-20	Factotum
Chemical Weight Fraction	prod_factotum_202009	Sep-20	Factotum
Collected Data on Functional Use	functional_use_data_05242022	May-22	Factotum
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker"
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	-	-	CDR website
HTTK	v2.1.0	May-22	HTTK

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Version 2.0.1 - Summer 2022

• Feature Updates
  • New About section including Release Notes
  • Support of Google Analytics
  • New mechanism to set the default view to tiles for the chemical lists
  • Access to chemical lists without case sensitivity
  • Send chemical to batch waits until all chemicals are loaded
• Resolved Issues
  • Bioactivity concentration-response plots are now visible
  • All data are now visible in the Hazard table
  • Batch search warning for duplicate chemicals is working
  • Chemical list download spinning wheel resolved
  • Fixed overlapping comments
  • Sizing error for small screens is fixed
  • Send To Batch Search is working properly for long chemical lists
  • Correct data displayed in Assay Endpoints Citation
  • SDF V2000 file download issues are addressed
  • Toxics Release Inventory data is now visible

Data Sources

The table below offers information on the data sources used for this release of the Dashboard. For descriptions of data sources and how they are used in the Dashboard, visit the About page. For more information on and access to downloadable data, visit the Downloadable Computational Toxicology Data page.

Source Name	Version	Snapshot Date	Reference
DSSTox	prod_dsstox_202202	Feb-22	-
PhysChem and Environmental Fate/Transport Properties	20191118_ChemPROP	Nov-19	-
ToxValDB	v.9.1.1	Apr-21	ToxValDB v9.1.1
invitroDB	v3.5 (prod_internal_invitrodb_v3_5)	May-22	invitroDBv3.5
Product & Use Categories	prod_factotum_202009	Sep-20	Factotum
Chemical Weight Fraction	prod_factotum_202009	Sep-20	Factotum
Collected Data on Functional Use	functional_use_data_05242022	May-22	Factotum
Predicted Probability of Associated Functional Use	-	Feb-20	Publication data
Biomonitoring Data	-	-	R package "bayesmarker"
Exposure Predictions	General-Exposure-Predictions-2022-05-16	May-22	R package "SEEM3"
Production Volume	-	-	CDR website
HTTK	v2.1.0	May-22	HTTK