Core LIMS Training: Data Maintenance You will often need to keep the data that you initially capture in the LIMS current with the most recent information. Here are some slides that describe ways that administrators can manipulate the data in order to keep records accurate in the LIMS. Click on a slide whenever you are ready to move to the next page.

Data Maintenance Tasks Unless you restrict their permissions, end users will usually be able to: Edit attributes or associations of single entities (except published experiments) Update an attribute or association with a common value across a list of entities Deactivate (NOT delete) a single record or a list of records Administrators can additionally: Make an non-editable attribute or association temporarily editable Batch create multiple records from a spreadsheet This can be exposed to end users for a specific entity type Useful for legacy data entry Batch update multiple records with different values from a spreadsheet Unpublish experiments so end users can edit them again Edit chemical structures This slide points out what types of tasks end users can typically do to maintain their own data and what specific tasks are typically reserved for those with administrative access by default. Note that in some cases you can alter a user’s access in order to modify these privileges. By default, end users can generally edit the attributes or associations on any single entity by just editing the Details page for that entity. The main exceptions are published experiment records or specific attributes or associations that you have set to be non-editable in the Main Admin Panel. If they want to update the same value across many records, end users will be able to use the List Functions page to update records in batch. End users can also deactivate a single entity or a list of barcodes at the same time using the List Functions page. Administrators will be allowed to do additional tasks to update data. You can go into the Main Admin Panel to temporarily switch a non-editable attribute or association to an editable state while you make some updates and then convert it back when your edits are complete. You can also use a spreadsheet to either create new records or update many records that have different values at the same time. If users need to commonly create many records from a spreadsheet (for example a batch sample registration process), you can provide them with a menu to allow them to do that without using the Main Admin Panel. Admins will also need to unpublish experiments whenever users need to modified published data. However, this privilege can be given to an end user if needed. If you have chemical structures, this is also typically limited to administrators to avoid accidental creation of duplicate records, but this privilege can also be extended to end users. CONFIDENTIAL

Editing a Single Record For most records in the system, you can just click on the Edit Icon in the Action Toolbar, make changes, and save the updates If a field is not editable, admins can temporarily configure the attribute to be editable, make the changes, and then reconfigure the attribute back Published experiment records need to be unpublished before any data can be edited The simplest way to modify a single record in the LIMS is to click on the Edit Icon on an Entity Details page. This will change the view from read-only to an editable form. Users can then make any changes directly on the page and then save the changes back to the LIMS. Note that some fields that may be automatically calculated, copied from another database field with a trigger, or imported from a file may be set by the administrator to be non-editable. Published experiment records will need to be unpublished before they can be modified. CONFIDENTIAL

Editing a Non-Editable Attribute If a field has been configured to be non-editable, navigate to the appropriate Entity Type in the Main Admin Panel and temporarily change the editable status so you can edit the data and change the editable status back when you are done If you have a non-editable field that needs to be modified, the administrator will need to change the setting on the Entity Type before any data can be changed. Look for the Editable column and set it to yes. You can change it back after the data is modified if you need to. CONFIDENTIAL

Deactivating a Single Record Records are never deleted from the system Records can be deactivated so that they will be removed from most queries, reports, and calculations Any user given the access to edit a record can deactivate it The record can be made active again later This is the method to deactivate a single record, multiple records can be deactivated from the List Functions page 1) Click on the Edit Icon 2) Deselect the Active Checkbox 3) Click the Update button Deactivating a record is a universal action for all entity types, but remember: Deactivating an experiment only removes the general information about an experiment from most views – the experiment should be unpublished to remove the individual sample data from views Deactivating a sample does NOT automatically deactivate related lots or containers – be sure to check that you have deactivated every record you want If you make a mistake that can’t be fixed by changing the original record (such as creating an extra unwanted entity), you can always deactivate the record to remove it from any calculations, reports, or searches. Deactivation never permanently removes any data from the LIMS so that it can be retrieved if specifically searched for or reinstated if you change your mind later. While it is tempting to completely purge our mistakes, remember that sometimes small mistakes can be the source of important scientific data. CONFIDENTIAL

Deactivating Multiple Records Every Entity Type will have a List Functions page The options on the page will vary by Entity Type, but they all have a Make Inactives option You can navigate directly to this page from a menu or have samples transferred automatically to this page from a Smart table or another page You can also deactivate records from the List Functions page if you have a lot to do at once. Although the List Functions page may vary depending on which Entity Type you are working with, all List Functions pages will have a Make Inactive option you can select. CONFIDENTIAL

Updating Many Records With 1 Value The List Functions page also allows you to edit attributes or associations across a list of entities For attributes, select which one to update and enter the common value to write for all records in the list For associations, select the desired record(s) from the list Any previous values will be overwritten Any List Functions page will also give you a space to update many records with a common value for an attribute or a selection for an association. Note that only editable attributes and associations will be displayed on the page. If you need to update an attribute for many records with different values, you will need to use a spreadsheet which will be discussed next. CONFIDENTIAL

Batch Data Inserts & Updates Best practice is: Edit a single record: Use the Edit Icon Create single new record: Use the Create New page (navigate from menu or gadget) Edit a list of records with the same value: Use the List Functions page Edit a list of records with one or more fields having different values: Load a spreadsheet into the Load Entities Tool Create multiple records: Load a spreadsheet into the Load Entities Tool Exceptions: Multiple structures should be inserted via Batch Registration of SD files; Plate-to-plate transfers has a separate interface Tip: Check a few records on a small scale in a Test system before doing a large batch!! This slide reviews which of the data maintenance processes we have been discussing are the best to use for each use case. CONFIDENTIAL

3) Select Load Entities of the desired Entity Type Using the Load Entities Tool 1) Navigate to the Main Admin Panel 2) Select List All Types of the desired Super Type 3) Select Load Entities of the desired Entity Type Data that is uploaded by a spreadsheet is done through a LIMS feature called the Load Entities Tool. You can use this same tool to batch insert many new records or batch update many existing records for any Entity Type in the LIMS. It is very useful for loading legacy data from any previous database systems you had. You can create menus for end users to upload spreadsheets to this tool for common Entity Types that need to be created in batch. However, in general, this tool should be limited to administrators because it is powerful enough to overwrite a large amount of data accidentally or create many records with incorrect data that need to be cleaned up. Even for experienced admins, it is a good idea to test a few records first to make sure your spreadsheet is set up correctly before submitting large numbers of records. Since this is primarily an admin tool, it is usually accessed from the Main Admin Panel. Click on the Load Entities hyperlink next to the Entity Type that you are trying to create or update. CONFIDENTIAL

Preparing the Spreadsheet Include a BARCODE column in the first column – if you are updating a record, fill in the appropriate barcodes of records to update; if you are inserting new records, it is recommended to leave the cells blank and let the system generate the correct sequence Copy any column headers for data that you want to upload into an Excel file from the Entity Type Details page (remove any hyperlinks) Add the data that you want to upload – one row per record Do NOT include any columns that you do not want to change (blank cells will overwrite existing data with null values) You can upload multiple columns at a time, column order does not matter If there is a controlled vocabulary, be sure to use terms in the list (in the correct case) Make sure you include any required fields Be sure to save as a .xls or .txt file (NOT .XLSX!!) The most critical step for the successful use of the Load Entities Tool is to get the correct column headers for the spreadsheet that you want to upload. There are several hardcoded column headers that you can use and these are listed in the documentation. The most common one that is used for almost all spreadsheets is the BARCODE column. This column tells the LIMS whether you are creating new records or updating existing records. Blank BARCODE cells next to rows that have data in other columns means to create a new record. If you list an existing barcode in the BARCODE column the LIMS will update that record with the new values in the spreadsheet. The barcode column should be on the left and have all capital letters. Other column headers names will come from the Entity Type Details page. You can copy the name of the attribute directly (be sure to remove any hyperlinks from the spreadsheet) or you can use the display name for the attribute. For associations, use the Context name. You do not have to include every column for an Entity Type in your spreadsheet, especially if you do not have data for any of the rows. You do need to make sure that all required attributes and associations are in the spreadsheet and that any attributes that use controlled vocabularies have values that are spelled the same. Each row in the spreadsheet will be for a single entity in the LIMS. When you are done populating the spreadsheet, be sure to save the file as either a tab delimited text (.txt) file or as the older excel format (.xls). CONFIDENTIAL

Uploading the File 1) Browse to the saved file 2) Click Preview to check for any errors 3) Use Browser back button to return to this screen 4) If file is OK, click Upload button From the Load Entities hyperlink, you will be prompted with a simple screen to input the spreadsheet you just created. Use the Browse button to find where you have saved your file locally. Next you can use the Preview button to verify that the LIMS is interpreting your spreadsheet correctly. You should check the number of records matches and you are not inserting any blank rows. You should also be sure that the LIMS indicates it is creating or inserting the type of records you expect. If you do not get the results you anticipated, modify your spreadsheet and try again. Once your Preview page gives you the correct results, click on the back button of your browser. The file you previously browsed to should still be cached. You can now click on the Upload button to create the records. If you have any errors with a specific row of data, the LIMS will give you an error message and not commit any changes to the database. You can then modify your spreadsheet as needed and try again. CONFIDENTIAL

Successful Upload For updates, the new changed values plus the original values of other fields are displayed Click on individual records to view details The uploaded Excel file will automatically be attached and can be viewed by clicking on the Files icon Entity Types that support versioning can compare versions before and after updates If there are no errors in your spreadsheet, the Load Entities tool will create or update all of the records together and return the new data in a Smart table. You can click on hyperlinks to view any of the individual records you created or edited. The spreadsheet file that you uploaded will automatically be attached to every record that you created or modified. CONFIDENTIAL

Special Note on Samples You can update Sample, Lot, and Container information in the same spreadsheet While it is fine to use the Load Entities tool to update Sample or Lot records, multiple chemical structures should be entered through a Batch Registration of an SD file Even if there is only Lot attributes to update, you will need to use the Load Entities Tool from the Sample pages You can use multiple ways to specify the same record, for example: Entity Type = SMALL MOLECULE, BARCODE = SM1, LOT = 1 or use BARCODE = SM1-1 to update a lot record See Sample Registration Chapter for more details Generally, the Load Entities Tool is used to load or edit data for a single Entity Type. For example, only employee attributes could be put in the Employees Load Entity Tool or only location names and attributes could be loaded with the Location Load Entities Tool. However, the Sample Load Entities Tool will allow you to enter information for samples, lots, and containers in the same spreadsheet. You will not be able to load this spreadsheet directly into the Lot Load Entities Tool. We will go into more details about this in the Sample Registration sections in later tutorials. Also take note that if you have chemical structures, there is a separate process to load structures using an SD file. CONFIDENTIAL

Common Spreadsheet Columns Notes Header Definition Examples "Primary" Headers for the Entity Type you are creating or updating ("LOT" is specific to 'Sample' Super Type) ENTITY TYPE Primary entity type you are creating or updating SMALL MOLECULE, CRYOVIAL, 9X9Box NAME Unique Name of Object SM1, CRY123, 9X9Box1 BARCODE Unique Barcode of Object SEQ Sequence # of Object 1, 123, 1 LOT Lot # of sample to update; leave blank to create new 1, blank Can be used alone as a unique Sample_Lot identifier either as a "Primary" object or associated to Containers being loaded LOT BARCODE Unique identifier for updating an existing lot SM1-3 Associations can be made to containers when uploading Sample and Lot information as the "Primary" Objects CONTAINER TYPE Type of container used when creating new container objects CRYOVIAL, 4DRAM CONTAINER BARCODE Leave blank to create new containers (use w/Container Type), or include to update existing container CRY123 Container associations can be used when containers are either your "Primary" objects being loaded, or your associated objects when loading Sample_Lot information AMOUNT Amount associated to container. Should not be 0 or null 10 AMOUNT UNIT   mg, uL CONCENTRATION Concentration associated to container. CONCENTRATION UNIT uM, mM LOCATION BARCODE Barcode # of location to place container FRZ1, BOX123 POSITION If location barcode references matrix box (10X10, 9X9, etc.), position indicates "cell number" where container will be placed 1,2,3-100; 1,2,3-81 DESTINATION CELL If you are updating wells in a plate, the cell number indicates where the sample will be placed 1,2,96 Additional Configured Attributes or Associations Date Received Color Vendor Tare This slide shows some of the hard-coded column names you can use in your spreadsheets for the Sample Load Entities Tool. For now this is just for your reference – we will be going into more detail on this spreadsheet in the Sample Registration tutorials. CONFIDENTIAL

Unpublishing Experiments Published experiments need to be unpublished before data can be edited Depending on your corporate rules, unpublishing experiments may be limited to administrators After the data is edited, it needs to be republished for all users to see it One other mainly admin function is to unpublish experiments. Scientists can only enter and modify experimental data when it is in an unpublished state. When they are done making their modifications they can publish the data to make it available to their colleagues in reports and queries. If they later realize they need to make further modifications, an administrator will need to unpublish the data to make the experiment editable again. This will be discussed further in lessons on Entering Experimental Data. CONFIDENTIAL Click on the minus or the Unpublish link to unpublish

Editing Chemical Structures Depending on your corporate rules, editing chemical structures may be limited to admins – anyone with edit permissions for structures will see a Sketch Tool, all others will see the structure displayed in a non-editable box Calculated properties will be automatically updated when the structure is changed For businesses that work with chemical structures, editing the structures is usually limited to admins since editing a structure requires a structure search for duplicate records and chemical properties need to be recalculated. This concludes this brief tutorial about how to update and maintain your data in the LIMS. Be sure to see the documentation or other tutorials for further information. CONFIDENTIAL