Modifications in QSAR Toolbox v2.3
Modifications in Toolbox v2.3
1.Profiling
2.Metabolism
3.Databases
4.Import/export
5.Other modifications
6.Bug fixes
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Profiling
The total number of the profilers in Toolbox 2.3 is 37. Below are
presented the updated and new profilers:
Updated profilers
1 ECOSAR (v1.10)
2
OECD HPV Chemical
Categories
3
Protein binding by OASIS
4
Protein binding by OECD
5
Protein Binding Potency
6
DNA binding by OASIS
7
DNA binding by OECD
8
Skin irritation corrosion
Inclusion rules by BfR
1
2
3
4
5
New profilers
Carcinogenicity (genotox and
nongenotox) alerts by ISS
In vitro mutagenicity (Ames
test) alerts by ISS
In vivo mutagenicity
(Micronucleus) alerts by ISS
Organic functional groups
(extended)
Organic functional groups
(nested) (extended)
9 Chemical elements
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Profiling
• Modifications in the updated profilers include corrections in:
 some of the category names
 some of the structural boundaries
 supporting justification – help files
• Previously presented Mutagenicity/Carcinogenicity alerts by Benigni/Bossa profiler was
split to Carcinogenicity (genotox and nongenotox) alerts by ISS and In vitro mutagenicity
(Ames test) alerts by ISS
• Each of the extended versions of Organic functional groups and Organic functional
groups (nested) is consisting of 464 categories (each of the previous versions include
227 categories)
• The “nested” version of the extended OFG profiler is derived automatically
• New category informing for Overlapping groups appears in the profiling result from the
extended Organic functional groups (nested) – the user can see the groups which are
overlapped in the explain form
• The previous versions of Organic functional group and Organic functional groups
(nested) will be available in Toolbox 2.3 too
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Metabolism
• Documented
Updated observed metabolism
1
Observed Microbial metabolism
(551 maps)
New observed metabolism
1
Observed Mammalian metabolism *
• Simulated
Updated simulators
1
Skin metabolism simulator
2
Liver metabolism simulator
* Short descriptions of the newly added database with observed metabolism is presented on next slide
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Metabolism
Observed Mammalian metabolism - Metabolic pathways documented for 100
chemicals with 630 studies in different mammals are stored in a database and
available in version 2.3.
Short description: The collection includes chemicals with variety of functionalities,
aliphatic amines, alkyl and aryl halides, ethers, esters, carbamates, carboxylic acid
esters and multifunctional compounds. In vivo and in vitro studies were used to
analyze the metabolic fate of chemicals. Metabolic maps with the in vivo studies are
predominantly for the collection of studies (347 studies included in 49 maps).
Microsomes prevail over the other experimental systems included in the in vitro
studies (around 50% of studies). Around 50% of administration routes included the
in vivo studies refer to oral route of administration. Different sources including
monographs, scientific articles and public web sites were used to compile the
database.
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Databases
New Databases
Updated Databases
1 Skin Sensitisation
1
MUNRO non-cancer
2 GENOTOXICITY Oasis
2
Bacterial mutagenicity ISSSTY
3 Micronucleus ISSMIC NEW
3
Hydrolysis rate constant
4
Carcinogenicity&mutagenicity
ISSCAN
5 HESS Repeated dose toxicity
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Import/export new features
• Support of IUCLID 5.3 (import/export via i5z and web services)
• Added IUCLID Web Services logging for easier problem identification
• Renamed "Save as" to "Export" in the Profiling editor
• Changed horizontal export. It separates value and unit into different
columns
• Changed vertical export to separate value from unit. Unit is now in the
"Unit" field of the metadata header.
• Changed export form datamatrix popup - it now selects all sub-nodes.
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Import/export new features
• Fixed repainting of columns in vertical import
• Added Duration field for some IUCLID mappings
• Added "Save to file…" feature to import report form for IUCLID import as
well as generic import
• Added check for LIST-CLOSED fields during IUCLID5 export
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Other new features
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EPIWin v4.10 instead v4.00 is included
All databases are pre-calculated with ChemAxon module for pKa
Optimized caching of profiling (faster profiling)
Faster gather data on server version.
Input by chemical list - if some of the identifiers (CAS or SMILES) is missing the
system asks the user to search in the database by the other
Profile statistic: now user can group by category
Gap Filling module registers any kind of data points removals not described by the
prediction domain
TPRF introduces a new item in section 4.2. "Unambiguous algorithm (OECD
Principle 2)", which reports the above data points removals
The domain of any newly created model could be saved as a profiler category
Added points count to "Possible data inconsistency" form
Changed data gather prompt behavior. It now only asks once
Changed the Add/Remove of prediction to be accurately reflected by the statistics
Added caption to repeating values check form which shows the number of
chemicals, groups and data points.
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Other new features
• Added message after data gather with total data points and chemicals number.
• Added scaling for 2D depiction
• Disabled is starting of Toolbox two times. Second instance can make wrong
ECOSAR profiling
• Sub-categorization window – display count of remaining chemicals
• Copy information from cells of data matrix
• Library with known units is expanded with over 200 new units and their
conversion formulas
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Bug fixes
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HESS database about count of imported data was wrong
After import of new database show about was very slow ~1minute
Tab order in IUCLID5 Web Services login page
Bug which caused the 2D not to be cleared when clearing the Search
clause
Clearing the profiles list
Distorted images by PDF export in reports section are fixed
“Go forward” and “Go last” functionality in Gap Filling are fixed
A bug in QSAR import functionality is fixed
A missing part of the TPRF report (between points 4.2 & 4.4) is restored
Fixed bug where the "Data points" form would not display original data (in
case some scale transformation had been applied)
Removed "Multiple dimensions" prompt for QSARs with defined scale and
no data
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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Bug fixes
• Fixed repeating values check where some data was not distinguished
based on dynamic tree settings.
• (Q)SAR ranking function is fixed
• Grouping by (UNDEFINED) categories is fixed
• Strict category grouping when only part of targets categories are selected
is fixed
The OECD QSAR Toolbox for Grouping Chemicals into Categories
22.02.2012
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