User Manual Tips and Tricks
Contents
1. 9 00 2 d e N x juejsuo2 Me K1u9 jeyusuruodAu 3 uonnquysig pue yodsues yyodsuesy p i Structure 5 Return to matrix Trend aigalysis prediction for Environmental Fate and Transport Transport and Distribution between Environmental Compartments Henry s Law constant H making a linear approximation based on 1232 data points from 1232 analogue chemicals Observed target value N A Predicted target value 1 74 atm m3 mole a ink experimental Deg atm m3 male s L L L LI E a a a a L a E E L E a a a umo uj ume um cm cum Demo unc um ee cd cmm mc mnc donc anc unc uec Ca uno ee an Rooms eee selon ee ln n eee eee ums e mcm nn nmn eee nn mn E a a L a a 8 i i a a a a E a a E E E L i L L E E E a E a E a a a a E L a a a E E E E PR A Ran gt Profiling Descriptors Prediction Adequacy Cumul freq Statistic 2 is a 9 m 6 ontrol 2 OSAR Toolbox 2 0 60 597 Phys chem EPISUITE Read across Trend analysis Q SAR models Page 18 of 19 Document Version 1 1 February 2011 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 org2. Author s Website Disclaimer Options Help 0 Document 1 1 Then dialogue box Define new calculator CT OSAR Toolbox 2 060 597 Document 1 QSAR 9 option Main Modules Units Reports 9 Databases 8 Inventories Profilers Document 9 Grouping methods Metabolism Q SARs Search engine eg Installed modules Showr by providers Information for selected module ch User Manual Tips and Tricks es D About Update Donator s Text file with data SMILES TAB Value TAB Units Alternative calculator working in 29 Use values Only calculated values Only values from file From file and calculated Enter calculator title Select calculator type 20 30 Browse file with data HEH Define new calculato Delete Options A Help aax e About Update 0 Document_1 Document Version 1 1 February 2011 00 Page 14 of 19 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 d
3. 3 93E 00 COcOccoOocca clccci odccl 3 2E 00 Cl hyclececel 1 846 00 CLENCJccecc cl 1 66E 00 CLECNECIC ceeceL 1 7 9E 00 cl cljceetiojyce 2 26E 0 2 166 00 Document Version 1 1 Page 12 of 19 February 2011 QSAR TOOLBOX User Manual Tips and Tricks 2 Go to the Options by clicking on the Options icon in the shape of a wrench in the upper right hand corner 1 a gt Profiling Endpoint Select From Database Chemical Name Select from Inventory Drawing Select from File Delete Chemical Document Single Chemical 01010 ch Dane 8 10100 gt Data Gap Filling gt Category Definition gt Report Load Database Load Inventory IB Load Chemical List Chemical List About fer Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Developed by LMC Bulgaria Documents E Substance identity Physical Chemical Properties Environmental Fate and Transport HEcotoxicological Information ElHuman health hazards 0 Document 1 Document Version 1 1 February 2011 Page 13 of 19 QSAR TOOLBOX Click on Define new calculator 1 9 OSAR Toolbox 2 060 597 Document 1 m Databases Inventories Profilers Grouping methods E Metabolism Q SARs amp Search engine Short description Define new calculato amp Delete Name Donator s
4. 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 target value 4 01 log 1 mol L Predicted target value 3 99 log 1 mol L Model equation 3 29 0 392 log log 1 mol L LC50 obs log 1 mol L o w e D 60 80 90 100 110 120 130 140 150 160 Molecular weight Da Descriptor X Molecular weight iv 326 Aldehydes Mono Aquatic toxicit Data gap Filling A dialogue box asking for confirmation of replacing the descriptor pops up Only one model descriptor is allowed in trend analysis mode J Da you want to replace Ehe 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 1 Page 9 of 19 February 2011 QSAR TOOLBOX User Manual Tips and Tricks s th le 2 About gt Catego Profiling Endpoint Definition fi Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filling Method 1 Target b Read across T Trend analysis s HCx mE Q SAR models cia Target Endpoint EEE a 9 al Information Aquatic Toxicity lia Descri
5. C lt TAB gt 0 lt TAB gt 0 lt TAB gt 0O E TBO_DataCalculators Notepad File Edit Format View Help Title Path Units Is3D ISWS isinteger GSH Reactivity Physical Chemical Properties Gsh Reactivit oO 0 0 Boiling point experimental Physical chemical PropertiessBoiling point Deg c p 0 0 5 Save and close the DataCalculators cfg file The next time the QSAR Toolbox is opened this new descriptor will be availabel in the drop down menu of the Data Gap filling graph Document Version 1 1 Page 17 of 19 February 2011 User Manual Tips and Tricks QSAR TOOLBOX About Accept z ume um ome Developed LMC Bulgaria 3 prw The QSAR Toolbox for Grouping Chemicals into Categories Q OH B ou ozi CH NH gt CH3 N 0 ain d 5 6 Mndel equation 106 7 62F n3 Railing rimental Giowin gt Category Definition a i i i i L i i i gt Endpoint Half pint expe Biodeg Probability Biowin 1 odeg Probability Biodeg Probability giling p Biodeg Probability Biowin 2 Bio Bi a 3 00E 2 4 00 2 2 O0E 2 1 00 2 c ag yiodsue z7 0dsuei p Boiling point experimental a 7 T Q A E 5 E e e
6. data in the QSAR Toolbox for boiling point as an X axis descriptor the user should follow these steps 1 Open the TBO_DataCalculators cfg file 2 Find where the endpoint you wish to add is located in the endpoint tree of the Toolbox in order to define the path Document Version 1 1 Page 16 of 19 February 2011 QSAR TOOLBOX User Manual Tips and Tricks H Substance identity Physical Chemical Properties Autoflammability Self ignition temperature Boiling point Density Dissociation Constant pka Explosive properties Flammability Flash point GSH Reactivity Melting freezing point Other property Oxidation reduction potential Oxidising properties Particle size HParition Coefficient solubility in organic solvents fat solubility Stability in organic solvents and identity of relevant d surface tension Vapour pressure Viscosity Vater solubility 3 The path is indicated by separating each branching of the tree with In this case that means that the path for boiling point is Physical Chemical Properties Boiling point 4 This parameter is expressed in Deg C it is 2D it is not water solubility and it is not limited to integer values You can give any name you want to the descriptor e g Boiling point experimental Hence you would need to add to the file TBO_DataCalculators cfg the following line Boiling point_experimental lt TAB gt Physical Chemical Properties Boiling point lt TAB gt Deg
7. C 7 QCPE MOPAC 7 QCPE VV Vv www Uy 4 U NV YN CAU Ch I E 51 Schiff base formation with aldehydes Data gap filing m Document Version 1 1 Page 6 of 19 February 2011 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 s 61010 011 10100 About i b Profiling Endpoint A Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Fling Method Eb a Read across Trend analysis L Q SAR models Target Endpoint ogical Info siege n T AUD Toxicity 36 h Descriptors Prediction Adequacy Cumul freg Statistic Accept prediction or ates Ac ps opteryaii Fish i yecilia reti Return to matrix Poecilia ret
8. LES Tab Value TAB Units Please note that in case the descriptor is dimensionless each line should nevertheless contain a TAB 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 TAB 1 4 TAB C S CCCCC TAB 3 3 TAB C S CCCCCCC TAB 43 lt 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 1 Page 11 of 19 February 2011 QSAR TOOLBOX User Manual Tips and Tricks Example of external file with experimental parameter calculator values 1 1 3 30400 ci Ce O cccci 2 17E 00 0 3 65E 00 c1 C e Cl ce Cl cc1 3 93E 00 C C C C ctcce O ce1 3 72E 00 1 1 1 84E 00 5 c1 NC cccccl 1 66E 00 c1 CN C C cccccl 1 79E 00 1 1 2 26 00 1 1 2 16 00 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 Exp logKow TXT Notepad File Edit Format wiew Help CL CTIC CTiccccLl 3 30E 00 cLecicitycetciycecl 3 65E 0
9. The OECD OSAR Toolbox for Grouping Chemicals into Categories User Manual Tips and Tricks lt TOOLBOX User Manual Tips and Tricks Document history Version 1 0 December 2010 Tips and Tricks for Toolbox version 2 0 Version 1 1 February 2011 Amended section 3 Issue date February 2011 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 1 Page 2 of 19 February 2011 QSAR TOOLBOX User Manual Tips and Tricks Table of Contents FOr EWOO TT TID OE nn 4 1 Changing the X axis descriptor when performing trend analysis with the C E es naans cena seeds ec ann cases tem nana secs 5 Using experimental results for the X axis descriptor 11 Using experimental results from the Toolbox databases for the X axis e rely eee cet den 16 Document Version 1 1 Page 3 of 19 February 2011 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 acro
10. 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 log 1 mol L B mm mm mm mm eee eee 41 web ewe ed mew ede we ew de ew ww ole we ow dt m ms mm mm mm mm mme 8 w oO s in LC50 obs log 1 mol L 8 80 90 100 110 120 130 140 1 Molecular weight Da Descriptor X Y 326 Aldehydes Mono Aquatic toxicit Data gap filling B Document Version 1 1 Page 8 of 19 February 2011 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 01010 01 1 10100 About LI Profiling Endpoint category fey Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filing Method I Target jJ 5 Read across Trend analysis L Q SAR models 0 Target Endpoint lt ui xicological Information Aquatic Toxicity Mo 0 96h Animalia Descriptors
11. escriptor 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 experimental 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 lag Kow Type 2 D Text Ale with data SMILES 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 A 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 t
12. he steps explained in Chapter 1 Document Version 1 1 Page 15 of 19 February 2011 IR 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 Edit the DataCalculators cfg file The default location of this file is C Program Files Common FilesNQSAR Toolbox Ver 2 0Nconfig It can be edited with a simple text editor E TBO DataCalculators cfe Notepad File Edit Format View Help Title Path units Is3D ISWS 1sinteger GSH Reactivity Physical Chemical Properties GshH Reactivity mmol L oO 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 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 For instance in order to add the experimental
13. iculata 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 log 1 mol L lllBiodeg 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 Ano Document Version 1 1 Page 7 of 19 February 2011 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 sl 61010 ao 7 011 10100 About b Profiling Endpoint A fs Update The OECD QSAR Toolbox for Grouping Chemicals into Categories Control Developed by LMC Bulgaria Data Gap Filling Method 1 Target a L Read across P Trend analysis odi LE m Q SAR models 4 Target Endpoint Ecotoxicological Information Aquatic Toxicity lv h Animalia Descriptors Prediction Adequacy Cumul freq Statistic Accept prediction ebrates Actinopterygii Fish T Return to matrix Trend analysis prediction for LC50 making a linear approximation
14. lbox 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 endpoints e g aquatic toxicity alternative descriptors may be warranted for other endpoints e g vapour pressure for acute inhalation toxicity s th 10 About 5 b gt Profiling Endpoint A 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 log 1 mol L 50 4 i 0c 5 e 2 OO RE mm ET NE o ua MEN ORT E e 1 u 0 00 1 00 200 3 00 log Kow Descriptor X log Kow 326 Aldehydes Mono Aquatic toxicit Data gap filling Document Version 1 1 Page 5 of 19 February 2011 QSAR TOOLBOX User Manual Tips and Tricks There are two types of descriptors in the Toolb
15. ox 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 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 QSAR Toolbox for Grouping Chemicals into Categories Developed by LMC Bulgaria Data Gap Filing 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 Datapoints 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 9 Biowin5 Linear MITI Non Linear Biowin7 Anaerobic Linear Biodegradation half lives 1 br Adapted Stein and Brown OASIS OASIS OASIS OASIS MOPA
16. ptors Prediction Adequacy Cumul freg Statistic Accept prediction s Actinopterygii Fish Trend analysis prediction for LC50 making a linear approximation Roun men based on 15 data points from 15 analogue chemicals Observed target value 4 01 log 1 mol L Predicted target value 3 98 log 1 mol L Model equation 2 64 1 34E 02 Molecular weight Da log 1 mol L al n J approach c J i atc data 450 00 Make active descriptor 400 es 1 Remove active descriptor mar ME ee ee ee OE Collect data 2 3 00 Jl E _ Change descriptor units 30 40 50 60 70 8 amp 0 90 100 110 120 130 140 150 160 b 2 a Molecular weight Da Descriptor X Molecular weight 326 Aldehydes Mono Aquatic toxicit Data gap filling Document Version 1 1 Page 10 of 19 February 2011 lt 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 SMI
17. ss 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 grouping 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 applii 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 1 Page 4 of 19 February 2011 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 Too
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