BizInt Cookbook of Reports & Visualizations

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Learn how to use the BizInt tools to create powerful and effective reports and visualizations, with examples and step-by-step recipes.

C ookbook of R eports & V isualizations

www.bizint.com/Cookbook

Created with the BizInt Smart Charts Product Family

VP-SCE Version 12

june 2023

Using This Cookbook

STYLE CONVENTIONS USED

APPLYING THESE RECIPES TO YOUR DATA

Commands are shown in colored sans-serif type with the pipe(|) symbol used to divide sequential menu selections. For example, File | Combine indicates that you should first click on the File menu and then select Combine. Italics indicate a note, generally indicating steps that may be different depending on the dataset. "Text in quotation marks” indicates something you should type in to a text box or text that appears in the software outside of the menus.

We believe the methods in the recipes included here are applicable to other data sets and sources. However, because each recipe was built using a particular example dataset, you should take some caveats into consideration when applying recipe steps to your own data: Caveat One: When you combine charts from different sources, the source selected first (the “Key Chart”) will determine the names for common columns. For example, depending on the source, the column could be called Condition, Disease or Indications. While you may see different column names than those indicated in the recipe, the same steps should still apply. Caveat Two: Some recipes contain steps and guidance based on the content of the example dataset. For example, we provide suggestions for changing Common Trial ID assignment in cases where the automatically generated Common ID combines trials we want to be treated separately. How much this step is necessary depends on the dataset. Caveat Three: We revise these recipes based on user feedback, so check the latest edition of the Cookbook on our website to see if we have revised the recipe you're interested in.

Note: This edition of the Cookbook is a selection of some of our favorite recipes, updated for VantagePoint - Smart Charts Edition Version 12, and with some new visualizations. Minor updates were made to this edition of the Cookbook in 2023 to reflect Reference Rows and export changes. If you are using an earlier version of VP-SCE, please refer to the February 2018 or earlier versions of the Cookbook, as many VP-SCE functions have been redesigned in Version 11.

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the Journey continues…

Recipes Using This Cookbook........................................................................................................................... inside cover PIPELINE Extracting the Highest Phase for an Indication [Pipeline DP-4]. .................................................................. 2 Highest Phase for an Indication – Database Summary [Pipeline DP-5]...................................................... 4 Creating Pipeline “Piano Charts” in PowerPoint [Pipeline DP-13]................................................................. 6 Visualizing the Pipeline with a Bullseye [Pipeline DP-16] .............................................................................. 8 Creating a Butterfly Chart [Pipeline DP-17]. ....................................................................................................10 Analyzing Companies by Phase with a Bubble Chart and Multi Donut Chart [Pipeline DP-18].........12 TRIALS Training (1): Creating a trial “Piano” Chart [Trials CT-11]...............................................................................14 Training (2): Trial Completion Timeline [Trials CT-12]....................................................................................16 Summarizing Clinical Trial Enrollment [Trials CT-4]. ......................................................................................18 Creating a Milestone Timeline [Trials CT-13]. ..................................................................................................20 PATENTS Creating a Motion Bubble Chart [Patents PT-14]............................................................................................22 Analyzing Companies by Therapeutic Activity with a Bubble Chart [Patents PT-12]............................24 Summarizing Sequence Locations in a Patent Family [Patents PT-8]........................................................26 Filtering the Patent Family by Authorities [Patents PT-3].............................................................................28 TECHNIQUES Technique: Using List Cleanup. ...........................................................................................................................30 Technique: Extracting Year...................................................................................................................................32 Technique: Working with Thesauri.....................................................................................................................34 Technique: Extracting Keywords.........................................................................................................................36 Technique: List Comparison.................................................................................................................................38 Technique: Classifying Records. ..........................................................................................................................40

For More Information.... ........................................................................................................................................42

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Extracting the Highest Phase for an Indication [Pipeline DP-4]

In this example, we’ve used VantagePoint - Smart Charts Edition (VP-SCE) to filter the Indication Phase (Normalized table for a specific indication (Merkel Cell Carcinoma). In BizInt Smart Charts Drug Development Suite, we then run the“Extract High Phase in Column” tool to extract the highest phase from the filtered subtable into a new column.

SUBTABLE FILTERED FOR MCC

NORMALIZED HIGHEST PHASE

HIGHEST PHASE COLUMN EXTRACTED FROM THE FILTERED SUBTABLE

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Extracting the Highest Phase for an Indication [Pipeline DP-4] How did we create this?

START WITH: Any supported drug pipeline data already displayed in BizInt Smart Charts. In this example we used: A combined chart with Cortellis, Adis R&D Insight, and Citeline Pharmaprojects: Indication = Merkel Cell Carcinoma BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE - create your combined chart 1. Display the indication phase field: Use View | Apply Template and choose “BizInt Editor’s Choice - Multi-Database.” Alternatively, check that your chart has the Indication Phase (Normalized) column or use View | Choose Columns to add it. 2. Use File | Export to export as VantagePoint - Smart Charts Edition. VantagePoint - Smart Charts Edition (VP-SCE) should open and import the file. If not, launch it and choose the option to import the .vpxi file. Clean up your selected indication: Find Indication Phase (Normalized) on the list of fields. Click the black triangle to the left of the field name to display the Child fields (Indication and Phase). Right-click on the Indication Child field and choose List Cleanup. On the List Cleanup panel, click OK to go to the Dual View Cleanup Confirmation panel. 4. Drag and drop to combine: Drag and drop all the synonyms for your indication onto a single item. 5. Use the search box (optional): Enter a search term, like “merkel” into either search box (overwrite “(type to filter...)) to filter the list. For more information on using List Cleanup, see the Techniques: Using List Cleanup recipe. 6. Finish cleanup : Once you have combined all the terms for your selected indication, click Accept. Saving the thesaurus is optional. To create the filtered subtable, you do not need to cleanup any other indications. 7. Filter the subtable by your Indication : You will now have a new sub-field: Indication: (Cleaned). The first row should be your selected indication. Click on the row to select it. Under the Analyze tab, click on Run a Script | Filter Drug Development Phase . A new filtered Indication Phase field will be created. 8. Export back to BizInt Smart Charts : Under the Report tab click on Export to BizInt Smart Charts. In the Export Wizard, uncheck the boxes for all fields except the filtered Indication Phase (e.g. Indication Phase (Normalized): Merkel cell carcinoma). Click Export. BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE- extract the highest phase for the indication into a new column 9. When BizInt Smart Charts Drug Development Suite comes to the foreground, select the combined chart . It will redisplay with a new column at the end of the chart -- the new filtered Drug Development Phase subtable. 10. Extract the highest phase for your Indication into a new column : Select the filtered Drug Development Phase subtable and then use Tools | Extract High Phase in Column . You now have a column with the highest phase for your selected indication! You can compare this to the Highest Phase (All Indications) column to see where the highest phase for the selected indication differs from the highest phase for all indications. VANTAGEPOINT - SMART CHARTS EDITION - filter the Drug Development Phase for indication of interest 3.

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Highest Phase for an Indication – Database Summary [Pipeline DP-5]

In this example, we’ve taken the chart from the previous recipe (Extracting the Highest Phase for an Indication) and used BizInt Smart Charts Reference Rows to select a single value for each unique drug. And, we’ve used tools in BizInt Smart Charts Reference Rows to create a summary of the Merkel Cell Carcinoma Phase and Update Date for each related drug record.

SUMMARY OF MCC PHASE BY DATABASE AND UPDATE DATE

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Highest Phase for an Indication – Database Summary [Pipeline DP-5] How did we create this?

SEARCHES: Cortellis, Adis R&D Insight, and Citeline Pharmaprojects: Indication = Merkel Cell Carcinoma

BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE 1. Open your combined pipeline chart from the previous recipe [Pipeline DP-4] with the extracted highest phase for Merkel Cell Carcinoma column (Extracted Highest Phase) visible. 2. Rename columns: Right-click on the Extracted Highest Phase column and choose Column Properties. Rename the column to indicate it is the indication highest phase - “Highest Phase (MCC)” . Click OK. 3. Send the chart to Reference Rows using the toolbar icon (or File | Send to Reference Rows ). BIZINT SMART CHARTS REFERENCE ROWS 4. In the Selection View, green check marks indicate the items selected by the database ranking and rules. 5. (Optional) Apply rules to select most recently updated records: Right-click on the Highest Phase (Normalized) column, choose Edit Column Rule and from the Selection Rule drop down choose the Most Recently Updated rule and click OK to select the phase from the most recently updated record. Do the same for the Highest Phase (MCC) column. 6. Create a Summary Subtable : Run Tools | Create Subtable from Columns . 7. Double-click on items on the Available Columns list to add them. Select Database, Highest Phase (MCC) and Update Date in that order and click Apply. A new subtable will be created at the end of your chart with these three columns. 8. Double click on the new subtable column header to rename the column from Untitled Subtable (e.g.“Database - MCC Phase - Update Date”.) 9. Apply the Summarize rule to the subtable : Right-click on your new subtable column, choose Edit Column Rule and from the Selection Rule drop down choose the Summarize All Values rule and click OK to set the subtable column to display the content from all rows in exported reports. “Plus” marks in blue circles will appear in the cells. You will not see the summarized subtable until you export the report. 10. (Optional) Customize the chart: Use View | Choose Columns to hide columns you do not want displayed in your final report. 11. Create the HTML report: Use File | Export to export the report to HTML or Word and see the selected highest phases and the subtable column summarizing the Database/MCC Phase/Update data. You can use this report to review reported phase discrepancies between databases. You can now sort the Reference Rows report by the Highest Phase for MCC (highlighted in yellow at left) or the Highest Phase for all indications (highlighted in blue), since a phase has been selected for the group of records for each drug. These selected values for each drug can also be exported to VantagePoint - Smart Charts Edition to use in visualizations, as you will see in the Piano Chart and Bullseye recipes in this Cookbook.

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Creating Pipeline “Piano Charts” in PowerPoint [Pipeline DP-13]

This recipe describes how to build a piano chart visualization of a drug pipeline, which shows one box for each drug, boxes color-coded by field values, and boxes labeled by multiple fields. In this example we have built a “type of molecule” category using data found in different fields in different databases. We used this to color code the boxes.

If you have already followed the steps in the Bullseye recipe, you can skip to step 15 and build the piano chart.

Search results were exported from multiple pipeline databases to BizInt Smart Charts Drug Development Suite and then integrated with Reference Rows. VantagePoint - Smart Charts Edition (VP-SCE) was used to extract indication phase, create a category field, and clean-up and simplify drug and company name. The chart is then built using the “Create Piano Chart” dialog shown below and exported to PowerPoint (or Excel) where it can be further customized.

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Creating Pipeline “Piano Charts” in PowerPoint [Pipeline DP-13] How did we create this?

SEARCHES: For this particular example, we used a combined chart of COVID-19 vaccine records with data from Adis, Citeline, Clarivate, and GlobalData.

BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE - create your combined chart 1. Import data: Use File | Import to import the sample data from each database. Click OK to create the chart and choose either General Product Chart or Basic Information as the initial chart template and click OK. 2. Combine data: Use File | Combine to combine both charts, choosing the Citeline chart as your key chart. 3. Use View | Apply Template and choose BizInt Editor’s Choice - Multi-Database. 4. Use View | Choose Columns to add any needed columns not yet visible in your chart. You will need source fields for creating the category field, depending on your sources these can include: Chemical/Biological Class, Molecule Type, Origin of Material, Other Actions, and Therapeutic Class Status. 5. Extract the highest phase for Indication: if you want to use the highest phase for your indication, use the Extracting the Highest Phase for an Indication recipe (DP-4). 6. Select File | Send to Reference Rows to open the chart in BizInt Smart Charts Reference Rows. 7. Create the category field: To create the categories used for the bullseye slices, follow the Technique: Classifying Records recipe. 8. Use File | Export to export as VantagePoint - Smart Charts Edition. VantagePoint - BizInt Smart Charts Edition (VP-SCE) should open and import the file. VANTAGEPOINT - BIZINT SMART CHARTS EDITION - clean fields and build the piano chart 9. Set Phase as Data Type: If not already set, Right-click on the phase field you will be using (either Highest Phase (Normalized) or an extracted highest phase) and choose Set Data Type | Custom | Phase . 10. Create sub-dataset by phase: From the Summary Sheet, double-click on your selected phase field to view the list. Double-click on the column header to sort by phase. Use Shift+click to select phases you want to include. We selected only clinical phases. Under the Refine tab, click on Create Sub-dataset and then click OK. A new dataset appears with your selected phases. For a larger dataset you may wish to filter again by other criteria. 11. Cleanup company name: From the Summary Sheet, right-click on the Developer field and select List Cleanup and click OK. Under matching ruleset, select Organization Names (Pharma) and click OK. Use the Cleanup Confirmation panel to clean-up terms. For more information on using List Cleanup, see the Techniques: Using List Cleanup recipe. 12. Cleanup drug and company name: From the Refine tab, click on Concatenate Fields . Choose Drug Name and Developer (Cleaned) (or Company (Key)) for your first and second fields. Use a slash with a space on either side “ / “ as the separator and name the new field “Drug / Company.” 13. Cleanup the new field: Some Drug / Company pairs may not need modification. Under the Refine tab, choose List Cleanup. To edit an item, right-click on it and and use Rename Item. If you have multiple items for the same drug, you should drag and drop to combine. You can use the Detail Window panel to display additional company information if it was visible in your chart when you exported. Alternatively, you can export back to Reference Rows and make your changes there and export back to VP-SCE. 14. Build the Piano Chart: Go to the Report tab and click on Piano Chart . In Step 1, select the fields you want to include in your chart. Choose the Drug / Company (Cleaned) field for the Box Labels and your chosen phase field as the Field for the Phase. 15. In Step 2, choose your category field as the Field to Color Code the Boxes. The Drug / Company field will be automatically split into two rows in the boxes. You can now choose to add hyperlinks, split phase columns into two, and flip the chart to have the phase labels at the bottom instead of the top. 16. In Step 3, enter a title for your chart. In Step 4, select the radio button for PowerPoint and click “Create Piano Chart”. BIZINT SMART CHARTS REFERENCE ROWS

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Visualizing the Pipeline with a Bullseye [Pipeline DP-16] This recipe creates the latest type of chart we have been working on-- the bulls-eye. If you have already followed the Creating Pipeline “Piano Charts” in PowerPoint recipe, you can skip to step 15 and create the bullseye directly. The sample data we’ll be using is the same COVID-19 vaccine data used for our example visualizations, found at bizint. com/covid, from four different pipeline databases: Adis, Citeline, Clarivate, and GlobalData. It is not necessary to have the same set of sources to follow this example. You can also use the tools to help create a type of compound category that will be used for the sectors or slices of the chart. This generally involves both reviewing the data as well as a combination of tools. For this we have an additional recipe, Technique: Classifying Records. Note that there is some custom work involved in creating our COVID-19 vaccine bullseye examples. If you would like us to create something similar for you, just contact us at support@bizint.com!

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Visualizing the Pipeline with a Bullseye [Pipeline DP-16] How did we create this? SEARCHES: For this particular example, we used a combined chart of COVID-19 vaccine records with data from Adis, Citeline, Clarivate, and GlobalData. 1. Import data: Use File | Import to import the sample data from each database. Click OK to create the chart and choose either General Product Chart or Basic Information as the initial chart template and click OK. 2. Combine data: Use File | Combine to combine both charts, choosing the Citeline chart as your key chart. 3. Use View | Apply Template and choose BizInt Editor’s Choice - Multi-Database. 4. Use View | Choose Columns to add any needed columns not yet visible in your chart. You will need source fields for creating the category field, depending on your sources these can include: Chemical/Biological Class, Molecule Type, Origin of Material, Other Actions, and Therapeutic Class Status. 5. Extract the phase for Indication: To extract the indication phase, use the Extracting the Highest Phase for an Indication recipe (DP-4). 6. Select File | Send to Reference Rows to open the chart in BizInt Smart Charts Reference Rows. 9. Set Phase as Data Type: If not already set, Right-click on the phase field you will be using (either Highest Phase (Normalized) or an extracted highest phase) and choose Set Data Type | Custom | Phase . 10. Create sub-dataset by phase: From the Summary Sheet, double-click on your selected phase field to view the list. Double-click on the column header to sort by phase. Use Shift+click to select phases you want to include. We selected only clinical phases. Under the Refine tab, click on Create Sub-dataset and then click OK. A new dataset appears with your selected phases. For a larger dataset you may wish to filter again by other criteria. Our COVID-19 bullseye is now split by region. 11. Cleanup company name: From the Summary Sheet, right-click on the Developer field and select List Cleanup . Under matching ruleset, select Organization Names (Pharma) and click OK. Use the Cleanup Confirmation panel to clean-up terms. For more information on using List Cleanup, see the Techniques: Using List Cleanup recipe. 12. Create Bullseye labels: For our COVID-19 example, we add key company to the labels. From the Refine tab, click on Concatenate Fields . Choose Drug Name and Developer (Cleaned) (or Company (Key)) for your first and second fields. Use a slash with a space on either side “ / “ as the separator and name the new field “Drug / Company”. 13. Cleanup the new field: Some Drug / Company pairs may not need modification. Under the Refine tab, choose List Cleanup and click OK. To edit an item, right-click on it and and use Rename Item. If you have multiple items for the same drug, you should drag and drop to combine. You can use the Detail Window panel to display additional company information if it was visible in your chart when you exported. Alternatively, you can export back to Reference Rows and make your changes there and export back to VP-SCE. 14. Create Bullseye: Go to the Report tab and click on Bullseye . 15. In Step 1, select the cleaned Drug - Company (Cleaned) field as the Field to chart. Select your chosen phase field as the BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE BIZINT SMART CHARTS REFERENCE ROWS 7. Create the category field: To create the categories used for the bullseye slices, follow the Technique: Classifying Records recipe. 8. Use File | Export to export as VantagePoint - Smart Charts Edition. VantagePoint - BizInt Smart Charts Edition (VP-SCE) should open and import the file. VANTAGEPOINT - SMART CHARTS EDITION - clean up the data and create the Bullseye chart

Field for the Phase and your category field as the Category field for the pie slices. 16. In Step 3, select PowerPoint as the export format and click Create Bullseye.

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Creating a Butterfly Chart [Pipeline DP-17] A butterfly chart compares two items against another field. In this example we will be using drug pipeline data for COVID-19 vaccines. For the two sides of the butterfly we used the same regional division used in our two bullseye charts featured in our COVID-19 dashboard. We also use the Vaccine Type field created as part of the dashboard. See bizint.com/covid for more examples. You can create a butterfly with any two fields, but you can only show two values for the primary field. For the alternate example, we group clinical phases into a single group and compare with preclinical for top companies.

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Creating a Butterfly Chart [Pipeline DP-17] How did we create this?

START WITH: Any supported data already displayed in BizInt Smart Charts. In this example we used: A combined chart with Cortellis, Adis R&D Insight, Citeline Pharmaprojects, and GlobalData. Topic is COVID-19 vaccines.

BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE 1.

Display the two columns used to create the butterfly: Use View | Choose Columns to add columns if not already displayed in your chart. To create the alternate butterfly chart, add the Highest Phase (Normalized) and Companies (All) columns to your chart You will need two fields. For the primary field you will be looking at only two values, which form the right and left sides of the chart. The secondary field can have multiple values. In this example, the primary field is Region, created by grouping countries which appear in the Drug Development Phase subtable. The second field is the Vaccine Type, created for our COVID-19 dashboard bullseys. 2. Use File | Export to export as VantagePoint - Smart Charts Edition. VantagePoint - Smart Charts Edition (VP-SCE) should open and import the file. If VP-SCE does not launch automatically, launch it and choose the option to import the .vpxi file. VANTAGEPOINT - SMART CHARTS EDITION - Butterfly using curated fields 3. Select the primary field : Find your primary field, Region in this example, and double-click on the field name to display the contents. Select two rows for the right and left sides of the butterfly chart. 4. Create the Butterfly Chart : Under the Report tab, click on Butterfly Chart. When prompted to pick a field to analyze, select your secondary field from the drop-down. In this example, we selected Vaccine Type. Click OK to build the chart. You can click on Export Image to choose from a range of options to export your butterfly chart. VANTAGEPOINT - SMART CHARTS EDITION - (Alternate) Company vs Development Stage Butterfly You can also use the butterfly chart like a bubble chart of company vs. phase except with two broad groups rather than individual phases. 5. Cleanup Companies: Return to the Summary Sheet. Right-click on the Companies (All) field and choose List Cleanup. Under matching ruleset, select Organization Names (Pharma) and click OK. 6. Drag and drop to combine: Drag and drop company name variations onto your preferred company name to combine (for example, drag “Pfizer Japan” and “Wyeth” onto “Pfizer” to combine these terms and use Pfizer as the preferred term). 7. Use the search box (optional): Enter a search term into either search box to filter the list. You only want to cleanup the top 10-15 companies. For more information on using List Cleanup, see the Techniques: Using List Cleanup recipe. 8. Finish cleanup : Once you have combined all the terms for your selected indication, click Accept. Saving the thesaurus is optional. To create the butterfly chart, you do not need to cleanup all company names. 9. Select the top companies : Select the top 10-15 rows. Right-click and choose Add Selection to Group. Name the new group “top” and click OK. 10. Create the Clinical and Preclinical groups : Return to the Summary Sheet and double-click on Highest Phase (Normalized). Select all the clinical phases you want to include. Right-click and choose Add Selection to Group. Name the new group “Clinical” and click OK. Select the preclinical phases. Right-click and choose Add Selection to Group. Name this group “Preclinical” and click OK. 11. Create the primary field for the butterfly chart : Under the Refine tab, click on Create Field From Group | Names. Click Select All and then click OK. Use Ctrl+A to select all rows in the new field. 12. Create the Butterfly Chart : Under the Report tab, click on Butterfly Chart. When prompted to pick a field to analyze, select Companies (Cleaned) from the drop-down. Click the second drop-down to change from All Items to the top group. Click OK to build the chart. You can click on Export Image to choose from a range of options to export your butterfly chart.

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NEW!

Analyzing Companies by Phase with a Bubble Chart and Multi Donut Chart [Pipeline DP-18] Seeing a company’s pipeline by phase is often a useful landscape view. A bubble chart is a nice visualization option suitable for exploring a dataset to large to fit a piano chart or bullseye without filtering or selection. Small multiple donut charts are another way to view the same data, focused on how each company’s assets are distributed by phase.

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Analyzing Companies by Phase with a Bubble Chart and a Multi Donut Chart [Pipeline DP-18] How did we create this? START WITH: Any supported drug pipeline (or clinical trials) data already displayed in BizInt Smart Charts. Any combined drug pipeline chart created with current software will have the columns used here. BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE 1. Display the necessary columns: Use View | Apply Template and choose “BizInt Editor’s Choice - Multi-Database.” Alternatively you can use View | Columns to add a company name column and phase column visible in your chart. You can use the extracted highest phase for an indication if you have it. 2. Select File | Send to Reference Rows . BIZINT SMART CHARTS REFERENCE ROWS 3. Use File | Export to export as VantagePoint - Smart Charts Edition. VantagePoint - Smart Charts Edition (VP-SCE) should open and import the file. If VP-SCE does not launch automatically, launch it and choose the option to import the .vpxi file. VANTAGEPOINT - SMART CHARTS EDITION - create the bubble chart and/or donut chart 4. Set Phase as the Data Type for your phase field : Right click on the Highest Phase (Normalized) field, and from the “Set Data Type” submenu, select “Custom” and then “Phase”. This will cause phases to sort properly in your visualization. 5. Select phases to include (Bubble Chart) : Double-clcik on Highest Phase (Normalized) to view the list. Select the phases you want to include. You can use Ctrl+click to select non-adjacent items. Right-click and choose Add Selection to Group and name the group, such as “map” and click OK. 6. Create Phase Categories (Donuts) : Under the Refine tab, click on List Cleanup and click OK to use the default settings. Drag and drop phases onto a single item to combine into broad categories. For example, you can drag all the clinical phases onto a single item. Then right-click on the group and choose Rename Item. Rename the new group “Clinical”. When you finish creating and renaming groups, click Accept. You can skip saving the thesaurus. You should now have less than seven rows checked off in the map group. 7. Under the Refine tab, select Create Field From Group | Items . Check the box for the map group. Scroll down to change the New Field Name to Highest Phase (Groups) and click OK. 8. Remove company suffixes : Return to the Summary Sheet. (Optional) Right click on Developer and choose Further Processing | Remove | Company Suffix . Alternatively, remove text in parentheses: right-click on Developer and use Further Processing | Read Until - First | Paren . 9. Finish cleaning up Company Names : Click on List Cleanup . Under matching ruleset, select Organization Names (Pharma) and click OK. 10. Use the Cleanup Confirmation panel to clean-up terms : On either panel, drag and drop names to combine terms. (For example, drag “Genzyme” onto “Sanofi”). When you are done with clean-up, click the Accept button. You may wish to save the Thesaurus for future projects. If you choose an existing thesaurus when you save, you have the option to Merge. For more information on using List Cleanup, see the Techniques: Using List Cleanup recipe. 11. Select the top companies : A visualization with the full list will likely be too large and hard to read. Select the top 10 rows on the cleaned up list of companies. Right-click and choose Add Selection to Group and name the group, such as “Top” and click OK. 12. Create the Bubble Chart: Click on the Report tab and then on Bubble Chart. Select your cleaned companies field for Rows. Then select the group you created: click the Select a group radio button and choose your group from the drop-down. Select Highest Phase (Sort) for Columns and then click Run. 13. Create the Donut chart: Click on Multi Donut. Select your cleaned company field as the “field to use for each donut chart”. For

the “Field for Categories” use HIghest Phase (Groups). Scroll down and click Run. You can click on Export Image to choose from a range of options to export your chart.

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Training (1): Creating a trial “Piano” Chart [Trials CT-11] This is the first in a set of two training recipes designed to help BizInt Smart Charts users learn the key features of VantagePoint - Smart Charts Edition (VP-SCE). In these two recipes, you will learn how to clean-up data and create visualizations — a Trials Piano Chart and a Bullseye in PowerPoint and an Estimated Trial Completion Timeline in HTML. These recipes use a training.vpxi file which was created by searching for Merkel Cell Carcinoma trials in ClinicalTrials.gov and EU Clinical Trials (EudraCT), importing the results into the BizInt Smart Charts Drug Development Suite and then integrating results for each trial in BizInt Smart Charts Reference Rows. In Reference Rows we applied column rules and reviewed the data to select representative values for each trial and then exported to create the training.vpxi file.

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Training (1): Creating a trial “Piano” Chart [Trials CT-11] How did we create this? This recipe should be used with the training.vpxi file and provides detailed step-by-step instructions for cleaning up the data and creating a piano chart and bullseye

The training.vpxi file used in this recipe can be found at: www.bizint.com/vptraining

VANTAGEPOINT - BIZINT SMART CHARTS EDITION - Clean-up the data 1. Import data: : Open VantagePoint - Smart Charts Edition (VP-SCE) and select the option to Import XML (Smart Data Exchange) and click OK. Browse to the training.vpxi file and click Open. You can also double-click on the training.vpxi file to launch VP-SCE and open the file. 2. Clean-up sponsor names: On the Summary Sheet screen, right-click on the Sponsor field and select List Cleanup . Under “Matching ruleset”, select Organization Names (Pharma) and click OK. 3. Use the Cleanup Confirmation panel to clean-up terms. On either panel, drag and drop names to combine terms: e.g. drag “Incyte Biosciences International...” onto “Incyte Corporation” and “EMD Serono” onto “Merck KGaA” to combine these terms). When you are done with clean-up, click the Accept button. You do not need to save the Thesaurus. 4. A new field “Sponsor (Cleaned)” is created. For more information on using List Cleanup, see the Techniques: Using List Cleanup recipe. 5. Return to the Summary Sheet , using the tabs near the bottom of the screen, or the top drop-down menu. The Summary Sheet is where you can navigate between lists. You can right‐click on a field name and use Rename Field to rename a field. 6. Set Phase as the Data Type for your phase field: Right click on the Phase field, and from the “ Set Data Type ” submenu, select “ Custom ” and then “ Phase ”. This will cause phases to sort properly in your visualization. 7. Normalize phase: Right-click on the Phase field and choose Thesaurus . For “Select Thesaurus File”, select DrugDevelopmentPhases_ Arabic and click OK. Note: if you don’t see this file, click on the folder icon and go up one level to VantagePoint - SCE and select the Thesaurus folder. 8. Normalize status: Return to the Summary Sheet. Right-click on the Overall Status field and choose Thesaurus . Select the TrialStatus file and click OK. You will now have two more cleaned up fields “Phase (1)” and “Overall Status (1)”. 9. Having cleaned up sponsors, phases and trial status, you are ready to build your visualization. VANTAGEPOINT - BIZINT SMART CHARTS EDITION - Create the visualization 10. Build the Piano Chart: Go to the Report tab and click on Piano Chart in the “Smart Charts Report” section. 11. In Step 1, choose the Common Trial ID field for the Box Labels and choose your cleaned-up Phase (1) field for the Phase. See the “Create Piano Chart” window on the previous page 12. In Step 2, choose the cleaned Sponsor (Cleaned) as the “Field to add to the Boxes”. Choose the normalized Overall Status (1) field as the “Field to Color Code the Boxes” and select the second color palette. Check the box to “Add hyperlinks to records.” Note: record links can be followed in PowerPoint in the Slide Show view. 13. In Step 3, enter the title “MCC Trials” for your chart. In Step 4, select the radio button for PowerPoint and click “Create Piano Chart”. You can click on Piano Chart again and try different options - try other fields, a different color palette, or checking the option to Flip chart. 14. Some intermediate windows will appear and then VP-SCE will create a new document in PowerPoint and draw the piano chart, similar to the one shown on the previous page. Switch to PowerPoint to see the Piano Chart. Note: You can edit the chart in PowerPoint and follow links to the trial records in the PowerPoint show . 15. Build the Bullseye : On the Report tab, click on Bullseye . You can use the same data to build a different visualization. • In Step 1, choose the Common Trial ID field for the “Field to chart”, your cleaned-up Phase (1) field for the “Phase”, and the normalized status field, Overall Status (1) for the “Category”. In Step 2, give your chart a title “MCC Trials”. • In Step 4, select the radio button for PowerPoint and click “Create Bullseye”. Intermediate windows will appear and then VP SCE will create a new document in PowerPoint and draw the bullseye. Switch to PowerPoint to see it. 16. To save your work in VP-SCE, go to the Home tab and select Save to save as a .vpt file. Note: If you have problems at any step, go back and check that you did not skip a step. Do not hesitate to contact us at support@bizint.com for help!

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Training (2): Trial Completion Timeline [Trials CT-12] In this second recipe, you will clean-up trial completion dates and use your previously cleaned data to create a trial completion timeline. The timeline shows estimated completion dates for a set of trials arranged into horizontal categories, or lanes. This type of chart is also sometimes called a “swimlane” or “fishbone” chart. The trial completion timeline is created in VP-SCE and can be saved as an interactive HTML report.

LANE

BOX LABEL

ADDL BOX LABELS

COLOR CODE

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Training (2): Trial Completion Timeline [Trials CT-12] How did we create this? This recipe is a continuation of the first recipe in this series and uses the file already created in VP-SCE.

The training.vpxi file used in this recipe can be found at: www.bizint.com/vptraining

VANTAGEPOINT - SMART CHARTS EDITION - Clean-up completion dates 1. Remove text from completion date: On the Summary Sheet, right-click on the completion date field and select F urther Processing | Read Until - First | Paren . 2. Convert partial dates: Go to the Refine tab; under Thesaurus, select Find and replace . For the Name of the new field, type “Completion Date (Cleaned)”. Under Find and Replace, select FindReplace_MonthYYYY from the drop-down list and then click OK. Information in parentheses has been removed, and partial dates (e.g. June 2019) have been converted to the complete format needed for the timeline. VANTAGEPOINT - SMART CHARTS EDITION - Create the visualization 3. Create the Timeline: Go to the Report tab and click on Event Timeline . Then, select the fields that you want to include in your timeline. See the Event Timeline options panel on the previous page. • Field for Box Labels: used for the box label - white text on colored background (e.g. Common Trial ID in this example • Field for Lane Labels: used to label the lanes on the left of the timeline (e.g. Phase (1)). • Field for Date: the cleaned completion date, used to plot the boxes (e.g. Completion Date (Cleaned)). • First Year/Last Year: defines the date range of the launch timeline (e.g. 2017 and 2023). • Fields for boxes/tooltips: optional additional labels for the drug boxes (up to 3). These fields can also be used as “tooltips”when your mouse hovers over the drug box in the HTML version. (e.g Sponsor (Cleaned) with Boxes selected, and Completion Date (Cleaned) with Tooltip selected). • Field for color code: used to color code the trial boxes (e.g. Overall Status (1)). For the radio button, select “All items in field.” • Type “MCC Trials” for the Chart Title. 4. Click on the Create Timeline button to open your trial completion timeline in a VP-SCE window. Note: The timeline adjusts to the size of the window so your timeline could look different than the timeline on the previous page. 5. You can edit the title, subtitle and other information in the HTML window or the VP-SCE window. In VP-SCE, you can click on each box to get more detail. 6. Export the timeline: To save the timeline, click the Export Image camera icon on the right side of the toolbar. You can save as HTML or as a PDF, JPG or PNG image. Note: Timelines saved as HTML can be opened in a browser window and have some interactive features- you can zoom, scroll, see tooltips, and click on a trial id to view the record on CT.gov or EudraCT. 7. Optional: Try running the Create Timeline script again, but this time use Overall Status (1) for the Lane Labels and Phase (1) for the color code field, to create a slightly different visualization of the same data. We hope these recipes have helped you learn some of the basic features of VantagePoint - Smart Charts Edition (VP-SCE). The next step is to try the tools with your own project!

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Summarizing Clinical Trial Enrollment [Trials CT-4] This recipe shows how you can use Reference Rows to build a single row for each trial that includes a summary table showing enrollment number and update date from each database. The chart used here is the same set of trials for drugs targeting Merkel Cell Carcinoma used in other trial recipes in this Cookbook. You can also create a summary table showing the enrollment in each member state for each trial. The EudraCT (EU Clinical Trials) database provides trial records for a trial in each member country. BizInt Smart Charts tools help you identify related trials and summarize the data for all EU trials in a single row.

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Summarizing Clinical Trial Enrollment [Trials CT-4] How did we create this?

SEARCHES: We searched EudraCT (EU Clinical Trials) and ClinicalTrials.gov for Merkel Cell Carcinoma. This is the same data used in the Training recipes to create piano charts and timelines.

BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE 1. Import each set of search results into BizInt Smart Charts and use File | Combine to create a combined chart, selecting the ClinicalTrials.gov chart as the key chart (so that field names match the ones used later in the recipe.) 2. Run the Identify Common Trial IDs tool and sort by Common Trial ID. Review and make changes if needed. 3. Send to Reference Rows using the toolbar icon (or File | Send to Reference Rows ). BIZINT SMART CHARTS REFERENCE ROWS - Create the Trial Enrollment Summary 4. Create the Enrollment Subtable: Run Tools | Create Subtable from Columns . 5. Select the Database, Enrollment, Member State, and Enrollment in State columns in that order and press Apply. A new column will be created containing a subtable with these four columns. 6. Double click on the column header to rename the new column from Untitled Subtable to “Enrollment Summary”. 7. Change the column rule to summarize enrollment for each trial: Use Reference Rows | Column Rules... to set the rule for the new column to Summarize All Values . Blue hash marks will appear in the cells. 8. Hide any columns you do not want displayed in your final report. 9. Use File | Export to export the report to HTML and see the summary subtable — see example at left. Both EU Clinical Trials and ClinicalTrials.gov provide total enrollment numbers; EudraCT adds the ability to see the enrollment in each EU country.

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Creating a Milestone Timeline [Trials CT-13] The new Milestone Timeline combines features of our Duration and Event Timelines. You can plot trials showing start and end dates and milestones, both associated with a specific trial and global milestones applying across trials. Trials are organized into lanes as with the Event Timeline. In this example we will be plotting COVID-19 vaccine trials for children and adolescents. Both Moderna and Pfizer have a stated goal to have the vaccine available for the start of the new school year. By creating a timeline we can see how much of the trials might be completed by then. The milestones specifice to particular trials are added as a custom subtable with three columns: date, label, and category. Mutliple milestones for the same trial can be added as multiple rows in the custom subtable.

NEW!

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Creating a Milestone Timeline [Trials CT-13] How did we create this?

START WITH: Any supported clinical trial data already displayed in BizInt Smart Charts. In this example we used: A combined chart with ClinicalTrials.gov and TrialTrove. Topic = COVID-19 vaccine trials for children and adolescents.

BIZINT SMART CHARTS DRUG DEVELOPMENT SUITE 1.

Display the columns used for the timeline: Use View | Apply Template and choose “BizInt Editor’s Choice - Multi-Database.” This provides a good starting point and ensures standard names for columns. Alternatively, use View | Choose Columns to add necessary columns. 2. Add a column for the lane labels : E dit | Add Column . This creates a new Untitled column at the end of your chart. Double click on the column header and change the name. Enter content in the new column to create a category column for thelanes of the timeline. To enter a line break in the labels use a pipe symbol: | For this example we use the name “Vaccine - sponsor” and enter vaccine and sponsor information for each trial. Alternatively, you can use View | Choose Columns to add a field you want to use to determine the lanes, such as Phase or Overall Status. 3. Add Columns for the milestones : Edit | Add Column . Double click on the column header and change the name to “Milestone Data.” Repeat to add two more columns - “Milestone Text” and “Milestone Type”. 4. Add milestone data : Enter data for all three milestone columns for each trial associated milestone you want to include. For multiple milestones for the same trial, enter the information for additional milestones on a new line. 5. Create the milestone subtable : Use Tools | Create Subtable from Columns . Add the three new milestone columns in order: Milestone Date, Milestone Text, and Milestone Type. Click Apply to create the subtable. 6. Select File | Send to Reference Rows . BIZINT SMART CHARTS REFERENCE ROWS 7. Use File | Export to export as VantagePoint - Smart Charts Edition. VantagePoint - Smart Charts Edition (VP-SCE) should open and import the file. If VP-SCE does not launch automatically, launch it and choose the option to import the .vpxi file. VANTAGEPOINT - SMART CHARTS EDITION - create the milestone timeline 8. Normalize phase : Right-click on the phase field and choose Thesaurus. Under Thesaurus, select DrugDevelopmentPhases_ Arabic and click OK. Note: if you don’t see this file, click on the folder icon and go up one level to VantagePoint - SCE and select the Thesaurus folder. 9. Create bar labels : Under the Refine tab, click on Concatenate Fields. We choose Phase (1) as the First Field and Subject Age as the Second Field. Click OK and then enter a colon followed by a space “: “ as the string between the terms and click OK. 10. Create Bar Category Field : Return to the Summary Sheet. Right-click on Subject Age and choose List Cleanup. On the List Cleanup panel click OK to go to the Dual View Cleanup Confirmation panel. Drag and drop to group similar items. Then right click on each top level item and choose Rename Item. Enter a name for the group, such as “Children” and “Teens & Adults” in our example. Click Accept when you are done. You can skip saving as a thesaurus. 11. Cleanup start and end dates : Return to the Summary Sheet. Right-click on the completion date field and select Further Processing | Read Until - First | Paren . Return to Summary Sheet and repeat with the Completion Date. 12. Create the Milestone Timeline : Under the Report tab, click on Milestone Timeline. Select the fields you want to use. • Milestone Data: The custom subtable containing the data for the milestones (Milestone Data in this example). • Custom Global Milestones: Added text and date for custom milestones. Click the plus sign to add each milestone. • Chart Title and SubTitle: Title and subtitle for the chart. These can be edited after the timeline is created, 13. Click on the Create Timeline button to open your trial completion timeline in a VP-SCE window. In VP-SCE, you can click on each box to get more detail. 14. Export the timeline : To save, click the Export Image camera icon and choose HTML to edit it. 21 PAGE • Field for the Lane Labels: used to label the lanes on the left of the timeline (e.g. Vaccine - sponsor). • Starting Date and Ending Date: the cleaned dates (e.g. Completion Date: Read Until - First/Paren) • Bar Label Field: used to label trials bars (e.g.Phase (1): Subject Age in this example) • Bar Category Field: : used to color code the trialb ars (e.g.Subject Age (Cleaned) in this example).

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