1. Core LIMS Training: Querying and Reporting

2. Course Topics Common Canned Reports (sample/experiment/assay)
Using Query Pages
Reports from List Functions Page
Using the Smart Table
Report Formats
Using Lists
Reports
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3. Common Canned Reports
Core LIMS already has pages built to answer several common questions:
Show me my work
Show me all experimental data on a lot or sample
Show me all data for an experiment
Show me all data across an assay
Show me all information for a project
In addition, you can build your own custom reports
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4. Show Me My Work
Reports are hyperlinked from your user record
My Files – a list of all the files (for a selected file type) that you have attached to records
My Experiments – a list of the experiments (for a selected experiment type) that you have created
My Samples – a list of the samples (for a selected sample type) that you have registered
My Lists – a list of any private lists (for a selected list type) you have saved
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5. Show Me All Data for a Sample or Lot
Multiple hyperlinks to many useful reports
These hyperlinks are configurable so you may have different ones
Similar reports are available for both the Sample Details and the Lot Details pages
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6. Common Sample Report Hyperlinks
Single Data: all experimental data on all lots of this sample. Each assay will be listed in a separate table. Each data point will be listed as a separate row in the table and will not be averaged (even if the lot and experimental protocol is the same).
Rejected Single Data: any experimental data that the scientist rejected prior to publishing an experiment
Sample Average Data: all experimental data on this sample. Each assay will be listed in a separate table. Multiple data points from different lots using the same experimental conditions or protocol will be averaged together. This report will just list the averaged value and %CV (and not include all the other aggregate statistics).
Sample Aggregate Data: same as Sample Average Data report plus other aggregate statistics
Lot Average Data: similar to Sample Average data. Multiple data points from different lots will not be averaged together, but multiple data points from the same lot using the same experimental conditions or protocol will be.
Lot Aggregate Data: same as Lot Average Data report plus other aggregate statistics
View Inventory: report shows you the quantity, locations, and container IDs of all lots of the sample
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7. Show Me All Data for an Experiment
Experiment Details page gives you generic information that applies to the whole experiment
Click on the View Report link to see the detailed data for individual samples or Aggregate Data to see duplicate points averaged
Export to Excel exports the detailed report
Use the Assay links to view reports across experiments
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8. Experiment Report
These are samples that were tested together in the same experiment
Follow the hyperlinks to see the Lot, Assay, Protocol, Container, etc. Details
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9. Show Me All Data Across an Assay
Once on the Assay record, click on one of the reports to view the data
These are all the samples that were tested in the same assay from multiple experiments
All tables in reports and lists are sortable and filterable, click on a column header to toggle between an ascending/descending sort
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10. Show Me All Information for a Project
From a list of Projects or from a Project record directly, there are hyperlinks to reports that give an overall perspective of all records associated to a given project
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11. Searching for Records
Quick Find – fastest way to look up a single record
Query Pages – provide you ways to filter records by attributes and associations; can be accessed by magnifying glass icon on records or from menus
Sample Query (Short) – search by sample attributes
Sample Query (Full) – search by sample & lot attributes as well as by assay criteria
Lot Query – search by lot attributes
Other Query Pages
List Functions Pages – way to look up multiple records at a time and apply a variety of reports to them
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12. How Do I Use the Quick Find?
1) Use the pull-down menu to define what type of item you are searching for (if not searching a barcode or record name)
2) Type in a single number in the box OR scan/type the barcode OR enter the record name (case sensitive)
3) Hit the arrow icon to start the search
Note: Since there is only one “hit”, you will be taken directly to the record that you requested
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13. Common Query Workflows
Generate Report
Review hit list
Select interesting subset – send to a List Functions page
Save/Add to List
Search for records that meet criteria on Query Pages
Filter List using Smart Table (optional)
Generate Report (apply Report Format)
Add to queue
Core LIMS is flexible enough to accommodate many different scenarios for searching – this workflow shows some common actions that users can perform to help them find and process data
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14. General Tips for Query Pages
Type in values/use pull-down menus/pop-up calendars to narrow your results to records that are most interesting to you
Filling in multiple criteria is an “AND” query (i.e. a record must satisfy both conditions to pass the filter – to make an “OR” query, do a search for each condition individually, save the compound lists, and then combine them later in the List Functions page)
Performance speed is directly proportional to the # of hits in your answer set – narrow your query as much as possible
Since most searches have multiple answers, you will be usually taken to a Smart Table to view all results
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15. Sample Query (Short)
Short Query page is to search by Sample-level attributes only
Searching with no filters = List All records
Can specify fields to sort returned results by
If you have chemistry module, you can do exact, substructure, or similarity searches
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16. Lot Query
Very similar to the Sample Query (Short) except that the attributes to filter by are batch-specific information
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17. Sample Query (Full)
When all the options have been set, hit the Search button
This comprehensive search page has a section for Sample, Lot, and Assay criteria. There are many options, but it is powerful!
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18. List Format vs Report Format
List Format – returns all attributes (of either sample or lot) for the list of records returned
Report Format – returns user-defined specific attributes based selections on the fly or stored in a report format record
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19. Query Hits Can Be Returned in a List
Further data may be stored underneath tabs
To transfer rows to the List Functions page (where you can apply reports to the set), select the Send to list functions menu beneath either the All or Selected Items sub-menu
Note: These menus are configurable
Select individual rows using the Shift or Control keys to highlight desired rows
To drill down into the details of any individual record – click on one of the hyperlinks
Every record that passed the filters is listed in a table, 1 record per row
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20. Results Can Be Sent To a List Functions Page
A wide variety of reports and tasks can be performed from here (more details later…)
3) Hit the Submit button
1) The list can be automatically transferred from a Smart Table
(Alternatively, you can start from this page, type or copy/paste a list of identifiers in, and apply a report to search for information on multiple samples/lots at the same time)
2) Choose one of the reports or tasks
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21. Waiting For a Long Query?
How do I know it’s doing something?
If you don’t get an instant result, it may not be as obvious that the system is working on your request – depending on your browser if there is a circle spinning, the system is “thinking”
If something appears to be “stuck”, then it is probably a better idea to stop your current process (typically hit Esc) first, then resubmit the task
Sometime you can see a progress bar or messages at the bottom of the screen
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22. Common Reports From List Functions Page
Once you have identified a group of records that meet certain criteria, you may want to get a report with key information from those records
Three very common reports can be derived from the List Functions page:
How do I get all data in the system on a group of samples/lots? (All Single Data)
How do I get all data for a specific assay on a group of samples/lots? (Single Data In)
How do I get a table of data that contains key values across many assays? (Generate Report)
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23. All Single Data
The All Single Data Report will return all published data in the system on a group of samples
Single Data returns all points when a sample is run multiple times in an experiment
Aggregate Data will average points when a sample is run multiple times under the same conditions
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24. All Single Data Reports
Each sample in the list will be listed sequentially
Every assay that has data will have a table on the right
Sample and Lot Details are displayed on the left
Go to experiment report to compare with other samples in an experiment
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25. All Single Data In
The Single Data In Report will return all active data for a selected assay on a group of samples/lots
Once Assay Type is selected, the Assay list will be populated
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26. Generate Report
The Generate Report gives you a table with key values across many assays
Can select from a variety of public or customized private reports
Can view in a web page, Excel table, or export as a SD file
Tip: for Excel pages, the structures are sortable images, but cannot perform any advanced chemistry functions (like editing structure settings, etc.). If you have tools that can embed structures in a spreadsheet, you may want to import an SD file into an Excel table or convert smiles into a structure instead
Selecting All Lots will give one row for each available lot;
Deselecting All Lots will concatenate values from different lots into a single row
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27. Generate Report in Excel
The Excel table will open in a web browser. In the browser menu, go to File>Save as and choose .xls as a file format. Then you can open the report directly in Excel and have access to all standard Excel functionality.
Note: The structures are non-embedded images, but they will move if data in other columns are re-sorted as long as they are not undocked from their original cell
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28. HTML Report: Use the Smart Table to Filter
HTML reports will output an interactive Smart table that can aid your decision-making process
Click on a column header to get menus with useful functionality
You can hide columns that you don’t need to currently view
You can also filter rows that you don’t need to currently view
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29. Hands-On Practice Use the Quick Find to navigate to a sample record
Look at one of the lot records related to that sample
Use the Sample Query (short) page to find records that have registered within the last few days
Transfer the hits to the list page and apply a report from the Generate Report function
Use the Sample Query page to find records that have been created after a certain date and have data for a specific assay
Transfer a few of the hits to the list page and apply the All Single Data report
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30. Can I Choose What Columns Go in a Table?
Yes! You can use any pre-defined public report format OR you can define your own customized report
The Report Format is where you define what data columns you want to see in a table
You can select any combination of columns from all assays in the system
You can also choose from any sample or lot attributes
Once your columns are defined, the Report Format can be applied across any list of samples to build your own custom report
For report formats of entity types other than sample/lot/assay, you can just select the attributes on that entity type or attributes on entity types that are associated to that entity type
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31. How Do I Make A Report Format?
Create Report Format allows you define a new list
List All allows you find (and potentially edit) Report Formats that are previously defined
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32. Create a New Report Format
Type in a descriptive name that will be easily recognizable in a pull-down menu
Assay Entity Type will also allow Sample and Sample-Lot fields; other Entity Types will just provide fields within that Entity Type and any fields associated to that Entity
If you check the box, only you can see this report in Core. If you do not check it, you can share the report format with others on your team, but sharing too many reports will make a long pull-down menu for everyone.
Select a project and hit the Create New button
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33. Report Format Record
Click on the Add/Remove Members link to start defining what columns you want to put in your reports
Report Formats automatically create a database view in the schema that other applications can point to
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34. Choosing Sample or Lot Report Columns
3. Click Update List to save the new column(s) to your report
1. Select 1 or more columns from the pull-down menus. (Use Shift or Control keys to multi-select)
2. If you want to re-name a column, type the desired name in Alias field (if multiple columns selected, all will get the Alias name)
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35. Choosing Assay Report Columns
1. Select Assay Type to populate other menus
3. Select any other options:
Sample Centric - average different lots with same conditions
Grouping – if the assay has pre-defined sets of groups (like different concentrations tested) you can pick one to add to report
Protocol – you can specify compounds that follow a specific protocol be reported
Aggregate Function – you can get other statistics besides an average (add 1 row at a time to get multiple statistics in report)
User Defined Equation – you can perform math operations on a database column
2. Select Assay and Data Types
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36. Modifying the Report
To reorder the columns in your table, click on the Sort Members link
Edit the Alias field if you want to rename any columns
Select the Remove box if you want to delete unwanted columns later
Continue to add more columns as desired (one at a time)
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37. Sorting Report Columns
1. Type in desired sort order
2. Click Save Sort Order to save new order
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38. Editing a Finished Report Format Later
Edit Icon can be used to deactivate record if you want to remove it from view. It does NOT edit the columns in the report.
Go to Report Formats > List All to find your record
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Click on Add/Remove Members to add or remove or rename columns
Go to Sort Members to reorder the columns

39. Applying Your Report to a Set of Compounds
Now you can pull the data for the specific columns in your Report Format for any list of compounds using the Generate Report on the List Functions page
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40. Applying Your Report to a Query
You can also apply the same report columns to queries. Set your filter criteria as normal but select Report Format and choose the Report Name you want.
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41. Making a Report Format From a Query
You can directly start a new Report Format from a Sample Query page. Select ‘Derived from criteria’ as your Report Name and give a new unique Report Name under Save Report.
Sample or lot filter criteria you set will not automatically be included as a report column and you can display columns that were not used to filter data. Check the boxes in the Select column on the right to choose columns for a report format.
Assay filter criteria will automatically be included. If you want to include an assay column, but not filter data by it, choose the Select for report option
This is a great way to quickly start a report and you can go edit column order or rename columns later.
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42. Can I Save a Common Set of Samples?
Yes! You can save any list of samples as a List
These lists can be public lists shared with everyone OR you can define your own private customized lists
You can start a new list or add to an existing list from the List Functions page
Once your list is saved, you can quickly apply any report or task to those compounds
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43. Starting a New List
2) Type in a descriptive name that you can recognize in a pull-down menu
1) Transfer a list from a query or paste a list of compounds into the box on the List Functions page
3) If you check the Private box, only you can see this list in Core. If you do not check it, you can share the list with others on your team, but sharing too many lists will make a long pull-down menu for everyone.
4) Select a List Type
5) Select the radio button
6) Hit the Submit button
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44. Viewing Your List
In View Member Details section, you can view or remove compounds
Click on Forward to List Functions to transfer the list for reports or actions
Click on Sort Members to reorder the list
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45. Adding New Compounds to a List
1) Like before, transfer a list from a query or paste a list of compounds into the box on the List Functions page
2) Select from previously saved lists
3) Hit the radio button
4) Hit the Submit button
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46. Quick Data Reports With Create Report
A quick way to get up to the minute data on a standing report without going through the List Functions page…
1) Pull-down your pre-saved compound list
2) Pull-down your pre-saved Report Format
3) Hit the Generate Report button
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47. Hands-On Practice Create a new Report Format
Add several columns of interesting data in the Add/Remove Members section
Resort the order of the columns
Query for a few recent compounds and transfer them to the List Functions page; Add the compounds to a new compound list
Run the Create Report using your Report Format and compound list
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48. Reports, Gadgets & Dashboards
(Scheduled or Live)
Gadgets
Dashboards
A report is a set of results from a stored query returned in a Smart Table.
The reports can be pre-run on a schedule or dynamically run when the report is called.
A report can be easily incorporated into a gadget (as a table or a plot).
Gadgets can be any type of dynamic web content. It can be a table, plot, link to another web page, external widget, etc.
Many gadgets can be combined into a single dashboard page.
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49. Reports Start From Query Results
Run a query to look for incomplete work orders
Save the query as a report from the Smart Table menus
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50. Reports
For scheduled reports, users can re-run a report as needed for latest results, but stored results are viewable immediately
Live Reports will re-run the query automatically when the record is called
Query results will be at the top of the page
Query details are at the bottom
You can edit the query to refine it later
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51. Viewing Key Reports
You can return to a favorite report (and re-run for latest data) at any time by:
Finding the report by name or barcode in QuickFind Tool
Like the page to find it in the Favorites section
Make the report a menu item by associating it to an application
Make a gadget to hold the report and add it to a dashboard
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52. Make a Report Menu Item
If you add the Report Super Type to an application and associate a report to the application, it will automatically create a menu item to navigate to the report record
Associate the report to an application
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53. Make a Gadget for the Report
Copy the gadget code from an existing Smart Table example and modify the title
Associate the gadget to the report with the data
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54. Add Gadgets to a Dashboard
You can add several gadgets in any order to a dashboard page
The LIMS will automatically position them using an algorithm to minimize white space
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55. Display the Dashboard Page in the Application
Dashboards can be application home pages or standalone pages that users select from a menu
To convert a dashboard to an application home page, you need to edit the application and associate the desired dashboard record
Gadgets can be interactive – click on area to drill down to underlying data table
Select the desired dashboard record to be the application’s home page
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