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1. Select a feature template if applicable for that template additional fields will now appear ONDA ND In case no appropriate template is available as yet select add modify and create a new feature template 9 Each additional field should describe a specific characteristic for the measurement Items name and unit are already mandatory but other fields need to be added describing main features of Short manual Phenotype v1 0 20150219 6 of 8 the experiment whereby it is heavily recommended to report these features according to minimum information guidelines 3 2 2 Importing of features When creating multiple features of the same type of measurement importing of features will provide a quick way of uploading them to the module section Of note should be that the descriptive field items themselves cannot be imported in this manner but should be created beforehand However the content of these fields can be created in Excel and uploaded in one session for multiple field items See Appendix I for an example 2 N Go to the module menu choose the appropriate module Select in the Import menu the option Features Select the Excel file containing information on the features Choose the appropriate data template Feature template It is indicated that the data template is not required but leaving this empty results in the use of the standard feature template This will give p2. events e g biological marker was measured on material from a subject e g from a blood sample Go back to study for which you ve imported subjects Short manual Phenotype v1 0 20150219 4 of 8 1 Go to the Browse menu and choose Edit your study Click on step 3 Events Choose the type of event treatment or sampling event and an Event template Both for events and sampling events predefined templates are present 4 If no appropriate template is present select add modify and create a new sampling event template 5 Click add 6 Continue adding all events you need Below a description will be given of a Group Change the name of the Group to be more informative e g name of measured biological marker 8 Click on quick save and then next 9 An overview of subjects and sampling events is now created Mark the subjects that belong to the created sampling event group 10 Click quick save and then next 2 4 Samples After defining your events see section 2 3 an overview screen will appear with the to be generated sample names the name consists of the subject ID Event name Group and sampling event template Depending on the sample template used additional fields will be present which contains information on the sample type which can be completed here Click next 2 5 Assays To be able to link your measurements to a sample for a par
3. v1 0 20150219 708 8 Select the Excel or CSV file containing the results measurements Please make sure that the setup of the file to be imported is correct Click on allowed layouts text for examples Click next 9 Select sample layout sample or subject Click next 10 Check that samples were matched to the correct subject features and event otherwise make adjustments here or click on previous if applicable 11 Click next if all data have been matched correctly Your data has been added to the assay and can be viewed and exported 5 Export You can export data from Phenotype Database in order to perform calculations or visualisations on the data or to obtain an export file for upload into for example the data integration platform tranSMART 5 1 Export study meta data 1 Go to the GSCF Go to the Export menu choose Export studies to SimpleTox file Select the study of interest and click Export The downloaded file will contain information on subjects sampling events and sample names 5 2 Export study meta data and measurements 1 Go to the Export menu and choose Export assay data to file 2 Select your study and the assay 3 In the next screen mark the items of interest It is also possible to export only the measurements Choose the type of export file in most cases European csv and click on submit Click ok in the next screen to downl
4. 1 of 8 Phenotype Database Quick start user manual for entering study meta data in the Generic Study Capture Framework amp Assay Modules Mariska Bierkens Jolanda Strubel Short manual Phenotype v1 0 20150219 2 of 8 1 Introduction This short manual explains the steps required to create a study in Phenotype Database It includes the definition of the study creating of subjects creating samples and linking data of measurements to these samples using so called assays For a full description of Phenotype Database go to the extended user guide available on the website Please note before starting with uploading data in Generic Study 5 Capture Framework Module e g SAM Phenotype Database GSCF Create templates for each part of the study Fields within the templates represent data that needs to be entered Creating templates beforehand will enable the user to directly match their data columns to the particular Platform template fields see Chapter 3 of the user manual for description on templates Data files that need to be uploaded should adhere to a specific structure to allow matching of column headers to the desired template field see Paragraph 2 3 of the user Feature manual for some examples In this manual a walkthrough will be given in which a study is set up Section 2 platforms and features are created Measurement Section 3 measurements are uploaded Section 4 and data is exported Section 5 In Fi
5. Import file Click on upload to select the Excel file with subject information a Leave the date format dd MM yyyy Select sheet containing data Indicate columns header row number Select data type being uploaded here Subject Select study o 2 9 0 Select type of the data template If no appropriate template is available select add modify and create new template g Fora subject template two fields are mandatory subject identifier and species Add other variables to describe subjects as desired e g gender age tumour pathology etc but when using systems such as e g OpenClinica take care not to completely copy data already present within this tool h Click next Page 2 Assign properties Match fields in the subject template to the column headers present in the Excel file name IDENTIFIER field should be matched to the Excel column with the subject identifier etc Click next Page 3 Check the imported data Overview of the to be imported subjects Check variables and where necessary make corrections additions Page 4 Confirmation If everything has been matched all right click next otherwise click previous and make changes Page 5 Done Subjects have been imported to the study 2 3 Define sampling events In this part you need to state what happened to the subject i e what events e g treatment with a drug diet challenge or sampling
6. gure 1 the general setup of the Phenotype Database and the relation between the different elements is shown Figure 1 General overview of elements within the Phenotype Database One subject indicated by 1 can have more than one number N sample s and one sample can have more than one number N measurements in the same assay 2 Generic Study Capture Framework section set up your study In this section it is explained in short how to set up your study how to add subjects define events and create samples in the Generic Study Capture Framework GSCF section of the Phenotype Database For more details please refer to the extended user manual Short manual Phenotype v1 0 20150219 3 of 8 2 1 Create a new study 1 2 3 Go to menu Create and select Create a new study Select a predefined template or choose the add modify option to create a new template Choose General Study template in case you are not sure of the fields you need This template contains the fields title description code startdate and contacts Help text is available under the question mark icons Complete the mandatory fields indicated by a green arrow Click on Quick save 2 2 Importing subjects using an Excel file 1 2 3 Go to the menu Import and select A part of the study design Make sure that the Excel spreadsheet you use contains unique subject names Page 1
7. oad The downloaded file will contain information on subjects sampling events sample names event groups and the measurements Short manual_ Phenotype v1 0 20150219 8 of 8 Appendix I Example of fields within a qRT PCR feature For qRT PCR measurements the following additional fields describing a real time quantitative experiment should be added to a feature 1 2 3 10 11 12 13 14 15 16 17 18 19 Target gene full name s full name s of the target gene e g NCBI definition Target gene symbol HGNC name of the target gene using HGNC term for human subjects Target gene ontology NCBI code GI code Target gene forward primer forward primer sequence orientation given as standard 5 3 in nucleotides Target gene reverse primer reverse primer sequence orientation given as standard 5 3 in nucleotides Annealing temperature of target gene primers in Celsius Target gene primer manufacturer Reference gene full name s full name s of the reference housekeeping or control gene e g NCBI definition Reference gene symbol HGNC Reference gene ontology NCBI code GI code Reference gene forward primer forward primer sequence orientation given as standard 5 3 in nucleotides Reference gene reverse primer reverse primer sequence orientation given as standard 5 3 in nucleotides Annealing temperature of reference gene primers in Celsius Reference gene primer manufactu
8. propriate predefined Platform template is available select add modify and create the needed fields for the platform Click create 4 Click back to list Please note that it is possible to choose a different platform type referring to the different modules available here In case you have created a platform but can t find it under the expected module please check the other module and edit the platform type for the platform 3 2 Creating a feature A feature describes the actually measured item e g a biological marker laboratory parameter etc and the associated metadata for this measured item It is important to add as much information to this feature as required in order to reproduce or trace back the results according to minimum information guidelines such as MIQE Features should be present for all types of measurements in your study and should be uploaded to the appropriate platform You can manually define features in Phenotype Database section 3 2 1 or import them using an Excel file section 3 2 2 3 2 1 Manual creation of a feature 1 Go to the Module menu choose the appropriate module Select in the Browse menu the option Features All current features are shown If no appropriate feature is available yet select create new feature Indicate the platform to which this new feature belongs Give the new feature a meaningful name mandatory and if applicable a unit
9. rer Reporter dye manufacturer Description description on how the qRT PCR was performed Can be reference to a published article or a reference to the protocol It is also possible to enter a field with experimental protocol and upload the protocol file itself Machine used for qRT PCR manufacturer Software used for analysis of results software manufacturer and version Analysis calculation unit value of the measured feature Short manual_ Phenotype v1 0 20150219
10. roblems in the next step as the descriptive fields from the Excel file cannot be matched Select platform Click next Match the headers in the Excel file to the descriptive fields present in the selected feature template Discard all columns and rows that do not need to be imported Click next Check whether everything was matched correctly If not use the prev to go back to the previous step Click next You can now use these features to add measurements to your study 4 Importing data measurements At the moment the Phenotype Database only handles the import of numeric values In case you have data in text format dichotomise that data if possible by coding them in the Excel file for instance Yes 1 No 0 unmethylated U 0 methylated M 1 Go from the module back to the GSCF by clicking on Go to GSCF 1 Choose from the Browse menu the My studies or All studies option Click on the view icon for the appropriate study Go to the tab Assays You will now see an overview of all assay names modules a column Link with a hyperlink to the eventual measurement details and the sample names Click on details of the respective assay No measurements are present as yet Click on the word importer in the text Use the importer to import your data to upload results into the assay Select the correct assay Click next Select the correct platform Short manual Phenotype
11. ticular sample event you need to create a so called assay 1 Select an assay template Give this assay a meaningful name e g name of the measured biomarker Choose the appropriate module for this measurement e g gPCR Click add Continue until you have defined all needed assays Click quick save and then next NOOR OD An overview screen appears showing all sample names for all subjects and the defined assays Check the boxes to indicate which samples belong to what assay Click next You have now created a study with subjects sampling events samples and assays which are awaiting data To be able to upload the data you need to define platforms and features which will be explained in section 3 Short manual_ Phenotype v1 0 20150219 5 of 8 3 Creating platforms and features Go to the Module menu and select the module section which you want your assay to appear in e g QPCR Now you need to choose or create a platform section 3 1 and then features section 3 2 3 1 Creating a platform Platforms have been predefined in the module section A new platform may be created to distinguish between types of techniques e g RT PCR SYBR Green To create a new platform 1 Select Browse In case no appropriate platform is available select Create new platform Complete the fields Name Platform version Platform type Comments and Template In case no ap
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