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User manual Database Import Wizard

1. 47 Appendix Import example for database with Human health hazards 59 Document version 1 0 Page 3 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard 1 Executive summary The QSAR Toolbox Database Import Wizard together with the IUCLID 5 import wizard see guidance document IUCLID 5 Import Export via Webservices is the entry point for importing custom user data to the QSAR Toolbox database It can import XLS files Excel 97 2003 version as well as TXT UNICODE plain text files Both file types pertain to how the data is read by QSAR Toolbox but not how the data is parsed afterwards 2 QSAR Toolbox data model The QSAR Toolbox operates with the following data model Data point record Value Link to chemical ID CAS SMILES Endpoint string Metadata type String Endpoint description string Dastin Velde Is Private Boolean Title 1 Value 1 Is Observed Boolean Title N Value N Metadata type Value Title 1 Value 1 Title N Value N Value is defined as Mean Qualifier lt Mean Value Low Qualifier lt Low Value floating point Upper Upper Value floating point gt gt etc floating point gt gt etc number Qualifier number number Figure 1 Database structure of the QSAR Toolbox Document version 1 0 Page 4 of 70 April 2011
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3. Data Mea 23 Positive Positive an health Positive an health hazards Carcinogenicity Negative an health hazards Carcinogenicity Negative H Nea stive 2 Fils Wizard stay uf Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side radio buttons Denter D The Scale Carcinogenicity 1 185 has been defined advance Accordingto this scale chemicals fromthe database are classified as Positive and Negative This is the default scale Document version 1 0 Page 52 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Note Scale editor pilo wizard step 4 0f 1 Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side io buttons health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity Scales definition PPL LEE EEE TEE EET di a li uw The user should select one of the scales from the Scale list panel or define a new scale Document version 1 0 Page 53 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select
4. dika Teen md nis Dred peed ert s t Brel peed mikon froen mam Bac fe aperi Pom Author Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni 01 9 Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni 01 9 Romualdo Benigni 01 9 Database is imported successfully Click Document version 1 0 April 2011 Next Finish Page 44 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Load imported database Q OSAR Toolbox 0 0100 Category Definition Data Gap Filling Substance identity Physical Chemical Properties Fate and Transport BHuman health hazards QSAR Tootbex 2 0 60 97 Document 1 FIA d 2 e QSAR VY T 10100 Profiling Category Definition Data Gap Filling 2 Document version 1 0 Page 45 of 70 April 2011 QSAR TOOLBO
5. 0 A When defining the metadata record the user should organize his her own metadata by using existing field labels This ensures that the same fields do not multiply under different names For example effects from the experiment should be placed in a column named Effect the type of the test method such as Ames test should be placed in a column named Test type etc The metadata fields can be organized in Set tree hierarchy panel Right click on endpoint tree to set the hierarchy Document version 1 0 Page 30 of 70 April 2011 QSAR TOOLBOX Appendix II Import example for a database with QSAR Toolbox User Manual Database Import Wizard ecotoxicological information The example below uses a file that is already prepared Guidance on how to prepare file for horizontal import can be found in Appendix I The destination for example files is Install folder Examples The default path is C Program Files QSAR Toolbox QSAR Toolbox 2 1 Examples Ecotoxicological example xls Cia 9 11022634 44 Ecotoxicological example xls Compatibility Mode Microsoft Excel x 2 Insert Layout Formulas Data Review View Developer E pee BD or Copy e a Fit vaste SES EES A aj Merge amp Center 55 2 Conaitional Format cen Insert Delete Format sot Find am
6. TOOLBOX QSAR Toolbox User Manual Database Import Wizard The Import s function is to translate the information in a file be it XLS or TXT separate it in different chunks see the figure above and write them into the database The information consists of the chemical connected with numerical and meta data In other words the point of the import is to define a list of data points the number that the user sees in the data matrix and uses for gap filling with its corresponding metadata namely the additional information on duration test organisms endpoint etc In order to properly parse the information the import expects one of two file layouts as outlined below 3 Import layouts The two layouts the QSAR Toolbox can parse are the so called Vertical layout and the Horizontal layout The Horizontal layout has each data point with its corresponding chemical and metadata defined in a single row In a way each row is a single record hence horizontal The Vertical layout on the other hand can have multiple records on each row with the metadata for each record defined on a column by column basis hence vertical 3 1 Vertical layout This layout is used where there is a list of chemicals and a result for each chemical but all results have the same metadata So the chemical is defined in the first columns and the next columns are used for the data points For each data column there is one set of metadata This means the ver
7. sel elete Forma 0 J Format Painter En Formatting as Table Styles 2 Cea Filter Select Clipboard Font Alignment g Number fs Styles Cells Editing Al fe cas 2 92177 49 6 Nitroso 2 oxopropyle Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 3 15973 99 6 di N Nitroso pernydi CICCN CN1N O Human health nazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 4 75881 18 4 1 Nitraso 3 4 5 trime C1C N C CN1N Human health hazards Carcinagenicity Carcinagenicity ISSCAN Positive Summary carcinogenicity 5 625 09 0 N Nitrosobis 2 2 2 tri N N CC F F F C Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 6 51 15 1 4 Nitrosochlordrazepox 2 Human nazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 7 73785 40 7 N Nitrosocimetidine O NN C NICXN Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 8 114282 83 0 N Nitrosodithiazine 1 1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 9 10595 95 6 Nitrosoethyimethylan CN CC N O Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 10 55557023 Nitrosoguvaco
8. 3 3 1 2 Ecotoxicological Informations Aquatic To 776692 sekas lanta ete sl ToC cuc abinm MA miele Tar D I caa VV V V V V V V V V A A A A VI VIV Select CAS 578112 111918 wizard step Zot 3 Select one more columns from the grid Scales below and then assign the selection to a editor region by choosing from the lefthand side radio buttons Data Mean value Scale value gical Information Aquatic 2 98 gical Information Aquatic Toxi39 gical Information Aquatic Toxi57 otoxicological Information Aquatic Toxi29 1 O C ec2eceece2W CC C O NC O JN1Ecotoxicological Information Aquatic 2995 767 2 2 2 sl stian A ca Tavit 112 Document version 1 0 April 2011 Page 34 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select Chemical name step 2013 Select one or more columns from the grid Scales below and then assign the selection to a editor region by choosing from the lefthand side radio buttons Informationst Aquatic Toxi12 98 gical Informations Aquatic Toxi39 ogical Informations Aquatic Toxi57 ogical Informationst Aquatic Toxi29 xicological Informationst Aquatic Toxi2995 767 cobavicalacics Teen skiem heiskie Tevit nno 112 Select one or more columns from the grid Scales below and then assign the selection to a region by choosing from the lefthand side gical In
9. Feat eA Select one or more columns from the grid O Low qualifier O Upper value below and then assign the selection to a or 1 O mean qualifier value GQunit region by choosing from the lefthand side DRE O Mean value Scale valO Upper qualifier Undefined radio buttons Ca O Upper qualifier O Mean value Scale39 Unit O Low qualifier Undefined firmnaliees shdika m Document version 1 0 Page 39 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Add undefined parameter Solubility step 2 0f Select one or more columns from the grid O Low qualifier Upper value Scales below and then assign the selection to a O Low value Uni editor region by choosing from the lefthand side O Mean valuefScale valO Upper qualifier O Undefined radio buttons O Mean qualifier Upper value O Mean value Scale Unit Lifestage Immobilisation Juvenile Daphnia magna Physiology Juvenile Daphnia magna Mortality Juvenile Daphnia magna Mortality Juvenile Vibrio fischeri Behavior Adult firanelices shits e Mart sli 2 5 step 4 9f Define value Select one or more columns from the grid O scale O Low qualifier Upper value below and then assign the
10. Scales editor W I have a header row Upper value Unit Low qualifier Low value Effect Ceriodaphnia affinis Daphnia magna Daphnia magna Daphnia magna Vibrio Fischeri sheik Physiology Mortality Mortality Behavior Maer sliksa Document version 1 0 April 2011 Cancel Immobilisation Select one or more columns from the grid below and then assign the selection to region by choosing from the lefthand side radio buttons Lifestage Water type Salinity Temp E Juvenile 3 Juvenile Juvenile Juvenile Adult Page 38 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Fils step 703 62 Define value Select one or more columns from the grid O Scale O Low qualifier Scales below and then assign the selection to O Mean qualifier value editor region by choosing from the lefthand side CEE O Mean value Scale valO Upper qualifier radio buttons Define value 8 Osce Mean qualifier 115 Mean values Elimination phase duration Elimination 5xT50 O Low qualfier Embryotoxic teratogenic effect Endpoint 92 Olen valus Data Mean qualifier Data Unt Endpoint Test organisms species Duration Mean value Scale value Duration Unit Solubility Unit Effect C50 Ceriodaphnia affinis Daphnia magna Daphnia magna Daphnia magna Vibrio fischeri franelices skis
11. DATA Main Value Scale value step 703 File layout O Vertical Private data Select one or more columns from the grid Scales below and then assign the selection to a editor region by choosing from the lefthand side radio buttons Endpoint Summary carcinogenicity Summary carcinogenicity Summary carcinogenicity Summary carcinogenicity Summary carcinogenicity v I have header row os region by choosing from the lefthand side radio buttons Speer vole Data Mean value Scale value arcinogenicity I ISSCAN arcinogenicity I ISSCAN arcinogenicity I ISSCAN arcinogenicity I ISSCAN The type of the column is specified by clicking on the column and Document version 1 0 Page 54 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard then clicking its type CAS Chemical name SMILES from the list box in the Define new region panel or selecting a metadata field label from the list box in the Metadata panel To remove designations click a column and then click on Undefined from the list box IT All fields fields defined with the Define new region panel are color distinguished from the fields of the Metadata panel Fileimpot wizard step 0113 Scroll bar File layout What do different layouts mean O Vertical a header row Private data Define new region 79 Define
12. Upper qualifier Undefined radio buttons CO Mean qualifier Mean value Sca Select Mean value Scale value ITT EN endpomt Test organisms species Duration Mean value Scale valueDuration UnitSolubility Mean value Scale valueUnit Ceriodaphnia affinis Daphnia magna Daphnia magna Daphnia magna Vibrio fischeri skis Document version 1 0 Page 41 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select Unit of defined Solubility parameter e File impot wizard step 703 Select one or more columns from the grid O Low qualifier O Upper value below and then assign the selection to a or O Mean qualifier O Low value Uni O Mean value Scale valO Upper qualifier Ov Undefined radio buttons Ele vate O Mean qualifier Upper value O Mean value Scal Unit O Low qualifier Undefined Endpoint Test organisms TETTE EEE value Scale valueDuration Unit Solubility Mean value Scale valu S Ceriodaphnia affinis 48 h Daphnia magna Daphnia magna Daphnia magna Vibrio fischeri shes olubility Unit Effect i d region by choosing from the lefthand side Select one or more columns from the grid O Low qualifier Upper value 8 editor Mean qualifier value 9 Unit O Mean value Scale valO Upper qualifier undefined Ee vake radio buttons O Mean qualifier Upper value O Mean value
13. 1 ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity 1 ISSCAN Carcinogenicity I ISSCAN acm m m mn mm mie ALL Database title Carcinogenicity amp mutagenici example Note the user could change the name A Itis very important that the thousands and decimal separators properly set while importing Especially with TXT file this could lead to erroneous parsing of data values Document version 1 0 April 2011 Page 49 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Step 2 Horizontal import v I have a header row 2 21111710 yard step 4 oF 3 99979999999 Select one or more columns from the grid below and then assign the selection to a p region by choosing from the lefthand side 25081 31 6 26921 68 6 70415 59 7 55984 51 5 9 69658 91 9 16219 99 1 N Nitrosobis 2 2 2 trifluoroethyl amine Nitrosochlordiazepoxide N N imetidi N Nitrosodithiazine Nitrosoethylmethylamine 1 Nitrosohydantoin Nitrosohydroxyproline health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health
14. METHYL METHANESULFONATE 5 Human health hazards Genetic Toxicity Uracil mustard USAN CI mO C WCCCKCC ONC O NI Human health hazardssGenetic Toxicity 1 5 NITROFURFUR YLIDENE AMINO JHYIC 1 C NN2C ONC 0 C2 CC CiN Human health hazards Genetic Toxicity Methylnitronitrosoquanidine C N N C M O NN O O Human health hazardss Genetic Toxicity 1 FLUORO 2 4 DINITROBENZENE cl F e N O O ec N O O cc1 Human health hazardsitGenetic Toxicity ETHYL_BROMIDE C C Br Human health hazards Genetic Toxicity TRIBROMOMETHAME Br Br r Human health hazards Genetic Toxicity 2 CLC C Br Human health hazards Genetic Toxicity TRIIODOMETHANE COXTM Human health hazards Genetic Toxicity PROPYLENIMINE CI C CM1 Human health hazards Genetic Toxicity TERT BUTYL_HYDROPEROXIDE C C CX C OO Human health hazards amp Genetic Toxicity DIOXATHION CI SPI SNOCC OCCIC SPI SKOCOOCMuman health hazards Genetic Toxicity 1 2 DICHLOROPROPANE 1 2 0 Human health hazards Genetic Toxicity 2 3 DICHLORO 1 PROPENE Human health hazards Genetic Toxicity Bromoacetic Acid C ONO CBr Human health hazards Genetic Toxicity AAA eee ef A Vm i baca be sala dit nkla dalles gj Database title GENOTOXICITY example Database title GENOTOXICITY example Note the user could change the name Importto The userhasto choose
15. Scale Unit O Low qualifier O undefined 6 O Low value Water type Salinity TemperaturepH Water alkalinity Water HardnessDATA QUALITY Author WARNE AND SCHIFKO JANSSEN AND PERSOONE Document version 1 0 April 2011 region by choosing from the lefthand side Page 42 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Scroll the bar to review data column designations Click on Next button 598 12111791 wizard step 7 0713 Select one or more columns from the grid O Low qualifier Upper value Scales below and then assign the selection to a O Low value Qunit editor region by choosing from the lefthand side O Mean value Scale valO Upper qualifier Undefined radio buttons Ee vate O Mean qualifier Upper value O Mean value Scale Unit O Low qualifier Undefined O Low value Year Title Comment a 1999 End point is Fluorescence od Daphnia with 1993 Comment End point is Fluorescence od Daphnia with Kramer 2 Miles Richardson 5 Pierens SL1998 Reproductive impairment and induction of Aquat Toxicol 40 335 360 End point egg production Female Kramer 2 Miles Richardson 5 Pierens SL1998 Reproductive impairment and induction of Aquat Toxicol 40 335 360 End point inhibition of vitrellogenin in male Reproductive impairment and induction of Aquat Toxicol 40 335 360 Male fish only Egg refers to sperm Sperm exposed for 1 Phipps GL Mattso
16. Test organisms 8 Endpoint tree pathation Aquatic Tox al cotoxicological Informationst Aquatic 39 cotoxicological Informations Aquatic To otoxicological Informations Aquatic 29 otoxicological Informations Aquatic 299 Select one or more columns from the grid Ei and then assign the selection to a region by choosing from the lefthand side radio buttons STER 2 Information Aquatic 39 cotoxicological Informations Aquatic Toxd5 cotoxicological Information Aquatic 29 otoxicological Information Aquatic 299 Document version 1 0 Page 37 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard The type of the column is specified by clicking on the column and then clicking its type CAS Chemical name SMILES from the list box in the Define new region panel or selecting a metadata field label from the list box in the Metadata panel To remove designations click a column and then click on Undefined from the list box IT All fields fields defined with the Define new region panel are color distinguished from the fields of the Metadata panel s File importwicand step 703 File layout CO Vertical Private data Define new region SMILES Endpoint tree path Data Mea Upper qualifier lis val Define value Scale Ones Add test Duration data What do different layouts mean
17. V BFF IUCLIDS phrasegroup P165 IUCLIDS phrasegroup P105 IUCLIDS phrasegroup 20 IUCLIDS phrasegroup C47 IUCLIDS phrasegroup 23 IUCLIDS phrasegroup T116 IUCLIDS phrasegroup T46 2 IUCLIDS phrasegroup T46 1 IUCLIDS phrasegroup IUCLIDS phrasegroup T143 IKUDS phrase roup 102 Skin sensitisation TIT LIMU Imitation Corrosion I LIMU RCSD Severe skin irritation Danish EPA Car nogenicity CPOB Skin Irritation Corrosion Eye Imitation Corrosion IUCLIDS 2 phrasegroup 16 IUCLIDS 2 phrasegroup PIOS IUCLIDS 2 phrasegroup PA IUCLIDS 2 phrasegroup 047 IUCLIDS 2 phrasegroup 23 E TH KHOA 2 nhescennmiim TIIA A When defining the data record the user should define I For categorical data Scale column for the scale name This should contain a name of a scale exactly as defined in the scales list in the QSAR Toolbox database or as defined by the user The Mean value Scale value column should contain only values Document version 1 0 Page 27 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard that scale members For value data At least one column for the Mean Min Max values Qualifiers and Unit are optional Metadata information These are fields for metadata such as Duration Organ Tissue Route of administration etc which are not mandatory for the import 50 Cenodaphriz 48 h Juvenile Fre
18. g AnSalmonella typhimurium in vitro bacterial reverse mutation assay e g AnSalmonella typhimurium lt NEE am WEEN M Scroll the bar to review data column designations Click Next button e fale import wizard step 4 9f 3 O mean qualifier O Low value Unit region by choosing from the lefthand side DEN O Mean value Scale valO Upper qualifier C Undefined radio buttons Select one or more columns from the grid O Low qualifier Upper value or Year CommentChemical info Document version 1 0 Page 67 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Click on Finish button s step d 9f Reference source NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Progr
19. hazards Genetic Toxicity an health hazards Genetic Toxicity 1 CN ClH C C COc2eceee2 CCC an health hazards Genetic Toxicity C OS O O OCC an health hazards Genetic Toxicity OS C O O an health hazards Genetic Toxicity sman Document version 1 0 Page 63 0f 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select DATA Scale 4 9f 3 v I have a header row Select one or more columns from the grid Low qualifier Upper value Scales below and then assign the selection to a 2 rs Mean Low value Ount editor region by choosing from the lefthand side 1 O Mean value Scale valO Upper qualifier radio buttons Water alkalinity Water flow Water Hardness Water media type Water type WaterType Weekly exposure days week Wet Dry Year Undefined ndefined Smiles ILES O O Endpc an health hazards Genetic Toxicity 1 CN CH C C COc2ecece2 CCC an health hazards Genetic Toxicity C OS O O OCC an health hazards Genetic Toxicity OS C O O File layout O Vertical Private data Select one or more columns from the grid re Important The endpoint tree path should point to a leaf of the predefined endpoint tree For more information check chapter 4 Endpoint tree path in Water
20. imported to any of its leaves In the QSAR Toolbox 2 0 however the data matrix displays not only the predefined part of the endpoint tree but also builds a dynamic part based on the metadata of the currently displayed data points and or QSARs To check which part is predefined and which part is dynamic press the Ctrl key and the predefined part of the tree will be underscored Document version 1 0 Page 7 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard 5 Building the dynamic tree The dynamic tree is a feature of the QSAR Toolbox where the endpoint tree is expanded with nodes that organize the data point s metadata In essence it is a way to visualize the data the user has gathered from the database The data is assigned to a path what we call predefined path The dynamic part of the tree is a function of the data point s metadata It is an instruction that the user has given to the QSAR Toolbox software requiring that the data point s metadata are connected with metadata fields in a specific order The metadata fields and their hierarchy are called the Set tree hierarchy feature It is important to make the distinction between what is the data point s endpoint tree path and on what node the data point is displayed on the data matrix The first one is an immutable attribute of the data point and the latter is an undefined path that is build at runtime based on the endpoint tree path the
21. mutation Gene mutation Gene mutabon Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Sequence of steps Click on bacterial reverse mutation assay e 0 Ames test bacterial reverse mutation assay e g Ames test bacterial reveree mutation assay e g Ames test bacterial reverse mutation assay e 0 Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mutation aseay e g Ames teet hactenal reverse mutahon assay eg Ames test bacterial reverse mulalion assay e g Ames lest bacterial reverse mutation assay c g Ames test bacterial reverse mutabon assay e g Ames test bacterial reverse mulation assay e g Ames lest bacterial reverse mutation assay c g Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mutation assay 9 Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mutation aeeay e g Ames teet bacterial reverse mutation assay 9 Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mutation sessy e g Ames teet bacterial reverse mutation assay e 9 Ames test bacterial reverse mulation assay e g Ames lest bacterial reverse mutation assay c g Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mulalion assay e g Ames lest bacte
22. mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Data Mean value Scale v 3 Positive bao oth Cossu ded tuum abis Pome oss Select CAS 578112 ard step 4 0f 3 Select one or more columns from the grid Scales below and then assign the selection to a region by choosing from the lefthand side Document version 1 0 April 2011 radio buttons health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity sman heslth Tavicibu Data Mean value Scale v Page 62 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select Chemical name pilo wizard step 4 0f 3 Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side radio buttons Undefined Data Mean value Scale v health hazards Genetic Toxicity health hazardsa Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity sman heslth ene Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side radio buttons Year CEE an health
23. path has two components predefined and dynamic e Predefined Ecotoxicological Information Aquatic Toxicity Dynamic LC50 Animalia Arthropoda Invertebrates Branchiopod a branchiopods Daphnia magna 48 h In the Import wizard these two translate to Endpoint tree path Figure 5 and metadata Figure 6 The Animalia Arthropoda Invertebrates Branchiopoda branchiopods part is a separate feature in which Kingdom Phylum Class information is inserted before the field Test organisms species In this respect the user should take extra caution to import species information to the Test organisms species metadata field Endpoint path Endpoint tree Aquatic Tox cotoxicological Information Aquatic cotoxicological Information Aquatic cotoxicological Information Aquatic Tox cotoxicological Information Aquatic Tox Figure 5 Endpoint tree path ndpoint Duration Mean value Scale valueDuration Unit Test organisms species 550 48 h Daphnia magna c h 48 h Daphnia magna 550 48 h Daphnia magna 48 h Daphnia magna 48 h Daphnia magna 1550 48 h Daphnia magna 48 h Daphnia magna 48 h Daphnia magna Figure 6 Metadata Document version 1 0 Page 11 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard A Metadata information should always be provided for the fields Test organisms species Duration and Endpoint 6 R
24. rtant The end pol nt tree pat h Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity should pO nt to a leaf ofthe p redefined Ecotoxicological Information Aquatic Toxicity end po int tree For more information Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity check cha pter 4 En d nt tree pat h of Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity this document Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity Endpoint tree path This is a field containing the endpoint tree path related to the endpoint for which experimental data is to be imported The endpoint tree is separated in a predefined and a dynamic part o The predefined part determines the basic structure of the endpoint tree e g substance identity physical chemical properties environmental fate and transport ecotoxicological information human health hazard ordinary endpoint data is related to this predefined part o The dynamic part of the endpoint tree builds additional layers of the tree depending on the data implemented in the databases ordinary metadata is related to dynamic part Enpoint data is assigned to a predefined part of the endpoi
25. value Select one or more columns from the grid OScale Low qualifier Upper value Scales below and then assign the selection to a Low value unit editor O Mean value Scale valO Upper qualifier O Undefined region by choosing from the lefthand side radio buttons Weekly exposure days week Wet Dry Year mm Undefined lt Type of methodType of genotoxicity Test type Summary carcinogenicit 1 Summary carcinogenicib Summary carcinogenicits Summary carcinagenicit Se Se Y Document version 1 0 Page 55 of 70 April 2011 QSAR TOOLBOX uuu wizard step 703 Jndefined QSAR Toolbox User Manual Database Import Wizard Scroll the bar to review data column designations Click on Next button H O Mean qualifier O Low value O Mean value Scale valO Upper qualifier O undefined Sexual maturation offspring Route Comment s step 3of3 Sexual maturation offspring Route Comment Document version 1 0 April 2011 gdatitikikikididikiiiititi Summary carcinogenicity data Positive Summary carcinogenicity data Positive Summary carcinogenicity data Positive Summary carcinogenicity data Positive Summary carcinogenicity data Positive Reference source http potency berkeley edu cpdb html http potency berkeley edu cpdb htmil http potency berkeley edu cpdb html http
26. 0 LOEL NOEL Skin sensitisation Endpoint Carcinogenicity Ames Chromosomal aberration Estrogen receptor binding Duration years months days hours minutes seconds Daphnia magna Lepomis symnetricus Oncorhynchus mykiss Poecilia reticulata Tetrahymena pyriformis Test organisms species Effect Effect type Metabolic activation Sexual maturation offspring Strain Test type Type of genotoxicity Type of method Organ Route Document version 1 0 April 2011 Immobilization Mortality Reproduction Maternal toxicity Developmental toxicity Fetotoxicity Embryotoxicity with S9 without S9 no S9 info with and without Male Female Male Female TA 98 TA 100 TA 104 New Zealand White Swiss Fischer 344 DuCrj bacterial reverse mutation assay e g Ames test in vitro mammalian cell micronucleus test bacterial gene mutation assay acute subacute chronic developmental static semi static flow through Gene mutaion Chromosomal aberration DNA damage and or repair genome mutation in vivo in vitro other Lung Liver oral inhalation dermal implantation intramuscular intraperitoneal Page 10 of 70 TOOLBOX QSAR Toolbox User Manual Database Import Wizard This means that if a user wants to have a consistent display of the endpoint tree he she must import the metadata to the aforementioned fields before defining additional fields For instance the above long
27. 5 70 0 0087 0 00007 A A A A VO MM Document version 1 0 Page 25 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard When the user defines data of a Categorical type e g positive negative s he should follow a scale definition 1 The file for import should have a Scale column for the scale name This should contain a name of a scale exactly as defined in the scales list in the QSAR Toolbox database for example Gene mutation I is a scale from the QSAR Toolbox database scale list red colored fields Scales definition Scales list Scale conversions MAL Defauk scale Gene mutation Carcinogenicity LLi Th A Ordinal Gene mutation 1 Er Frai Oasis Micronucleus I Respiratory sensitization I Skin sensitisation I Oasis Mutagenicity Skin sensitisation II ECETOC ee Gef 2 62500 ETHYL C C OS C a0 Human heath hazan Gene mulaton Positive 3 eg Soe Human heath Que mutation H tie TET 4 61922 Phenowybenzar CH H Human heath hazan Gene mutation sive skin sensitisation IV GPMT 5 64675 Disthyl_Sultate CIC OS O C Human heath Gene mutation Positive Skin sensitisation BFR amp 66273 UETHVI METH COS CM 0 0 Human heath hazar Gene mutation Positive IUCLIDS phrasegro
28. 6 Mortality Adult Freshwater 26 13 50 29 3 DDT C CIXCIN Ecotoxicological 70 gt EC50 Hemicentrot 225 h Egg Saltwater 15 14 50 29 3 DDT C CI CI i Ecotoxicological 0 0087 mg L EC 50 Penaeus van 48 h Juvenile Saltwater 20 285 15 50 29 3 DDT PP C CI CI Ecotoxicoloaical 0 00007 ma L EC50 Hyalella azte 240 h Mortality Freshwater 22 16 50 29 3 DDT PP C CIXCIN Ecotoxicological 0 00123 gt mg L 50 Chironomus 240 h Mortality Freshwater 22 1 50 48 6 C1ZC CrEcotoxicological 21 580942 gt mg L EC50 vibnofiscner 0 25 n Benavior Adult Saltwater 18 50 48 AMITRYP c12C Ci Fontaxicological 36 89287 moi 50 Ampelisca at 24 h Martality Saltwater 19 50 48 6 c12C C Ecotoxicological 0 776692 gt EC50 Scrobicularia 24 h Mortality Freshwater 20 50 48 6 c12C C Ecotoxicological 0 804431 lt mg L 50 Brachionus c 24 h Mortality Freshwater 21 50 54 4 QUINIDIN c12c c C Ecotoxicological 836 584 mg L EC 50 Vibrio fischer 0 25 h Behavior Adult Saltwater 22 50 54 4 QUINIDIN c12c c Ci Ecotoxicological 273 3837 s mg L 50 Ampelisca at 24 h Mortality Saltwater 23 50 54 4 QUINIDIN c12c c Ci Ecotoxicological 8 291145 lt 50 Scrobicularia 24 h Mortality Freshwater 24 50 54 4 QUINIDIN 12 Ccotoxicological 0 66462 gt CC 50 24 h Mortality Treshwater 25 50 63 5 CHLORO 1 Ecotoxicological 86
29. 6 712 gt EC50 Vibriofischer 025 h Behavior Adult Saltwater 26 50 63 5 CHLORO c1 NC C Ecotoxicological 2042964 gt EC50 Ampelisca at 24 h Mortality Saltwater 2 50 63 5 CHLORO C1 NC C Ecotoxicological 11 65934 gt mg L EC 50 Scroblcularla 24 h Mortality Freshwater 28 50 63 5 CHLORO c1 NC C Ecotoxicological 4 38515 gt EC50 Brachionus c 24 h Mortality Freshwater 29 50 78 2 ACETYLSC O O Ecotoxicological 26 12175 gt 50 Vibriofischer 025 Behavior Adult Saltwater 30 50 78 2 ACETYLS 0 0 Ecotoxicological 381 918 EC50 Ampelisca at 24 h Mortality Saltwater 31 50 78 2 ACETYLS C O O Ecotoxicological 177 9882 mg L EC 50 Scrobicularia 24 h Mortality Freshwater 32 50 78 2 ACETYLSC O O Ecotoxicological 141 41775 mg L EC 50 Brachionus c 24 h Mortality Freshwater 33 51 28 5 DINITROI c1 O c Ni Ecotoxicological 05 mg L NOEC Oncorhynchu 720 h 8710 mg L Growth Early lifestage Freshwater 12 34 51 20 5 DINITI3OI c1 O c Ni Ccotoxicological 0 0 mg L NOCC Oncorhynchu 720 h 0710 mg L Growth Carly lifestag l reshwater 17 35 51 28 5 DINITROIc1 O c Ni Ecotoxicological 09 NOEC Cyprinodonv 672 8710 Growth Early lifestage Saltwater 15 22 36 51 28 5 1 Ecotoxicological 11 NOEC Oncorhynchu 1440 h 8710 mg L Growth Early lifestage Freshwater 7 37 51 28 5 DINITROI c1 O c Ni Ecoluxiculugical 13 myl NOEC 1440 h 8710 myl Murlalily Early lifeslagtFre
30. 740 mgl met 15 22 8710 mgl Freshwater 1 H ril 0710 mat Lat feste get mat 8710 tab Ean ir EI E mL DEC h Embryo Freshwater LIA an 1 MEC Eariy Map tage Fre walter 41 mL MOEC 15 2 4 F KEC D s 25 22 Endpoint data region Structural information chemical identity 1 CAS field Column with CAS Registry numbers 2 Name field Column with Chemical Name s 3 SMILES field Column with SMILES string Document version 1 0 Page 22 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard 50 00 0 FORMALDEHYDE 50 00 0 FORMALDEHYDE 50 00 0 FORMALDEHYDE 50 00 0 FORMALDEHYDE 50 06 6 PHENOBARBITAL C1 O c c2ccccc 2 CC CI 50 06 6 PHENOBARBITAL C1 O c c2ccccc2 CC C 50 06 61 PHENOBARBITAL C1 O c c2ccccc2 CC Ci 50 06 6 PHENOBARBITAL C1 O c caccccc 2 CC CI 90 28 2 BETA ESTRADIOL 1 c12c C P 3C P C P 4 50 28 2 BETA ESTRADIOL 1 c12c C P 3C P C P 4 50 28 2 BETA ESTRADIOL 1 12 3 4 50 29 3 DOT C CKCMCN C1cec Clhec 50 29 3 DDT C CIMCIMCI C c 1Tcec Cl ec 50 29 3 DDT C CINCINCI c1ece Cl cc Field with Endpoint tree path Predefined path Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information Aquatic Toxicity Im po
31. E_OXE 1 2 02 Human heath nazarc Gene mutation 1 2 3 DBROMO 1 8 8 Human health hazarc Gene mutation 1 1 3 DICHLORO C ONCCI CCI Human heath hazarc Gene mutation Z AMINO 4 6 DI C1 N e O e N Human neath hazarc Gene mutation 1 2 4 DINITROANI c1 N c N 0 Human health hazarc Gene mutation 1 4 3 0 1 1 Human heath hazarc Gene mutation 1 BENZOTRICHLC 1 Human heath hazarc Gene mutation ALPHA Al PHA cI C CI CI ecor Human neath Gene mutation BENZENE 1 3 c1 N 0 O cc Human heath hazarc Gene mutation NITRO TOL c1 C c N cc N Human heath hazarc Gene mutation 4 NITRO O PHF CI N C N CC N Human neath Gene mutation 1 Import New Database Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutaton Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutabon Gene mulation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation mutation Gene mutation Gene mutaton Gene mulation Gene mutation Gene mutation Gene
32. ISSCAN Negative Summary carcinogenicity 41 149 29 1 Patulin OC1C2 CC 0 C Human health hazards Carcinogenicity Carcinogenicity 155 Negative Summary carcinogenicity 42 57590202 Pentanal methylform CCCC C NIN C Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 43 2257 09 22 gt C1 CCN C S C Human health nazards Carcinogenicity Carcinogenicity ISSCAN Equivocal Summary carcinogenicity 44 02 84 2 Phenothiazine N1C2 C C CC Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 45 103 72 0 Phenyl isothiocyanat 3 1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 46 108 45 2 m Phenylenediamint NC1 CC CC C Human health hazards Carcinogenicity Carcinogenicity I ISSCAN Negative Summary carcinogenicity 47 92 69 3 p Phenylphenol OC1 CC C C C Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 48 105650 23 5 PhlP HCI 1 2 Human health hazards Carcinogenicily Carcinogenicily ISSCAN Positive Summary carcinogenicity 49 56393 22 7 gt Sheet 2 4 Ready ScrollLock 71 Pildralazine CC O CN C C 1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Summary carcinogenicity Peete ee eee ee eee Import New Database Sequenc
33. The OECD OSAR Toolbox for Grouping Chemicals into Categories User manual Database Import Wizard QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Document history Version 1 0 Database Import Wizard for version 2 1 of the QSAR Toolbox Issue date April 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 0 Page 2 of 70 April 2011 SAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Table of Contents Document MISCOVV ang etes 1 Document histor 2 1 Executive SUMMA caen tus miun Farc 4 2 QSAR Toolbox data moGdbeLl cccccavexinii x waka a X Wi KO RR Teni w Rn ac aC OC RC a 4 3 IMPON E EE 5 3 1 2MSSEEIGJeaert Mee Miete 5 3 22 e Ce K SCHTEN 6 EnG pome tree DaED EEN 7 5 Building the GYNAMIC d EE 8 6 RUNNING the import wizard 12 Gl NEE 13 re E Uu UE 16 Appendix I Preparing file for horizontal import 19 Appendix II Import example for a database with ecotoxicological information31 Appendix III Import example for database with Human health hazards
34. Toolbox User Manual Database Import Wizard 3 A new scale could be defined during the process of import B File import wizard step of 3 Fia O Vertical Horizontal 11 have header row Private data Delra new regon SMILES Select ong or more columns from the grid Endpoint tree path balme and then the selection to A Data region by choosing from the lefthand side radio buttons Metadata Water Water flew Water Hardness Water media type Water type WaterType Weekly exposure days week Wet Dry ista Maan ode wate Data Lin t Patines CRC a health Toxicity oxybercamane hydrochloride OH LC Ce c2 CT heath Toxicity bere Pose Jethy LC let m 8 48 an haath ere E 5 Pere METHYL METHANESULFONATE OSC Kee kanan health Tock fv mutation Portie Benue 4 Enterthe name of the new Scale scales Note the name of the Scale has to be identicalto the one definedin the user excelfile Ge SIE 7 e of the scale Give typ Chromosome sberration 1 F I Ke Respiratory sensitization Skin sensitisation I Oasis i Skin sensitisation I ECETOC Cantinogenicity I ISSCAN Skin sensitization EC3 r atio EC3 Shan sensitization IV Skin sensitisation
35. Type of genotoxicity Type of method Metadata field Examples of metadata field values 50 10 EC 50 LOEL NOEL Skin sensitisation Endpoint Carcinogenicity Ames Chromosomal aberration Estrogen receptor binding Duration years months days hours minutes seconds Daphnia magna Lepomis symnetricus Test organisms a Oncorhynchus mykiss Poecilia reticulata species Tetrahymena pyriformis Effect Immobilization Mortality Reproduction Maternal toxicity Developmental toxicity Eileen Fetotoxicity Embryotoxicity Metabolic activation with 59 without 59 no 59 info with and without Sexual maturation Male Female Male Female offspring Strain TA 98 TA 100 TA 104 New Zealand White Swiss Fischer 344 DuCrj bacterial reverse mutation assay e g Ames test in vitro mammalian cell micronucleus test bacterial gene mutation assay acute subacute chronic developmental static semi static flow through 2 Gene mutaion Chromosomal aberration DNA Type of genotoxicity damage and or repair genome mutation Type of method in vivo in vitro other Organ Lung Liver Route oral inhalation dermal implantation intramuscular Document version 1 0 Page 29 of 70 Test type April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Metadata field AM of metadata field values intra intraperitoneal
36. X QSAR Toolbox User Manual Database Import Wizard Gather experimental data from ported database mu M 73 AN M Era 1 CSN 1 239 pll M 175 mal Hp CL LL DR LL LL LL LL LE ra nu uM 1 M BI mgl E mm 1285 115 1 a Document version 1 0 Page 46 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Appendix III Import example for database with Human health hazards Information example below uses a file that is already prepared Guidance on how to prepare file for horizontal import can be found in Appendix I The destination for example files is Install folder Examples The default path is C Program Files QSAR Toolbox QSAR Toolbox 2 1 Examples Carcinogenicity amp mutagenicity_example xls Carcinogenicity amp mutagenicity example xls Compatibility Mode Microsoft Excel 9 esm soi Cn dv x Home Insert Page Layout Formulas Data Review View Developer Document version 1 0 April 2011 LA Arial mmm RI wee tea General Past ARCOPY B 0 3 8 Conditional t Insert Delete t Sona Find i SS 4 2 li Merge amp Center a la onditional Forma
37. alkalinity Water flow Water Hardness Water media type Water type WaterType this document Weekly exposure days week Wet Dry Year Undefined ndefined 1 CN CH C C COc2cceee2 CCC C OS O O OCC an health hazardss Genetic Toxicity OS C O O an health hazards Genetic Toxicity Document version 1 0 Page 64 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select DATA Main Value Scale value 5 fale import wizard step Zof 3 Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side radio buttons Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation Gene mutation in vitro in vitro in vitro in vitro in vitro bacterial revers bacterial revers bacterial revers bacterial revers Gene mikstian Tenere in ura BY Select DATA Unit e step 5 Select one or more columns from the grid vote below and then assign the selection to a region by choosing from the lefthand side radio l Type of genotoxicity Type of methodTesttype Gene mutation in vitro bacterial revers 1 Gene mutation in vitro bacterial revers Gene mutation in vitro bacterial revers Gene mutation in vitro bacterial revers Gene mutation in vitr
38. am P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory NTP Program P amp G Inventory FRERES EEE RRR RRR RRR RRR RRA JHEEEEREEEEEHEEEEEEEEEEEHE JRRRRR RRR RRR RRR RRR RRR RRR AD Databaseis being imported Progress bar g rile inure step dur Document version 1 0 Page 68 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Database is imported successfully Click OK QSAR Toolbox 2 0 60 597 Decument_1 QSAR emm rr 7 4 Document version 1 0 April 2011 Ta HHN TTT File import wizard step 3 of 3 TON h Category Definition Data Gap Filing 27 9999999990 TTT smiles is correcbed aukomatichaj 1 n smiles is corrected automatich NaH N ected per EI The Row 2158 0 The smiles is corrected Row 2177 0 The smiles is corrected aukomaticha Row 2 5 0 The smiles corrected Row 2391 0 The smiles is correcbed automatici Row 2414 0 The smiles is corrected automatich Row 390708 The smiles is 4770508 The smiles ic corrected automatich Row 47 79 08 The smiles is corrected Row 4975 08 The smiles corrected aubomatichi Row 5019 08 The smiles is corrected Row 5952 0 The smiles i
39. anual Database Import Wizard Database is being imported Progress bar File weir slau 3 01 3 Sexual maturation offspring Route other other other other other other other other other other other other other other other other other other other other other other other other other other QSAR Toolbox 2 0 60 597 Document_1 QSAR 1 151 11111111111111141111111111 11111111111 ac Document version 1 0 April 2011 Reference source http potency berkeley edujcpdb htmi Romualdo Benigni Author http fpotency berkeley edujcpdb htmi http f pobency berkeley edu cpdb hitmi hittp f potency berkeley edu cpdb html http potency berkeley edu opdb html http potency berkeley edu epdb html http pobency berkeley edujcpdb html http potency berkeley edu cpdb html http potency berkeley edujcpdb html http potency berkeley edu cpdb html http potency berkeley edufepdb htmi hetp jpotency berkeley edufcpdb html http potency berkeley edu cpdb html http ffpotency berkeley edu cpdb html http fipotency berkeley edujcpdb htmi http ffpotency berkeley edujcpdb html http berkeley http ipotency berkeley edu cpdb html http potency berkeley edujcpdb html http berkeley edujcpdb html http berkeley edujcpdb html http potency berkeley ed
40. cifies the meaning of the different results columns In the example above it is only one RC50 value but the import can handle multiple columns at once To set the column metadata double click on the column or click on the column and press Set parameter metadata This will bring up the metadata editor Figure 10 Document version 1 0 Page 14 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard DAR Scale data Unit Endpoint Private data Data tree position Physical Chemical Properties Environmental Fate and Transport E Ecotoxicological Information Aquatic Toxicity Sediment toxicity Terrestrial Toxicity Human health hazards Metadata fields 1 Effect Value type Text CO value D 2 Duration Value eL Mean value O Text Lower value Upper value 3 Value Unit 3 Test organisms species value TTT Abarenicola pacifica Text CO value Add field vo Figure 10 Metadata editor The most important part of the metadata setup is setting the Data tree position it should be a leaf from the displayed endpoint tree If the column contains categorical data the user should check the Scale data checkbox and specify the Scale for the values in the column In the Metadata fields panel the user can enter a list of the metadata for
41. e of steps Click on Detailed information Page 47 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Import New Database 0 QSAR Toolbox 2 0 60 597 Document VE Le B Greet e TTT File import wizard step 1 of 3 money Asset Document version 1 0 April 2011 ONO Qi 1 10100 Category Definition Data Gap Filing separators Thousands gt OSAR Toolbox 3 48 0170 QSAR TOOLBOX File wird slan 0113 Open ie Preview of D Transfer Import test example Carcinogenicitymutagenicity_exanple xis QSAR Toolbox User Manual Database Import Wizard Used separators ChemName Nitroso 2 oxoprooylethanolamine di N Nitroso perhydropyrimidine 1 Nitroso 3 4 5 trimethylpiperazine N Nitrosobis 2 2 2 trifluoroethyl amine Nitrosochlordiazepoxide N Nitrosocimetidne N Nitrosodithiazine Nitrosoethylmethylamine vent Geet Smiles N CC C ONCCOJNIO CICCN CNINSQ NSO CIC N C CNINSO C C C NIN CC FXPF F CC FXF F O Thousands Endpoint tree path Human health hazards Carcinogenicity Human heath hazards Carcinogenicity Human heakh hazards Carcinogenicity Human health hazards Carcinogenicity cl C2cSe cee Chc3 N C N C N 0 CN 2 Human heath hazards Carcinogenicity O NN O NICXN NCCSCCI C N CNI Human heath
42. eci Ecotoxicological Informations Aquatic ToxiO 00123 AMITRYPTYLINE 12C mCCCN C C e3e occc3 CCelecc2 Ecoboxicological Information Aquatic Toxi21 580942 AMITRYPTYLINE c12C SCCCN C C e3e ecec3 CCelecc2 Ecotoxicological Informations Aquatic 36 89287 AMITRYPTYLINE c12C SCCCN C C e3e ecec3 CCelenxc2 Ecotoxicological Informations Aquatic Top 776692 AMITRYPTYLIME c12C mCCCN C C e3e ocec3 CCelecc2 Ecoboxicological Informations Aquatic 804431 d PRIRA NET SUP d A wn m ha ef eee Naass Fe nnn mina Ta umm omm Fe I UP Put VIA MM WM WV Ww WV A A A A MM WM WM Database title Ecotoxicological example LI Importto The userhas to choose whetherto 3 importthe file as new database orwhetherto add Database title Ecofoxicological example the data to a database already existing inthe Note the user could change the name Toolbox It is very important that the thousands and decimal separators properly set while importing Especially with TXT file this could lead to erroneous parsing of data values Document version 1 0 Page 33 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Step 2 Horizontal import Fils inure isd step 4 0f O Horizontal Select one or more columns from the grid below and then assign the selection to a region by choosi
43. es test Document version 1 0 April 2011 BROME C C Rr Human heath Gene mutation 1 TRDROMOMETIC Dr Dr Dr Human heath hazarc Gene mutation 2 Bromopropan C C C Br PROPYLENMINI C1 C CN1 Human heath hazarc Gene mutation Human neath nazarr Gene mutation Human heath hazarc Gene mutation TERT BUTYL HC C C C OO Human heath hazarc Gene mutation DOXATHON CI SP S OC C Human heath Gene mutahon 1 2 DICHLOROF C C CI CCI Human heath hazarc Gene mutation 1 2 3 DICHLORO C C CI CCI Human heath hazarc Gene mutation 1 Bromoacebc A C UMU CBr Human neath hazarc Gene mutation 1 DICHLOROACE Human health hazarc Gene mutation 1 2 NITROPROPA C C C N 0 Human heath hazarc Gene mutation 1 1 AMNO 2 4 DI c12C 20 c3c C Human heath hazarc Gene mutation 1 1 8 DHYDROX 12 0 Human heath nazarc Gene mutation 1 9 1 ANTHRAQL 12 0 Human heath hazarc Gene mutation 1 1 NITRONAPHT c1 N 0 O c2 Human heath hazarc Gene mutation 1 PICRY1 _CHLOR CI N 0 O e 1 Human neath Gene mutation O NITROANISO c1 OC c N O Human heath hazarc Gene mutation 4 NITRO 1 c2ccc N Human heath hazarc Gene mutation S NITROBENZIM C12c CC N O Human Gene mutation 1 2 AMINOPHENC c1 O c N cccc Human health hazarc Gene mutation 2 AMINO 4 MET c1 O c N cc C Human heath hazarc Gene mutation 1 STYREN
44. eshwater 22 1 PhppsG 1995 Melatve Arch Conta 1 OVitew ether 025 h Behavior Saltwater 22 Calle 1994 ECO Ampeisragd 2 h Mortality Saltwater 22 1804 19 Sembeuana M h Morta ty Freshwater 22 Cal 1984 ECS Brxhonusc 24 h Mortaity Freshwater 22 Calle 1064 mu ECO V noftaher 025 h Behavior Adut Saltwater 22 1954 2 50 24 h Mortality Saltwater 22 Calley 1994 3 ECS Scobcuana 24 h Mortality Freshwater 22 1994 Brachonuse h Mortality Freshwater 22 1994 a 025 Behar aleja 1994 Mortality 1664 24 Cale 1994 n 24 h Morta ty 1994 nm 025 n Cen 1994 EI Document version 1 0 Page 20 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Content of file for import Any file to be imported should contain o fields with structural information chemical identity o a field with the Endpoint tree path o fields with endpoint data information experimental results and metadata A The endpoint tree path should point to a leaf of the predefined endpoint tree For more information check chapter 4 Endpoint tree path of this document Document version 1 0 Page 21 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Bi Endpoint tree Structural 4 Experimental information li
45. esignations click a column and then click on Undefined from the list box The definition of the Data region has its particularities The data record can contain categorical data which would require two columns one for the Scale and one for the Value of the record On the other hand the data record can contain a value which the QSAR Toolbox is a packet of Mean Min Max value plus corresponding qualifiers and a Unit These two are combined in the Define value panel part of the Define new region panel Document version 1 0 Page 17 of 70 April 2011 SAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard A When defining the data record the user should define I For categorical data Scale column for the scale name This Should contain a name of a scale exactly as defined in the scales list in the QSAR Toolbox database The Mean value Scale value column should contain a value that is exactly one of the scale s members II For value data At least one column for the Mean Min Max values Qualifiers and Unit are optional Second is the Metadata panel The data there is not mandatory for the import but can be used to import additional data to the data value Defining numerical metadata is just like the data record value definition process The third stage of the horizontal import is for review purposes It is recommended that the user should look again at each column that is to be imported The data record region
46. fier Upper value Scales below and then assign the selection to a Data Mean qualifier Low value Unit editor region by choosing from the lefthand side v Mean value Scale val Upper qualifier Undefined radio buttons Metadata 1 Test material equivalent to subn is value a 9 Test material identity richtext Test material identity freetext Test material identity ID Test material identity identifier Test method Data source Test organisms species Test organisms species detai Test Purity Test Radio Label v Mame SMILES Endpoint tree path Data value DIMENSIONS Endpoint Duration Mean value Chemi SMILESe cC2 c2cc3X c3cc c4ccc5 c5 c1l Endpoint tree pathd Transport BioaceD ata Mean value Scale value Uni BCF 1 2 2 3 3 4 5 5 14 Fate and Transport Bioace2 69019608 BCF c c ccl ccc2 c2cc3 c3cc c4ccc5 c5 c1 Envi i 2 BCF c c ccl ccc2 c2cc3 c3cc c4ccc5 c5 c14 Environmental Fate and TransporkitBioac 3 3636119799 BCF c c ccl1 ccc2 c2cc3 c3cc c4ccc5 c5 c14 Environmental Fate and TransportitBioaci3 4243915544 BCF RCE Figure 11 Import wizard step 2 horizontal import A The type of the column is specified by clicking on the column and then clicking its type CAS Chemical name SMILES from the list box in the Define new region panel or selecting a metadata field label from the list box in the Metadata panel To remove d
47. fines a record in its entirety At import time the user specifies which columns contain chemical identity data CAS Name SMILES which columns contain the Value the result that is seen in the Data matrix and used for Data gap filling and which columns contain the metadata e g Organ Duration Temperature Dose Species Endpoint etc Document version 1 0 Page 6 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard 4 Endpoint tree path When a data point is imported into the QSAR Toolbox the database engine needs to assign it to a leaf node in the endpoint tree However the way the endpoint tree is constructed differs significantly from version 1 1 of the QSAR Toolbox For the user the tree looks similar in both versions but the underlying logic has changed In Toolbox 1 1 reien This would predefined endpoint tree leaves Aquatic Toxicity SECS Animals In Toolbox 2 0 A Arthropoda lnvertebrates IBranchiopodaibranchio 4 of which the data is assigned This has two components Predefined part Ecotoxicological Information Aquatic Toxicity Daphnia magna Dynamic part ECSO Animalia Arthropoda Invertebrates Branchiopo da branchiopods Daphnia magna 48 h Figure 4 Endpoint tree in Toolbox version 1 1 vs Endpoint tree in QSAR Toolbox version 2 0 In Toolbox 1 1 the tree displayed in the data matrix was predefined and data could be
48. for horizontal import Each row defines a record in its entirety At import time the user specifies which columns has chemical identity information CAS Name SMILES which columns contain the values what is seen in the Data matrix and used in Data gap filling and which columns contain the metadata Organ Duration Temperature Dose Species Endpoint etc Document version 1 0 Page 19 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Horizontal example compact view Ecotoxicological example 4 22 34 cam Jee eeng 1 3 23 1999 Physic Juvende Freshwater 20 A JAMSSEr 1993 8 Mortality Juverie Freshwater 20 3 JANSSEP 1993 E h Mortality Luvende Freshwater 20 3 JAMSSER 1893 si Behavior Adut Saltwater 22 1804 1 h Mortality Saltwater 22 Caja 1994 h Mortality Freshwater 22 1994 1 h Mortality Frestrwater 22 1994 10 h Reproduc Freshwater 28 81 317 1 Kramer 1998 Aquat Tomcol 4 End pow R parer Freshwater 26 81 317 1 Kramer 1008 Reprodu Aquat Toxicol 4 End Mortality Adult Freshwater 26 B1 317 1 Kremer V 1998 Reprodu Aquat Toxicol 4 Male n Reprodu Egg Saltwater 15 WYNBEF 1989 Egg Mortality Sakwater 20 285 3 REVES 1566 15 lortality Freshwater 22 1 1995 Relawe Arch Em Coma Fr
49. formation Aquatic Toxi12 98 gical Information Aquatic Toxi39 ogical Informationst Aquatic Toxi57 gical Informationst Aquatic Toxi29 gical Informations Aquatic Toxi2995 767 Document version 1 0 Page 35 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select Endpoint tree path e fale import wizard step Zot 3 v I have a header row Important The endpoint tree path Select one or more columns from the grid below and then assign the selection to a el EE should point to a leaf of the predefined endpoint tree For more information check chapter 4 Endpoint tree path in this document Select one or more columns from the grid Scales below and then assign the selection to a editor region by choosing from the lefthand side radio buttons al Ceriodaphnia affinis 3 cotoxicological Informations Aquatic 239 Daphnia magna cotoxicological Informations Aquatic Tox Daphnia magna mm a Aquat Toxg29 Daphnia magna PQQ Vibrio fischeri mnalers shdika _ Document version 1 0 Page 36 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select DATA Mean qualifier 5 fale import 703 Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side radio buttons Data Mean value Scale value Data Mean qualifier Unit Endpoint
50. hazards Carcinogenicity NI CSCSCI N O CN CC NmO OC O CI9 CCCN CI N O CI NC CNINSO SO sO C ONO CICC ONIN OJO N Nitrosomethyl 2 hydroxyethyl amine CN CCO NSO N Nitrosomethyl 3 hydroxypropyl amineN N CCCOK O N Nitrosomethyl 2 oxopropvl amine ON CC C OJN O Human health hazards Carcinogenicity Human health hazards Carcinogenicity Human health hazards Carcinogenicity Human health hazards Carcinogenicity Human heath hazards Carcinogenicity Human health hazards Carcinogenicity Human health hazards Carcinogenicity Human heath hazards Carcinogenicity Human healkh hazards Carcinogenicity N Nitrosomethyl 2 tosyloxyethyl amine NC COS O O CIC CC C CC I ON Human heath hazards Carcinogenicity 3 Nitrosomethylaminopyridine Cl CC C C N1N N 0 C Cl eCC CC N1N N O C Human health hazards Carcinogenicity Human heath hazards ECarcinogenicity CImCCmC C C mO OC C2N NmO CCCC2 Human heath hazards Carcinogenicity w n mmm um um o um ee mom m P Importto The userhasto choose whetherto importthe file as a newdatabase orwhetherto add the data to a database already existing in the Toolbox 2 Database title carcnogeniciyemutagencty example Scale Carcinogenicity 1 ISSCAN Carcinogenicity 1 ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity
51. hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity Scale Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN Carcinogenicity I ISSCAN AER na nh deL uidet Ame ss ks al bowen de dI uuum tuam m mah STROM ART Select CAS Q pila impot wizard step 4 9f 3 region by choosing from the lefthand side Select one or more columns from the grid ae below and then assign the selection to a or radio buttons health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity aman arrimananisikis Positive Positive Positive Positive Negative Negative Document
52. inogenicity Carcinogenicity ISSCAN Equivocal Summary carcinogenicity 31 64224 21 1 Oltipraz CC1 C SSC1 S Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 32 73590 58 6 Omeprazole O S C 1 NC2 C Human health hazards amp Carcinogenicily Carcinogenicily ISSCAN Posilive Summary carcinogenicily 33 65 86 1 Orotic acid monosoc 1 Human health hazards Carcinogenicity Carcinogenicity I ISSCAN Equivocal Summary carcinogenicity 34 23135220 Oxamyl O C C NOC O Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 35 3096 50 2 9 2 C12C3 C C CC Human health Carcinogenicity ISSCAN Positive Summary carcinogenicity 36 14898 29 4 Oxolinic acid 0 01 2 0 3 Human health hazards Carcinagenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 37 110559 85 8 1 2 Oxopropyl nitros O C N CC C O Human health hazards Carcinogenicity Carcinogenicity ISSCAN Equivocal Summary carcinogenicity 38 89837 93 4 2 Oxopropyinitrosour N C 0 N N 0 C Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 39 6452 71 7 Oxprenolol HCI C1 C CC CC 1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 40 102 77 2 N Oxydiethylenebenz N1 C SC2 C 1C Human health hazards Carcinogenicily Carcinogenicily
53. ity data Positive hitp potency berkeley eduj epdb html other Summary carcinogenicity data Positive http f potency berkeley edujcpdb html other Summary carcinogenicity data Positive http potency berkeley edufecpdb htmi other Summary cercinogenicity data Positive http ffpotency berkeley edu cpdb htmil other Summary carcinogenicity data Positive Attp potency berkeley edufepdb html other Summary carcinogenicity data Positive http f potency berkeley edujcpdb html other Summary carcinogenicity data Positive Attp potency berkeley edufepdb html other Summary carcinogenicity data Positive http f potency berkeley edujcepdb html Summary carcinogenicity data Positive http potency berkeley edujcpdb html Summary carcinogenicity data Positive http potency berkeley edusepdb html Summary carcinogenicity data Positive http j potency berkeley edujcpdb html Summary cercinogenicity data Positive http f patency berkeley edu cpdb hkml Summary carcinogenicity data Positive http ffpotency berkeley edufcpdb hitmi Summary carcinogenicity data Positive http potency berkeley edusepdb html The database 15 in the process of being imported For large databases this might take considerable time LAN Lee r 9 Deut 1 tmn aul 28 4 TT ai konos bon OOo of TEL MI palm
54. line OC 0 C1 CCCh Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 11 42579 28 2 1 Nitrosonydantoin C1 NC CN1N 0 Human health nazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 12 30310 80 6 Nitrasahydraxyproline lt Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 13 25001 31 6 0 0 Human health hazards Carcinogenicity Carcinogenicity IBSCAN Equivocal Summary carcinogenicity 14 26921 58 6 N Nitrosometny 2 h CN CCO N U Human nazards Carcinogenicity Carcinogenicity 1 ISSCAN Positive Summary carcinogenicity 15 70415 59 7 N Nitrosomethyl 3 h NIN CCCO C O Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 16 55984 51 5 2 CN CC C O N Human health hazards Carcinogenicily Carcinogenicily ISSCAN Positive Summary carcinogenicity 17 N Nitrosomethyl 2 t NC COS 0 0 Human health hazards Carcinogenicity Carcinogenicity I ISSCAN Positive Summary carcinogenicity 18 69658919 3 Nitrosomethylamin C1 CC C C N1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 19 16219 99 1 4 Nitrosomethytamin C1 CC CC N1 Human health nazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 20 55557 03 4 Nitrasameth
55. loaded data point s metadata and the current settings of the Set tree hierarchy feature How does the above pertain to the import All the Aquatic Toxicity data in the QSAR Toolbox is assigned to the Ecotoxicological Information Aquatic Toxicity path However when the user installs the QSAR Toolbox and loads data for aquatic toxicity the entire tree path is shown for example Ecotoxicological Information Aquatic Toxicity LC50 Animalia Arthropoda Invertebrates Branchiopoda bra nchiopods Daphnia magna 48 h Document version 1 0 Page 8 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Where do the other fields come from The other fields come from the data point s metadata The metadata fields build the dynamic part of the endpoint tree LC50 Animalia Arthropoda Invertebrates Branchiopoda branchiopod s Daphnia magna 48 h The data point itself is associated to the shallow predefined part of the tree Ecotoxicological Information Aquatic Toxicity Ecotoxicological Information pr part Aquatic Toxicity LC50 Animalia Arthropoda Invertebrates Dynamic part Branchiopoda branchiopods Daphnia magna 48h When a data point is read from the database and needs to be displayed to the data matrix the tree is expanded to display the metadata of the data points Set tree hierarchy feature Ecotoxicological Information Aquatic Toxicity Metadata labels Sub nodes C Show all labe
56. ls Endpoint Effect Test organisms species Effect type Metabolic activation Kin gd om Organ Organ Tissue Phylum Taxonomy data Route Sexual maturation offspring Class Strain Test type Tissue Type of genotoxicity Type of method Taxonomy A large diversity of species has been stored and organized in Toolbox Taxonomy library including more than 12 295 biological species Species have been distributed in five kingdoms Animalia Plantae Fungi Protozoa and Monera Biological information is organized in the following taxa Kingdom Phylum Class Scientific information is associated automatically to each of the biological species Figure 5 Endpoint tree hierarchy Document version 1 0 Page 9 of 70 April 2011 y IR TOOLBOX QSAR Toolbox User Manual Database Import Wizard The QSAR Toolbox has default settings regarding which metadata is displayed The default fields used are Endpoint Duration Test organisms species Effect Effect type Metabolic activation Sexual maturation offspring Strain Test type Type of genotoxicity Type of method Tissue Organ Route The list with default fields pertains to the whole endpoint tree For Ecotoxicological Information Aquatic Toxicity the default hierarchy is EffectZEndpointZDurationZ Test organisms species Table 1 Examples of metadata field values Metadata field Examples of metadata field values LC 50 10 EC 5
57. n Ankley GT Relative sensitivity of three freshwater b Arch Eny Contam Toxicol 28 281 286 Phipps GL Mattson Ankley GT Relative sensitivity of three Freshwater b Arch Env Contam Toxicol 28 281 286 Document version 1 0 Page 43 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Ma Database Import Wizard 19 Fils mud C sizaro stay 203 Sexual maturation offspring Route Comment Reference source other Summary carcinogenicity data Positive Attp potency berkeley edufepdb html other Summary carcinogenicity data Positive hitp potency berkeley edujepdb html other Summary cercinogenicity data Positive http potency berkeley edujcpdb html other Summary carcinogenicity data Positive http f potency berkeley edujepdb html other Summary cercinogenicity data Positive http f potency berkeley edujcpdb html other Summary carcinogenicity data Positive http potency berkeley edufecpdb htmi other Summary cercinogenicity data Positive http ffpotency berkeley edu cpdb htmil other Summary carcinogenicity data Positive Attp potency berkeley edufepdb html other Summary cercinogenicity data Positive http ffpotency berkeley edu cpdb htmil other Summary carcinogenicity data Positive Attp potency berkeley edufepdb html other Summary carcinogenicity data Positive http f potency berkeley edujepdb html other Summary cercinogenicity data Positive http potency berkeley edujcpdb html other Summary carcinogenic
58. ng from the lefthand side radio buttons Endpoint tree path cotoxicological Information Aquatic 12 98 cotoxicological Information Aquatic Toxi39 cotoxicological Information Aquatic 7 cotoxicological Information Aquatic 29 1 O C c2ceececec2 CC C O NC OJNIEcotoxicological Informations Aquatic Toxi2995 767 1 2O C c2ccccc2 CC C 20 NC O NI1 Ecotoxicological Informations Aquatic 0009 113 1 2O C c2ccccc2 CC C 20 NC O NIT Ecotoxicological Informationst Aquatic 212 2406 1 2O C c2ccccc2 CC C 20 NC O NT Ecotoxicological Informationst Aquatic Toxib178 729 12c C P 3C P C P 4C P CK C P Ecotoxicological Informationst Aquatic 0 00012 12c C P 3C P C P 4C P Ch C P Ecotoxicological Information Aquatic 0 000251 12 C P 3C P C P 4C P CK C P4Ecotoxicological Information Aquatic Toxi0 00115 CIMCIMNClelece Checl elece Checl Informations Aquatic Toxi70 CIMCIMNClelece Cheel elece Checl Ecotoxicological Informations Aquatic Toxi0 0087 CIXCIXCl C c1ece Cl eci eiecc Cl eci Ecotoxicological Informations Aquatic 005 CIMCIMAHClelece Cheel elece Chec1 Informations Aquatic Toxi0 00123 12 3 3 1 2 Ecotoxicological Informations Aquatic Toxi21 580942 12 3 3 1 2 Ecotoxicological Informationst Aquatic Toxi36 89287 12
59. nt tree i e it is assigned to a leaf of the endpoint tree Document version 1 0 Page 23 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Structure Substance identity Structure Leaf of predefined part Si immobilisation aLcen TS EJAnimalia LeyChordata vertebrates HE Actinopterygn F ish Leungepred Effect The predefined part can be visualized by holding the Ctrl button and clicking on the Endpoint tree The predefined part of the tree is underlined Document version 1 0 Page 24 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard Endpoint data information The QSAR Toolbox oparates with the following data structure Data point record Value Link to chemical ID CAS SMILES Endpoint string Metadata type String Endpoint description string Duration Is Private Boolean Title 1 Value 1 15 Observed Boolean Title N Value N Metadata type Value Title 1 Value 1 Title N Value N Value is defined as Mean Qualifier lt Mean Value Low Qualifier Low Value floating point Upper Value floating point gt gt etc floating point gt gt etc number Qualifier number number The user should therefore organize his her data as follows 29 2995 767 10009 113 1212 2406 5178 729 0 00012 0 000251 0 0011
60. o bacterial revers Tana miikskian Cane mit sting im utra harharisl revere 2 The type of the column is specified by clicking column and Document version 1 0 Page 65 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard then clicking its type CAS Chemical name SMILES from the list box in the Define new region panel or selecting a metadata field label from the list box in the Metadata panel To remove designations click a column and then click on Undefined from the list box II All fields fields defined with the Define new region panel are color distinguished from the fields of the Metadata panel Document version 1 0 Page 66 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Scroll bar pilo 11119108 77124143 4 0f Select one more columns from the grid O Low qualifier O Upper value Scales below and then assign the selection to Omean qualifier O Low value editor region by choosing from the side Mean value Scale valO Upper qualifier Undefined radio buttons Test organisms species Strain Species strainMetabolic activatio in vitro bacterial reverse mutation assay e g AmSalmonella typhimurium in vitro bacterial reverse mutation assay e g AnSalmonella typhimurium in vitro bacterial reverse mutation assay e g ArSalmonella typhimurium in vitro bacterial reverse mutation assay e
61. ond step During the second step the file s layout is selected which leads to two separate code paths vertical or horizontal Document version 1 0 Page 12 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard 6 1 Vertical File import wizard step 2 of 3 EIE File layout 5 vertical CO Horizontal WII have a header row Define new region CAS Select one or more columns from the grid Chemical name Scales below and then assign the selection to a editor What do different layouts mean region by choosing from the lefthand side Undefined radio buttons SMILES RCSO value Chemical namethoquinone 1 0 0050 ethyl trans 4 bromo 2 butenonate Br cJ C I 2 5 Dichlara 1 4 benzoaquinane 01 00 01 Bromo 1 d naphthoquinone 40 4 4 0 1 1 4 Naphthaquinane 01 4 401 8 1 2 5 Dichlara 1 4 benzoquinane ethyl 2 bromo 2 hutenonate C 4 Chlorochalcone 0 cieee cz cc 2 bromomethylacrylate OC 2 brormomethylacrelate ethyl trans 4 bromo 2 butenonate Figure 8 Import wizard step 2 vertical import The second step window Figure 8 contains the CAS Chemical name and SMILES columns Here is also a button that invokes the Scales definitions editor in case the user wants to impor
62. p Format Painter EI Merg 83 Formatting as Table Styles 2 Clear Filter Select Clipboard fa Font fe Alignment fa Number G Styles Cells Editing 141 ME 8710 F2 D 1 2 50 00 0 FORMALIC 0 Ecotoxicological 12 98 50 Ceriodaphni 48 h Immobili Juvenile Freshwater 23 3 50 00 0 FORMALI C 0 Ecotoxicological 39 gt EC50 Daphnia mat 1 h Physioloc Juvenile Freshwater 20 4 50 00 0 FORMALI C O Ecoluxiculugical 57 gt 50 24 Murlalily Juvenile Fiesliwaler 20 5 50 00 0 FORMALI C O Ecotoxicoloaical 29 EC50 Daphnia mat 48 h Mortality Juvenile Freshwater 20 6 50 06 6 C1 O CiEcotoxicological 2995 767 gt mg L EC50 Vibriofischer 0 25 Behavior Adult Saltwater 7 50 06 6 PHENOB C1 0 CiEcotoxicological 10009 113 lt mg L EC 50 Ampelisca al 24 n Mortality Saltwater 8 50 06 6 PHENOB C1 O Ci Ecotoxicological 12122406 lt 50 Scrobicularia 24 h Mortality Freshwater 9 50 06 6 PHENOB C1 O CiEcotoxicological 5178 729 lt 50 Brachionus c 24 h Mortality Freshwater 10 50 28 2 BETA ES c12c C P Ecotoxicological 0 00012 lt EC50 Pimephales 456 Reprodut Adult Freshwater 26 11 50 28 2 BETA ES c12c C P Ecotoxicological 0 000251 gt 50 Pimcphalcs 456 h Adult Freshwater 26 12 50 28 2 BETA ES c12c C P Ecotoxicological 0 00115 gt 50 Pimephales 45
63. port as Inmentory Decimal uu Thousands k Preview of D Transfer linport test example Ecotoxicological example xs LL CAS NAME Smiles Endpoint tree path Data Mean value Scale value Data Mean quis 5 File impot vizand stepi 1118 Ecotoxicological Information Aquatic 2 98 Ecotoxicological InformationdtAquatic Toxi39 Ecotoxicological Information Aquatic Toxi57 0 Ecotoxicological Information Aquatic Toxi29 C1 sO C c2eccecc2 CC C S O NC S O NI Ecotoxicological Informations Aquatic Toxi2995 767 Cl sO Cc c2ccecc2 CC C S O NC SO NI Ecoboxicological Informations Aquatic Toxil 0009 113 CI O C cZoccer2NCEKC ONNC O NI Ecotoxicological Informations Aquatic Toxi1212 2406 C1 sO C c2ccocc2 CC C O NC 0 NI Ecotoxicological Informations Aquatic Toxib178 729 BETA ESTRADIOL 17 12c C4P 3C4F HK C P M4C4P H CXC4P Ecotoxicological Informations Aquatic 00012 BETA ESTRADIOL 17 C12c C4P E3C4P K C P MC4P K CXC4P Ecotoxicological Information Aquatic 000251 BETA ESTRADIOL 17 Cc120 C4P 3C4F K C P HCAP KHCXCAP Ecotoxicological Informations Aquatic 0 00115 DOT CCC C eleee C eel elece Clerl Ecotoxicological Informations Aquatic Toxi70 DOT 1 1 Ecotoxicological Informations Aquatic 0087 DOT P P CCIM HC clece Aecl Ecotoxicological Information Aquatic Toxi7e 005 DOT P P C CIKCIXCIC clecc Clecl eleec CD
64. potency berkeley edu cpdb html http potency berkeley edu cpdb html Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side Scales editor radio buttons Author Year Romualdo Benigni 01 9 2008 Romualdo Benigni 01 9 2008 Romualdo Benigni 01 9 2008 Romualdo Benigni 01 9 2008 Romualdo Benigni 01 9 2008 Reference source Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Posi
65. rial reverse mutation assay c g Ames test bacterial reverse mutabon assay e g Ames test bacterial reverse mulation assay e g Ames lest bacterial reverse mutation assay c g Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mutation assay e 0 Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mutation sessy e g Ames teet bacterial reverse mutation assay e 9 Ames test Detailed information Page 59 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Import New Database R Bod Category Definition Data Gap Filino uuunuuuuunun T 1 1 4 QSAR Toolbox 2 0 60 597 Document_1 Ca Work Category Definition gt Data Gap Filling LELEELLLLLLLL Et AE 4 Document version 1 0 Page 60 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard File is open Used separators Inventory Decimal Thousands Preview of D Transfer Import gt test example GENOTOXICITY_example xts os Chemical name Smiles Endpoint tree path ETHYL METHANESULFONATE C C OS CKmO mO Human health hazardss Genetic Toxicity DICHLORVOS Human health hazards Genetic Toxicity Phenoxybenzamine hydrochloride USAW ON H CH C C COc2cecec2 Human health hazards Genetic Toxicity Diethyl Sulf ate C C OS OX O OCC Human health hazards Genetic Toxicity
66. s correcbed automatici 2CN3CN CN C3XC1 C2 CH b 7 CHA Au Na H 1 CDecl mM oof o H len e OM ERO d at eci 1 CH ci ee 4 CH A O4 Y CIC Act 01 57 Ce st PLA Cle it ean CHA 3 CCE n BRRARRARARARARARARARARARARAARRRARAARARARARARAARAARAARRRAARARRARARRARAARARRARRA Page 69 of 70 2 rue Andr Pascal 75775 Paris Cedex 16 France Tel 33 1 45 24 82 00 Fax 33 145248500 ehscont oecd org
67. s will be marked with color and text The metadata fields are marked with a bold text over the first row for each column The metadata of type value will be marked with name of metadata data subtype for example Duration Units Where all columns are set and double checked the user should press Finish After the process is finished an Import successful message will be displayed and the wizard will close Document version 1 0 Page 18 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Appendix I Preparing a file for horizontal import File layout A file prepared for import should follow the layout as shown in chapter 3 Horizontal layout this layout is used when the file is in the form where a row defines a single data point Here the user specifies which column is the data which column is metadata and the type of metadata G 1 CAS NAME SMILES Param descriptor 1 Param descriptor 2 Param descriptor N VALUE 2 CAS 1 1 SMILES1 Param descriptor value 1 1 Param descriptor value 2 1 Param descriptor value 1 1 Value 1 3 582 2 SMILES2 Param descriptor value 1 2 Param descriptor value 2 2 Param descriptor value 1 2 Value 2 A 5 CASEK SMILESK Param descriptor value 1 K Param descriptor value 2 K Param descriptor value 2 Value Figure 1 File layout for horizontal import Figure 1 illustrates the format of an XLS file
68. selection to a Omean qualifier O Low value region by choosing from the lefthand side O Mean value Scale valO Upper qualifier O Undefined radio buttons 4224242222934 a Ds value BEER Water media type Water type WaterType Weekly exposure days week Wet Dry Year Indefined Ceriodaphnia affinis Daphnia magna Daphnia magna Daphnia magna Vibrio fischeri Aronelices ahdika Document version 1 0 Page 40 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard 9 11016 step 710108 Define value Select one or more columns from the grid O scale Low qualifier Upper value Scales below and then assign the selection to a O Mean qualifier O Low value S unit editor region by choosing from the lefthand side 2 O mean value Scale valO Upper qualifier Undefined radio buttons aie value Solubility DIUI Water Hardness Water media type Water type WaterType Weekly exposure days week wet Dry Year Solubility Ceriodaphnia affinis 48 Daphnia magna 1 Daphnia magna 24 Daphnia magna 48 Mibrio fischeri 0 25 firanelicees nai l tmn mn mom lt iv Select one or more columns from the grid CO Low qualifier valu Scales below and then assign the selection to a O Mean qualifier Low value editor region by choosing from the lefthand side 2 OMean value Scale valO
69. shwater 23 2 2 EGO Daphnia ma i h Physiclec Juvenale Freshwater 20 3 EGO Daphnia rn 24 h Juvensk Freshwater 20 3 EGO Daphnia mac 48 h Moralky Freshwater 20 3 50 Vibiolischer 02 h Behavior Adult Saltwater 24 S50 Ampelisca x 24 h Mortality Saltwater 22 50 Scrohicularia 24 h Mortality Freshwater 22 50 Brachionus c 24 h Mortality Freshwater 2 2 50 Pimephales 458 h Reproche Freshwater 26 81 317 1 EGADO Pinephaes 458 h Reproche Adult Freshwater 26 B1 MT 1 ECS50 Pinephaes 458 h Moraky Freshwater 26 Bi 317 1 225 h Reproche Egg Saltwater 15 3 50 Penaeus van 48 h Juverale Saltwater 20 SE 3 EC S50 740 h Mortality Freshwaler 22 1 Metadata fields can be used for building the dynamic part of the endpoint tree The feature is accessible through the Set the hierarchy option The user sets what categories metadata he she wants displayed on the endpoint tree and their hierarchy Then when the data are loaded the tree is build with the contents of the corresponding fields Document version 1 0 April 2011 Page 28 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard e Human health Hspesr Genetit To sleloj Sub nodes Type of method Test type Endpoint Test organisms species Metabolic activation Strain Seal maturation offspring Strain Test type Tissue
70. sliwaler T 38 51 28 5 DINITROI c1 O c Ni Ecotoxicological 16 NOEC Oncorhynchu 720 h 8710 Mortality Early lifestagt Freshwater 17 39 51 28 5 DINITROI c1 O c Ni Ecotoxicological 18 mg L NOEC 720 h 8710 mg L Growth Embryo Freshwater 17 40 51 28 5 DINIIROI C1 O C NI ECotoxicological 19 NOEC Oncorhynchu 120 h 8 10 Mortality Early litestagi Freshwater 12 al 51 28 5 DINITROI c1 O c NI Ecotoxicological 1 9 Cyprinodonv 672 h 87101 Growth Early lifestage Saltwater 15 22 42 51 28 5 DINITROIc1 O c Ni Ecotoxicological 19 mg L NOEC Cyprinodonv 672 h 8710 Growth Early lifestage Saltwater 25 22 M 4 Sheet2 1752 4 Ready ScrollLock 24 Sequence of steps Import New Database Detailed information Document version 1 0 April 2011 Page 31 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Import New Database m WM vv Category Definition Data Gag Filing QSAR Toolbox 2 0 60 597 Carcinogenicityftmulagenicity example was deleted 5 QSAR LIJ gt Profiling Category Definition Data Gap Filling QSAR Toolbox emicals 4 Used separ mors Climport ss em thousands A Document version 1 0 32 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard File is opened Used separators L JIm
71. t Sort amp Find amp a SE 9 Formatting as Table Styles La Clear Filter Select Clipboard H Alignment la Number la Styles Cells Editing E8535 ETHYL METHA C C OS C 0 Human heath hazarc Gene mutation Gene mulation Gene mutation DICHLORVOS Human heath hazarc Cenc mutation Gene mutation Cenc mutation Pnenoxybenzar c1 CN CK Human heath nazarc Gene mutaton 1 Gene mutation Gene mutaton Dethyl Sulfate C C OS 0 C Human heath hazarc Gene mutation 1 Gene mulation Gene mutation METHYL METH 05 0 0 Human heath hazarc Gene mutation Cene mutation Cenc mutation Uraci mustard C1 U C N CCC Human neath hazarc Gene mutation Gene mutation Gene mutabon 1 S NITROFUFR C1 C NN2C 0 Human health hazar Gene mulation Gene mulation Gene mutation Methylnitronitro C N N C N O Human heath hazarc Cenc mutation Gene mutation Cenc mutation 1 FLUORO 24 c1 F c N 0 C Human heath hazarc Gene mutation Gene mutation Gene mutation bacterial reverse mulalion assay e g Ames lest bacterial reverse mutation assay c g Ames test bacterial reverse mutation assay e g Ames test bacterial reverse mulaliun assay e g Ames lest bacterial mutation assay c g Ames test bacterial reverse mutabon assay e g Ames test bacterial reverse mulaliuri assay e g Ames lest bacterial reverse mutation assay c g Ames test bacterial reverse mutation aeeay e g Am
72. t categorical data that has no available scale A The type of the column is specified by clicking on the column and then selecting its type CAS Chemical name SMILES from the list box above To remove designations click a column and then click on Undefined from the list box Document version 1 0 Page 13 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard File import wizard step 3 of 3 Set parameter metadata Select a data column and click Set parameter metadata to assign it ta a particular endpoint SMILES Chemical namethoquinone MILES O C C Br C Ojc2cl ethyl Erans 4 bramo 2 bubenanate 2 5 Dichlora 1 4 benzaquinane 01 1 2 1 4 401 4 00861 1 4 Maphthaquinane 201 40 4 4 1 2 5 Dichlara 1 4 benzaquinane ciciclhi cci oncicl ol ethyl 2 bromo 3 hutenonate 4 Chlorochalcone 1 2 lt LC Dr 0 2 bromomethy acrylate 0 ethyl trars 4 brormo Z hbutenonate 1 Octen 3 one lt Jint Hover over a data column to see what endpoint it is assigned Eo Figure 9 Import wizard step 3 vertical import The third step of the vertical import Figure 9 is where the user spe
73. the data point There are two types of metadata Text and Value The firstis a Document version 1 0 Page 15 of 70 April 2011 TOOLBOX QSAR Toolbox User Manual Database Import Wizard simple string while the latter is a Mean Lower value Upper value combination A The Vertical import imports the data column without qualifiers and only to the Mean part of the data point record If the user wants to enter qualified numbers or Mean Low Max combinations it is recommended to use the Horizontal layout After all metadata is set for all columns the user should press Finish After the process is finished an Import successful message will be displayed and the wizard will close 6 2 Horizontal The Horizontal layout is selected from a radio button group in the second step of the import There are basically two things the user can define marked 1 and 2 in figure 11 below First in the Define new region panel are the CAS NAME SMILES Endpoint tree path and Data items When they are defined the minimum is met Document version 1 0 Page 16 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard File import wizard step 2 of 3 File layout What do different layouts mean Vertical Horizontal v I have a header row Private data Define new region SMILES A Define value Select one or more columns from the grid Endpoint tree path O scale O Low quali
74. tical layout can import multiple values for a chemical Document version 1 0 Page 5 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard B C D E 1 CAS MAIVIE SMILES Experiment 1 Experiment 2 CASET1 NAME 1 SMILES 1 Value 1 Value 1 3 5 2 2 SMILES 2 Value 2 Value 2 A 5 6 58 SMILES Value Value Figure 2 Vertical layout Figure 2 illustrates the format of an XLS file for import The first three columns represent the chemical identity information and column D and E represent results from two different experiments a package of metadata such as Organ Duration Temperature Dose Species Endpoint etc 3 2 Horizontal layout This layout is used when each data point is defined in a row Here the user specifies in which column is the data the metadata and the type of metadata L A RS G 4 1 CAS NAME SMILES Param descriptor 1 Param descriptor 2 Param descriptor N VALUE 2 CAS 1 1 SMILES1 Param descriptor value 1 1 Param descriptor value 2 1 Param descriptor value 1 1 Value 1 3 582 2 SMILES2 Param descriptor value 1 2 Param descriptor value 2 2 Param descriptor value 1 2 Value 2 A 3 CAS K SMILESK Param descriptor value 1 K Param descriptor value 2 K Param descriptor value 2 K Value Figure 3 Horizontal layout Figure 3 shows how an XLS file could look like for horizontal import Each row de
75. tive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Summary carcinogenicity data Positive http potency berkeley edu cpdb html Author Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Romualdo Benigni Page 560f70 QSAR TOOLBOX QSAR Toolbox User M
76. ujcpdb html http potency berkeley edujcpdb html http potency berkeley eduycpdb html Cancel h Del Category Definition Data Gap Filling Page 57 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Error message log file QSAR Toolbox 2 0 60 597 Document_1 Work Category Definition r Data Gap Filling Q File import wizard step 3 of 3 LERMELLLLLLLELLLLLLLLLLELLLLL Imported database im Category Definition Data Gap Filling Y Grouping Categories Document version 1 0 Page 58 of 70 April 2011 QSAR TOOLBOX QSAR Toolbox User Manual Database Import Wizard Appendix IV Import example for database with Human health hazards Information A The example below uses a file that is already prepared Guidance on how to prepare file for horizontal import can be found in Appendix I The destination for example files is Install folder Examples The default path is C Program Files QSAR Toolbox QSAR Toolbox 2 1 Examples GENOTOXICITY_example xls GFENOTOXICITY_examplests Compatibility Mode Microsoft Excel 8 ej 4 9 Insert Page layout Formulas Data Review View Developer e FES 4 ES ra gra J Format Painter Arial lu gt Atal Ep Wrap Text General Bt DIE Merge Center 6 Conditional Format Cell Insert Delete Forma
77. unning the import wizard The import wizard is organised in a three step process First step Figure 7 The first window of the import wizard outlines the open file control 1 the file review pane 2 database name edit box 3 the used decimal and thousands separators and the import as inventory check box It is very important that the thousands and decimal separators are properly set while importing Especially with TXT file this could lead to erroneous parsing of results 1 a ror onore clone uu cansam dal Fate aad li ANT D ML ji Es tO LITER PT as a KC ei Klek Fest niani A sei Tr anf germerda xis lata Trent M Te maj ccm BOU remora aj Vato aluj Trara manda o ww d rf Eeer aj pes ed E Pss ged aj ale Ti rugo M Tran ES Tu Fe rpa s Traneport lf Tr ane Mie sr gf ECUS genre t ceo Ei Mol SR vw eo 0 sed Tarot cere a KOVI d Tr ru aj EC Tr SU fruaj ize ard Transportif Tare sz Toma re uj Trasporti Tran sz ul 1 uper ear e Trara ot sz e en E I pa e EN EN ku EN Eh ER a EN DN 4 Figure 7 Import wizard step one Sec
78. up_P16 rr 7 68751 Uraci mustard CI O C N CCC Human heath hazar Gene mutaten Positive IUCLIDS phrasegroup P105 8 87209 1 iS NITROFUF CI CeNNZC 0O Human heath hazar Gene mutation Equivocal IUCLIDS phrasegroup 20 Scale members 5 70257 Melhyiikron ro C NYN C N D Human heath hazar Gene mutation Positive IUCLIDS phrasegroup C47 10 70348 1 FLUORO 24 cl F c N O C Human heath haza Gene mutation Posdive IUCLIDS phrasegroup F23 11 Ta ETHYL_BROME C C Br Human heath hazan Gene mulaton Bosgtog IUCLID5 phrasegroup T116 13 75252 TRISROMOMETICIEME Er Human heath harari Gene mutation Positive IUCLIDS phrasegroup_T46 2 High Positive 13 15281 2 Bromapropan COC air Human heath hazan Gene mutation Positive IUCLIDS phrasegroup T46 1 Equivocal 14 75478 TRIODOMETHA Human heath hazan Gene mutation Positive IUCLIDS phrasegroup_T21 Negative 15 PROPYLENMINICT C CN1 Human heath hazad Gene mutation H Negative IUCLIDS phrasegroup T143 16 75812 TERT BUTYL HC CKCHC OO Human heath hazar Gene mutation Positiva IUCLIDS phrasegroup 102 17 HSH DIQXATHIOM 1 5845 Human heath hazan Gene mutation Positive skin sensitisation LIMU a 18 18875 1 22 DICHLOROF C CHCICCI Human heath harani Gene mulaton 2 The Mean value Scale value column should contain only values that scale members blue colored fields Document version 1 0 Page 26 of 70 April 2011 TOOLBOX QSAR
79. version 1 0 April 2011 Page 50 of 70 QSAR TOOLBOX QSAR Toolbox User Manual Database Impo rt Wizard Select Chemical name izand step 2 9f 3 Select one or more columns from the grid below and then assign the selection to a region by choosing from the lefthand side radio buttons Year DEEE health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity Select one or more columns from the grid Scales below and then assign the selection to a editor region by choosing from the lefthand side radio buttons heslth hsssrde arcinacenicitu an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity an health hazards Carcinogenicity iman heslth srcineeeniciu Data Negative Document version 1 0 April 2011 Page 51 of 70 TOOLBOX QSAR Toolbox User Manual Database Import Wizard Select Endpoint tree path Fi step 4 0f Select one or more columns from the grid Scales below and then assign the selection to a EE ekle Important The endpoint tree path should point to a leaf of the predefined endpoint tree For more information check chapter 4 Endpoint tree path in this document Endpoint tree path
80. whetherto importthe file as a new database orwhetherto addthe data to a database already existing in the Toolbox Itis very important that the thousands and decimal separators properly set while importing Especially with TXT file this could lead to erroneous parsing of data values Document version 1 0 Page 61 of 70 April 2011 QSAR TOOLBOX step 703 bee eee eee ee eee QSAR Toolbox User Manual Database Import Wizard Step 2 Horizontal import Select one or more columns from the grid ales below and then assign the selection to a region by choosing from the lefthand side health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity an health hazards Genetic Toxicity Scale Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene mutation I Gene
81. yiphenid C1 CC C C C t Human health hazardssCarcinagenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 21 4515 10 0 Nitrosopipecolic acid O NN CCC1 C C Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 22 5632 4 3 N Nitrosopiperazine O NN CCN1 CC Human health nazards Carcinogenicity Carcinogenicity I ISSCAN Positive Summary carcinogenicity 23 7519 36 0 Nitrosoproline O NN CC1 C C1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 24 81795 07 5 N Nilrosolhialdine CC1SC SC N1N Human health hazards Carcinogenicily Carcinogenicily 155 Positive Summary carcinogenicity 25 26541 51 5 N Nitrosothiomorphc O NN1CCSCC1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 26 23282204 Nivalenol Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 21 68 23 5 C C 12C C3c Human health nazards Carcinogenicity Carcinogenicity ISSCAN Positive Summary carcinogenicity 28 244 63 3 C12CAC CN C Human health hazardsstCarcinagenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 29 29002 74 4 Octachlorostrene 1 Human health hazards Carcinogenicity Carcinogenicity ISSCAN Negative Summary carcinogenicity 30 112 80 1 Oleate sodium C C C C CCCCC Human health hazards Carc

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