ELSA User Manual. KI Biobank Instruktion. Contents

Transcription

1 KI Biobank Instruktion ELSA User Manual Contents General Information... 2 ELSA explained... 2 What is needed to use ELSA?... 2 Issue reporting and support... 2 Using ELSA... 2 Important information... 3 Log in... 4 Choose current study... 4 Change password... 5 Register samples... 5 Register one sample and donor... 6 Register multiple samples for one study donor Approval of samples not approved during registration Search functions Search for samples registered for a specific donor View all data for the study Short instructions how to import CSV into MS Excel Ändringsmeddelande Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16) Utfärdad av: Staffan Bergh

2 General Information ELSA explained ELSA (External Logging of Samples Application) is a web based application provided by KI Biobank. Its primary purpose is to provide Biobank customers with an interface to register samples and study donors online. What is needed to use ELSA? To use ELSA you will need user credentials and a supported web browser installed on your workstation. All users must be provided with a username and password and these credentials must be held strictly personal for security reasons. Each user account may hold authorities to more than one study. To apply for a user account in ELSA, please contact your study coordinator which will send a request to biobank-support@ki.se. Supported web browsers are: Internet Explorer 6 and later (available in most PCs) Mozilla Firefox 3 and later (commonly found in Macintosh computers) Should you encounter any problems using the above browsers, please contact KI Biobank support as described in section Issue reporting and support Issue reporting and support If there are issues in, errors in or questions regarding the usage of ELSA, please contact KI Biobank support by sending a message to biobank-support@ki.se. To facilitate the handling of the issue at KI Biobank it is important to provide as much information as possible regarding the problem at hand. Important information is for example what actions were taken when the problem occurred, at what time it occurred, version of the current web browser and your operating system. Please attach error messages displayed by ELSA if possible, which could be done by copying the error message from the application to your support invoice. Please check your web browser version prior to contacting the support. Using ELSA ELSA is used to register samples in conjunction with study donors. To use the application s functions you must log into the application with your username and password, see section Log in. After logging in, users with access to more than one study must choose the study to work with, which is described in section Choose current study. After successful login the ELSA start view is displayed, see Fig. 1 Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

3 Fig. 1 ELSA start page At the start page, information about the current study such as number of logged samples and study donors is displayed, as well as a drop-down menu with available user actions. The menu items are; Register sample which is described in section Register samples Search, explained in section Search functions Change study described in section Choose current study Change password depicted in Change password To log out, follow the link Logout in the top right corner of the application window. Important information A very basic and important issue when using ELSA is to avoid using the browser s Back button. The Back button does not affect the state of already saved data. Hence, you cannot undo anything in ELSA by clicking the Back button. If you need your already entered data altered, please contact KI Biobank support. Entered data must be approved, which will lessen the risk of registration of erroneous data. Sample information is saved the moment the data is entered but the data will not be tagged as validated before the user actively approved the entries. The approval step provides the user with the opportunity to correct and review data and thus enhancing data quality. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

4 Log in Pointing your web browser to URL will display the ELSA login view, see Fig. 2. Fig. 2 ELSA login screen In order to log into ELSA, enter your user name and password and click button Login. Please be careful entering your password correctly as three failed attempts will lock your user account. This lock can be revoked only by KI Biobank, and the feature s purpose is to heighten the security level of ELSA. To change the user interface language, please choose any of the links in the top portion of the view. Svenska is the default setting and English toggles the language. The login view also contains links to the KI Biobank home page, the address to which support issues can be sent and a link where this document can be downloaded. The e- mail address is the primary choice if you experience problems in the usage of ELSA. Choose current study Users with access to more than one study must choose which study to work with after login, see Fig. 3. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

5 Fig. 3 Users with access to multiple studies must choose current study at login Choose a study and click OK after which the ELSA start page is displayed, see Fig. 1. This step is omitted for users with access to only one study. The menu item Change study allows users with access to multiple studies to change current study and enter data in more than one study without having to log out of the application. Change password In order to change your password, select Change password in the drop-down menu. Enter your current password and a desired new password, which must be repeated exactly. Your new password must be at least eight characters long. To save the changes, click Update. Fig. 4 Change password view Register samples To register samples select the Register samples item in the drop-down menu. If you have access to multiple studies, please check carefully that your currently chosen Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

6 study is the one intended. The name of the current study is displayed in the upper left portion of the view as shown in Fig. 5. The first view in the register sample flow prompts for type of registration and sample type, see Fig. 5. Fig. 5 First page of the sample registration flow ELSA currently supports two registration workflows. The first workflow assumes that there is only one sample to register for each study donor, allowing you to input both sample ID and donor ID on each registration, as described in section Register one sample and donor. The second workflow supports registration of multiple samples for each study donor, allowing you to specify a donor ID to which all following samples will be registered, so that only the sample ID must be entered on each registration. This is described in section Register multiple samples for one study donor Register one sample and donor If you wish to register one sample for each donor, choose the alternative One sample per donor on the first view in the registration flow, see Fig. 5. Select sample type in the drop-down menu and click OK. A sample entry view is displayed according to Fig. 6. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

7 Fig. 6 Sample registration screen which expects one donor per sample. In order to register a sample, enter study donor identity and sample identity and press OK. Registered samples will be listed below under the header Entered data, see Fig. 7. It is possible to review and edit entered data in this list. If the sample cannot be registered, which for example could occur if it is already in the system, an error message will be displayed. Note that all characters in the donor and sample identities are significant, e.g. leading zeros, hyphens, etc., are included! Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

8 Fig. 7 Registered samples are listed under Entered data To alter entered data, click on the link Edit to the right of the listed sample data. This opens a page where you may edit the data at hand, see Fig. 8. Press OK to accept the changes to your data. Fig. 8 Sample edit view To approve entered data, press button Approve. Up to 15 samples may be entered before the application prompts for data to be approved. Review data carefully, edit errors if there are any and approve before registration may continue. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

9 Fig. 9 A maximum of 15 samples can be entered before a mandatory approval is required It is possible to register samples of different types. Change sample type by pressing the Change button to the right of the currently selected sample type. Chose the desired sample type and press OK, see Fig. 10. Fig. 10 Choose sample type view Instructions for approval of samples that have not been approved while registering them can be found under section Approval of samples not approved during registration. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

10 Register multiple samples for one study donor Registering multiple samples for one donor differs from one sample per donor only in the sense that you are not prompted for the donor identity at each registration. The donor identity is instead entered before sample registration begins. To register multiple samples per donor, select this alternative after the Register sample menu option has been selected. Select sample type and press OK. A view where a donor identity can be entered is displayed, see Fig. 11. Fig. 11 Enter the donor identity for which multiple samples will be registered. Enter the donor s identity and press OK. A sample entry page is now displayed, as shown in Fig. 12. Fig. 12 Sample registration view for multiple samples per donor. Register samples by entering their identity and pressing OK. Just like described earlier in conjunction with the other entry scenario, the entered data is listed below the Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

11 sample entry form. To change sample type, press button Change beside current sample type. When registrations for the current donor is complete, press the button Change next to the current donor identity and enter the ID for the following donor. When all samples are registered, press To start page to exit the registration workflow. Editing and approval of data is done in the same way as in the workflow for single sample entries, described above. Instructions for approval of samples that have not been approved while registering them can be found under section Approval of samples not approved during registration. Approval of samples not approved during registration Normally, data is approved directly during registration of samples. If, for some reason, this has not been the case, for example due to a power out, there is an option to approve samples later. Samples that have been registered the same day but have not yet been validated will be listed under Entered data which allows you to restart registration if, for some reason, it has been interrupted. Note that samples may be downloaded to KI Biobank internal systems even if they remain unvalidated. It is therefore necessary to promptly validate samples. If there are any samples not yet approved in the current study, a message and a link to an approval view will be displayed on the start view as in Fig. 13. If there are no samples to approve, the ordinary welcome page will be shown, see Fig. 1. Fig. 13 Message displayed when there are samples in the study which have not yet been approved. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

12 The message informing the user about samples not approved will be shown to all users that have access to the study to which the samples belong. To enter the validation view, follow the To sample validation link which navigates to the view shown in Fig. 14. Fig. 14 Sample approval view Data about each sample is shown including the user name of the person who created it. It is possible to approve data entered by somebody else, but if you do so be sure to verify that data is correct. Mark the checkboxes next to the samples you wish to validate and approve them by pressing OK. If there are more samples to validate, a message will be shown. Otherwise the user is informed that no further validation is necessary. To cancel the validation, press Cancel. It is possible to edit data prior to approval as described under section Register one sample and donor. Note that all changes are persisted even if you choose to not approve data. If you wish to delete the sample, click Delete and confirm the deletion of the current sample. This is the only situation in which a user is permitted to delete samples. If you wish to delete a sample after approval, please contact KI Biobank support as described in section Issue reporting and support. Search functions ELSA contains a search view where it is possible to review data registered on the current study. To change the current study, see section Choose current study. To enter the search view, select Search in the menu. In the displayed view, you have the option of searching for all samples registered for a donor, which is described in section Search for samples registered for a specific donor or display all data in the currently selected study which is described in section View all data for the study. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

13 Fig. 15 ELSA search view. Search for samples registered for a specific donor To search for all samples registered for a specific donor, enter the donor ID in the designated field and press OK. The view displays the result, see Fig. 16, or shows a message that no samples were found for the given donor identity. Fig. 16 Result from a search for all samples registered on a donor. View all data for the study In order to view all data registered for a study, press the button Get all study data in the search view. The result view lists all data in a paged layout and displays the number of rows retrieved from data store see Fig. 17. Table headers may be used to sort data. Click once one the header to sort data in ascending order and yet another time to sort descending. Samples that have not been uploaded to KI Biobank LIMS system will display a yellow warning triangle in the rightmost column. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

14 Fig. 17 Result view of a search for all data in a study It is possible to export data from this view to a file in CSV format. This file may be imported into MS Excel for easier handling. See section Short instructions how to import CSV into MS Excel Short instructions how to import CSV into MS Excel 2003 The following is a short instruction how to import the ELSA generated file into MS Excel 2003, English version. The resulting file will have all columns in text format. This is necessary when donor or sample IDs contain leading zeroes, as MS Excel will remove these unless the data is converted to text format. NB: KI Biobank is normally not able to give support on the usage of MS Excel. The import into other versions of MS Excel may differ from this instruction. 1. Start MS Excel. If no empty worksheet is displayed, create one by selecting menu File New 2. Open the ELSA generated file, named elsa-data.csv by choosing menu Data Import External Data Import Data 3. A dialog (Fig. 18) is displayed where radio button Delimited should be selected. Field File origin should be left at its default value. Click Next Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

15 Fig In the following dialog (Fig. 19), Comma should be the delimiter. Click Next. Fig The third dialog (Fig. 20) lets you choose column format. Click the leftmost column in section Data preview, press and hold Shift and click the rightmost column. Then select radio button Text in section Column data format. Click Finish. Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)

16 Fig In the last dialog (Fig. 21) select Existing worksheet. Click OK and save the file with desired name. Fig. 21 Ändringsmeddelande Version Punkt Beskrivning av ändring Sign 01 NA Nytt dokument IP 02 NA Uppdatering för releaseversion AB NA Infört i Centuri CR NA Uppdatering för version BEF NA Tagit bort referenser till version, SB formattering NA Förtydligat att validering bör ske omgående; Dok.namn: ELSA User Manual Gäller fr.o.m: Dok.nr.-utgåva: (16)