User Manual Tips and Tricks
Contents
1. in the shape of a wrench in the upper right hand corner 1 01010 ch 01 1 E 10100 About gt Profiling gt Endpoint Acer old gt Data Gap nition Filling Report fer Update The OECD QSAR Toolbox fer Open EJ CAS Select from Database Load Database for Grouping Chemicals into Categories Save ER Chemical Name S Select from Inventory Load Inventory K Close Drawing Select from File Delete Chemical Load Chemical List Document Single Chemical Chemical List Developed by LMC Bulgaria Documents E Substance identity Physical Chemical Properties Environmental Fate and Transport HEcotoxicological Information Human health hazards LL 0 Document_1 10 0 Document Version 1 0 Page 13 of 17 December 2010 QSAR TOOLBOX Click on Define new calculator 1 EI OSAR Toolbox 2 060 597 Document 1 E Databases Inventories Profilers Grouping methods E Metabolism Q SARs amp Search engine Short description E8 Define new calculate EG Delete Name Donator s uthoris Website Disclaimer E Options Help 0 Document_1 i ET Then a dialogue box Define new calculator pops up CT OSAR Toolbox 20 60 597 Document 1 QSAR options Main Modules Units Reports E Databases S Inventories Profile2. log 1 mol L FE Model equation 2 64 1 34E 02 Molecular weight Da log 1 mol L al ith J approach E J i atc data 450 oe EEE EEE PE EEE EE Sooo eee ER Et 5 00 Make active descriptor 400 es CS Sue ee a Remove active descriptor E ee ee ee Collect data 3 00 i9 Change descriptor units v 30 40 50 60 70 8 amp 0 90 100 110 120 130 140 150 160 b AE 4 Molecular weight Da Descriptor X Molecular weight x 326 Aldehydes Mono Aquatic toxicit Data gap filling Document Version 1 0 Page 10 of 17 December 2010 SAR TOOLBOX User Manual Tips and Tricks 2 Using experimental results for the X axis descriptor The user also has the possibility to load datasets with experimental data to be used instead of the estimated descriptors This is illustrated with an example below of loading a database with experimental log Kow results 1 Prepare the external file with parameter calculator values The external file should be a text format with experimental data with the following structure SMILES lt Tab gt Value lt TAB gt Units Please note that in case the descriptor is dimensionless each line should nevertheless contain a lt TAB gt after the Value Example of a text file is presented in Box 1 Box 1 Format of a text file with experimental results C C S lt TAB gt 1 4 lt TAB gt C S CCCCC lt TAB gt 3
3. 3 see screenshot below Active descriptors are the descriptors that were used in the calculations for predicting the endpoint Inactive descriptors are all the other descriptors supported by the Toolbox but which were not used for predicting the endpoint 8 E gt Input gt Profiling gt Endpoint gt Category Definition gt Report The OECD QSAR Toolbox for Grouping Chemicals into Categories Developed by LMC Bulgaria Data Gap Filling Method Read across Trend analysis Q SAR models Cumul freq Target Endpoint Ecotoxicological Information Aquatic Toxicity Mortality LC50 96 h Animalia Chordata Vertebrates Actinopterygii Fish Poecilia reticulata Datapoints Corr R 14 0 9020 Available descriptors Name i Data points Corr R Biodeg Probability Biowin 2 Biodeg Probability Biowin 5 Biodeg Probability Biowin 6 Biodeg Probability Biowin 7 BioHC Half Life Biotransformation Half Life Boiling Point Calculated heat of formation Diameter effective Diameter maximum Diameter minimum Biowin2 Non Linear Model 4 Biowin5 MITI Linear Mode Biowin6 MITI Non Linear M Biowin7 Anaerobic Linear Biodegradation half lives 1 br Adapted Stein and Brown OASIS OASIS OASIS OASIS MOPAC 7 QCPE MOPAC 7 QCPE VV Vv www CU CN CU Uy IV NV YN NM NY 51 Schiff base formation with aldehydes Data gap filling BE Document Version 1 0 Page 6 of 17 Dece
4. 3 lt TAB gt C S CCCCCCC lt TAB gt 43 lt TAB gt Notes There should be no title line and no empty line at the bottom of the file i e no Carriage Return at the end of the last line The file has to be saved with a TXT extension e g Log KOW_internal txt Document Version 1 0 Page 11 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks Example of external file with experimental parameter calculator values c1 Chje Cl cccet 3 30E 00 c1 Ch e O cccct 2 17E 00 3 65E 00 lt c1 C e Cl ce Cl cc1 3 93E 00 C C C C ctcce O ce1 3 72E 00 C N ciccccci 1 84E 00 RS c1 NC cccccl 1 66E 00 c1 CN C C cccccl 1 79E 00 ys c1 Cl ccc O ccl1 2 26E 00 c1 O cc C cccl 2 16E 00 EE Copy these columns into the Notepad and save it as a file with txt extension When copying columns above please do not forget to include blanks in the last column so that there is a TAB between each Value and Unit PB Exp lopKow TXT Notepad File Edit Format wiew Help CL CTIC CTiceccLl 3 30E 00 cLecicitycetciycecl 3 65E 0 cL ecictcljycetcljcect 3 93E 00 Chcwecyecyclece o cel 3 72E O00 Cl hyclececel 1 846 00 CLENCJccecc cl 1 66E 00 CLECNECIC ceeceL 1 7 9E 00 cl cljceetiojyce 2 266 00 cltiojyecctitjyccec 2 166 00 Document Version 1 0 Page 12 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks 2 Go to the Options by clicking on the Options icon
5. The OECD OSAR Toolbox for Grouping Chemicals into Categories User Manual Tips and Tricks lt IR TOOLBOX User Manual Tips and Tricks Document history Version 1 0 December 2010 Tips and Tricks for Toolbox version 2 0 Issue date December 2010 Language English If you have questions or comments that relate to this document please send them to ehscont oecd org or visit the QSAR Toolbox discussion forum at https community oecd org community toolbox forum Document Version 1 0 Page 2 of 17 December 2010 lt IR TOOLBOX User Manual Tips and Tricks Table of Contents FOOD aE AER EAA ARAA EA 4 1 Changing the X axis descriptor when performing trend analysis with the Toolbox 5 2 Using experimental results for the X axis descriptor s s s2222222222 22222us22 11 3 Using experimental results from the Toolbox databases for the X axis descriptor 16 Document Version 1 0 Page 3 of 17 December 2010 SAR TOOLBOX User Manual Tips and Tricks Foreword This document is one of a series of guidance documents accompanying the OECD QSAR Toolbox Version 2 0 The main objective of the Toolbox is to allow the user to use Q SAR methodologies to group chemicals into categories and to fill data gaps by read across trend analysis and Q SARs For in depth background information on the concept of chemical categories the user is invited to consult the guidance document for groupin
6. endpoints e g aquatic toxicity alternative descriptors may be warranted for other endpoints e g vapour pressure for acute inhalation toxicity oO th 10 About 5 b gt Profiling Endpoint A e a Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filling Method Read across Trend analysis Q SAR models Target Endpoint Descriptors Prediction Adequacy Cumul freg Statistic Accept prediction rates Actinopterygii Fish Poecilia reticulata Return to matrix Trend analysis prediction for LC50 making a linear approximation based on 15 data points from 15 analogue chemicals Observed target value 4 01 log 1 mol L Predicted target value 3 99 log 1 mol L Model equation 3 29 0 392 log Kow log 1 mol L 50 4 0 77 5 2 OO RE mm r EA R oO EE eT Dy 5 1 Ww be 0 00 1 00 2 00 3 00 log Kow Descriptor X log Kow 326 Aldehydes Mono Aquatic toxicit Data gap filling Document Version 1 0 Page 5 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks There are two types of descriptors in the Toolbox active descriptors or Descriptors in use 1 and inactive or Available descriptor 2 Both types of descriptors are listed separately in the in the tab Descriptors
7. et value 4 01 log 1 mol L Predicted target value 3 99 log 1 mol L Model equation 3 29 0 392 log Kow log 1 mol L LC50 obs log 1 molL o w e D 60 80 90 100 110 120 130 140 150 160 Molecular weight Da Descriptor x Molecular weight ml 326 Aldehydes Mono Aquatic toxicit Data gap filling dialogue box asking for confirmation of replacing the descriptor pops up pp Only one model descriptor is allowed in trend analysis mode i a Do you want to replace the current model descriptor flog Kowt with the selected one Molecular weight By clicking the Yes button the trend analysis for the new X axis descriptor is completed Document Version 1 0 Page 9 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks oO th le 2 About i gt Catego Profiling Endpoint Definition fer Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filling Method 1 Target oo la Read across T Trend analysis Pr HCx Q SAR models ci Target Endpoint EEE al Information Aquatic Toxicity lia Descriptors Prediction Adequacy Cumul freg Statistic Accept prediction 3 Actinopterygii Fish Trend analysis prediction for LC50 making a linear approximation Roun cee based on 15 data points from 15 analogue chemicals Observed target value 4 01 log 1 mol L Predicted target value 3 98
8. g of chemicals published in the Series on Testing and Assessment of the OECD Environment Health and Safety Publications OECD 2007 ENV JM MONO 2007 28 http applil oecd org olis 2007doc nsf linkto env jm mono 2007 28 The current document is aimed at providing some guidance on some advanced features for using the Toolbox It will be updated and expanded as further guidance becomes available Additional guidance and training material will be made available on the internet site for the OECD Q SAR Project www oecd org env existingchemicals qsar and http www qsartoolbox org as well as the internet site of the Laboratory of Mathematical Chemistry http toolbox oasis Imc org There is also the OECD QSAR Toolbox Discussion Forum https community oecd org community toolbox_forum where users can exchange their experiences with using the Toolbox The user is invited to regularly consult these internet sites The OECD QSAR Toolbox has been developed with the financial assistance of the European Union Document Version 1 0 Page 4 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks 1 Changing the X axis descriptor when performing trend analysis with the Toolbox When performing a trend analysis within a category to estimate missing data with the Toolbox the default X axis descriptor is log Kow which is estimated with the EPISUITE program 1 see screenshot below While this descriptor may be pertinent for many
9. le is C Program Files Common Files QSAR Toolbox Ver 2 0 config It can be edited with a simple text editor TBO_DataCalculators cfe Notepad File Edit Format wiew Help Title Path Units I53D Tsws isinteger fen GSH Reactivity Physical Chemical Properties GsH Reactivity mmol L 0 0 The file contains a tab delimited table in the following format Title lt TAB gt Path lt TAB gt Units lt TAB gt Is3D lt TAB gt ISWS lt TAB gt IsInteger e Each row from this file defines a new calculator with Title this is the name of the calculator Path Position of the parameter in the endpoint tree where the data is associated with when read from databases Units defined units of the parameter Is3D is the type specification of parameter It is zero 0 for 2D OR one 1 if the parameter is 3D IsWS It is zero 0 if the parameter is not water solubility or one 1 if the parameter is WS IsInteger Parameter get integer values only for example Number of aromatic bonds if it is one 1 otherwise it is zero 0 Document Version 1 0 Page 16 of 17 December 2010 OECD 2 rue Andr Pascal 75775 Paris Cedex 16 France Tel 33 1 45 24 82 00 Fax 33 1 45 24 85 00 ehscont oecd org
10. mber 2010 QSAR TOOLBOX User Manual Tips and Tricks In the Prediction tab 1 the distribution of the observed data for the endpoint is plotted against any descriptor By default the Toolbox selects the first active descriptor to plot the available data In case of trend analysis the equation line of the model is also visible If the user changes the descriptor he she will see how the observed data for the endpoint is distributed against the newly selected descriptor It is possible to change the descriptor and re estimate the property For that the user has to click the box of Descriptor X under the trend analysis graph 2 A list of available descriptors appears The user can select a new descriptor from the list f 61010 ch O1 1 10100 About i i b Profiling Endpoint A fer Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Fling Method iw E E a Read across Trend analysis Q SAR models Target Endpoint 0 agical Info sine in DAME Toxicity 36 h Descriptors Prediction Adequacy Cumul freg Statistic Accept prediction ar ates JAC sy opterygii Fish i yecilia reti Return to matrix Poecilia reticulata Trend analysis prediction for LC50 making a linear approximation based on 15 data points from 15 analogue chemicals Observed target value 4 01 log 1 mol L Predicted target value 3 99 log 1 mol L Model equati
11. mental data 5 The user can choose an existing calculator to estimate the descriptor for chemicals not listed in the file with experimental data In this example log Kow calculated by the EPISUITE model could be chosen to fill data gaps in the experimental file 6 Please note that if an alternative calculator is chosen the radio button From file and calculated has to be checked 7 By clicking the OK button the file is imported as a new descriptor And the user can return to a normal work session Define new calculator Title Experimental log Kow Type e z D Text Ale with data SMILES TAE Y alue T AB Units S Applic EHS ADMINISTRATORS WichiOSAR_TBiExp logkow tet Alternative calculator working in 31 a5 Use walues only calculated values only values From fle Please Note For the newly defined parameter calculator to be active the system must be restarted 4 How to use the new parameter calculator Under Data gap filling the user can change the X axis descriptor with a parameter using external experimental data by following the steps explained in Chapter 1 Document Version 1 0 Page 15 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks 3 Using experimental results from the Toolbox databases for the X axis descriptor No interface is provided for this approach For this purpose one needs to e Edit the TBO_DataCalculators cfg file The default location of this fi
12. mm mm mm web ewe ed mew ede we ew de ew ww ole we ow ole mm mme SAER D dt m ms mm mm mm mm mme 8 w oO in oO LC50 obs log 1 molL 3 80 90 100 110 120 130 140 1 Molecular weight Da Descriptor x v 326 Aldehydes Mono Aquatic toxicit Data gap filling F Document Version 1 0 Page 8 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks At this stage however the equation is NOT yet re estimated To make a prediction using the newly selected descriptor the user must activate it This is done by clicking Descriptors data 4 on the right hand menu and then selecting Make active descriptor 5 or by dragging the new descriptor from the Available descriptors list to the Descriptors in use list in the Descriptors tab 61010 ch 01 1 10100 bout 5 b gt Profiling Endpoint category fey Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filling Method I Target fs 5 Read across Trend analysis H2C Q SAR models o Target Endpoint fk u Ec ctox xkicological Information Aquatic Toxicity Mo 096h Animalia Descriptors Prediction Adequacy Cumul freg Statistic Accept prediction Chordatal vertebrates Actinopterygii Fish Poecilia reticulata Trend analysis prediction for LC50 making a linear approximation ee based on 15 data points from 15 analogue chemicals Observed targ
13. on 3 29 0 392 log Kow log 1 mol L MEiodeg Probability Biowin 1 Biodeg Probability Biowin 2 Biodeg Probability Biowin 5 Biodeg Probability Biowin 6 Biodeg Probability Biowi Descriptor X log Kow LC50 obs log 1 molL 326 Aldehydes Mono Aquatic toxicit Data gap filling poer Document Version 1 0 Page 7 of 17 December 2010 QSAR TOOLBOX User Manual Tips and Tricks By clicking on the new descriptor in this example Molecular weight the selected descriptor is shown in the Descriptor X box 3 and the new descriptor appears also in the trend analysis graph f 61010 ES 7 O1 1 a 10100 About b Profiling Endpoint A far Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filling Method 1 Target a Read across f Trend analysis oe MeN E Q SAR models ON 4 Target Endpoint Juil Ecotoxicological Information Aquatic Toxicity rm Nv h Animalia Descriptors Prediction Adequacy Cumul freq Statistic Accept prediction ebrates Actinopterygii Fish r T E Return to matrix Trend analysis prediction for LC50 making a linear approximation based on 15 data points from 15 analogue chemicals Observed target value 4 01 log 1 mol L Predicted target value 3 99 log 1 mol L Model equation 3 29 0 392 log Kow log 1 mol L B mm mm mm mm eee eee ee ee ee mm mm mm mm mm
14. rs Document Grouping methods E Metabolism Q SARs Search engine eg Installed modules _ Show by providers Information for selected module ch User Manual Tips and Tricks es 6 D About Update Donator s Text file with data SMILES lt TAB Value lt TAB Units Alternative calculator working in 29 Use values Only calculated values Only values From file From file and caleulated Enter calculator title Select calculator type 2D 3D Browse file with data HEH Define new calculato Los Delete ef Options A Help aax D About Update 0 Document_1 Document Version 1 0 December 2010 _ 1 0 0 Page 14 of 17 IR TOOLBOX User Manual Tips and Tricks 3 The steps of introducing the external file with parameter calculator values in the Toolbox are see also screenshot below 1 Add a title In this example Experimental log Kow 2 Add a dimension or unit In this example the descriptor is dimensionless and the field is left blank 3 Select a type 2D or 3D The distinction is made depending on whether the descriptor could be calculated based on a 2D or 3D configuration of the structure Kow being usually derived from a 2D structure the 2D button can be selected 4 Indicate the path of the file containing external experi
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